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Yang JC, Hsu TH, Chen CS, Yu JH, Lin KI, Chen YJ. Enhanced Proteomic Coverage in Tissue Microenvironment by Immune Cell Subtype Library-Assisted DIA-MS. Mol Cell Proteomics 2024; 23:100792. [PMID: 38810695 PMCID: PMC11260568 DOI: 10.1016/j.mcpro.2024.100792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/30/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024] Open
Abstract
Immune cells that infiltrate the tumor microenvironment (TME) play crucial roles in shaping cancer development and influencing clinical outcomes and therapeutic responses. However, obtaining a comprehensive proteomic snapshot of tumor-infiltrating immunity in clinical specimens is often hindered by small sample amounts and a low proportion of immune infiltrating cells in the TME. To enable in-depth and highly sensitive profiling of microscale tissues, we established an immune cell-enriched library-assisted strategy for data-independent acquisition mass spectrometry (DIA-MS). Firstly, six immune cell subtype-specific spectral libraries were established from sorted cluster of differentiation markers, CD8+, CD4+ T lymphocytes, B lymphocytes, natural killer cells, dendritic cells, and macrophages in murine mesenteric lymph nodes (MLNs), covering 7815 protein groups with surface markers and immune cell-enriched proteins. The feasibility of microscale immune proteomic profiling was demonstrated on 1 μg tissue protein from the tumor of murine colorectal cancer (CRC) models using single-shot DIA; the immune cell-enriched library increased coverage to quantify 7419 proteins compared to directDIA analysis (6978 proteins). The enhancement enabled the mapping of 841 immune function-related proteins and exclusive identification of many low-abundance immune proteins, such as CD1D1, and CD244, demonstrating high sensitivity for immune landscape profiling. This approach was used to characterize the MLNs in CRC models, aiming to elucidate the mechanism underlying their involvement in cancer development within the TME. Even with a low percentage of immune cell infiltration (0.25-3%) in the tumor, our results illuminate downregulation in the adaptive immune signaling pathways (such as C-type lectin receptor signaling, and chemokine signaling), T cell receptor signaling, and Th1/Th2/Th17 cell differentiation, suggesting an immunosuppressive status in MLNs of CRC model. The DIA approach using the immune cell-enriched libraries showcased deep coverage and high sensitivity that can facilitate illumination of the immune proteomic landscape for microscale samples.
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Affiliation(s)
- Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Tzi-Hui Hsu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Jou-Hui Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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2
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Whiteaker JR, Zhao L, Schoenherr RM, Huang D, Kennedy JJ, Ivey RG, Lin C, Lorentzen TD, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Perry CD, Garcia-Buntley SS, Bocik W, Hewitt SM, Paulovich AG. Characterization of an expanded set of assays for immunomodulatory proteins using targeted mass spectrometry. Sci Data 2024; 11:682. [PMID: 38918394 PMCID: PMC11199596 DOI: 10.1038/s41597-024-03467-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024] Open
Abstract
Immunotherapies are revolutionizing cancer care, but many patients do not achieve durable responses and immune-related adverse events are difficult to predict. Quantifying the hundreds of proteins involved in cancer immunity has the potential to provide biomarkers to monitor and predict tumor response. We previously developed robust, multiplexed quantitative assays for immunomodulatory proteins using targeted mass spectrometry, providing measurements that can be performed reproducibly and harmonized across laboratories. Here, we expand upon those efforts in presenting data from a multiplexed immuno-oncology (IO)-3 assay panel targeting 43 peptides representing 39 immune- and inflammation-related proteins. A suite of novel monoclonal antibodies was generated as assay reagents, and the fully characterized antibodies are made available as a resource to the community. The publicly available dataset contains complete characterization of the assay performance, as well as the mass spectrometer parameters and reagent information necessary for implementation of the assay. Quantification of the proteins will provide benefit to correlative studies in clinical trials, identification of new biomarkers, and improve understanding of the immune response in cancer.
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Affiliation(s)
- Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Regine M Schoenherr
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Dongqing Huang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Chenwei Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Travis D Lorentzen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tessa W Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rhonda R Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph G Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua J Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Candice D Perry
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sandra S Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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3
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Zhang L, Nizhamuding X, Zheng H, Zeng J, Yuan X, Ma Z, Zhou W, Zhang C, Zhang T, Zhang C. An LC-MS/MS method for serum cystatin C quantification and its comparison with two commercial immunoassays. Clin Chem Lab Med 2024; 62:1092-1100. [PMID: 38253403 DOI: 10.1515/cclm-2023-0821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024]
Abstract
OBJECTIVES The standardization of cystatin C (CysC) measurement has received increasing attention in recent years due to its importance in estimating glomerular filtration rate (GFR). Mass spectrometry-based assays have the potential to provide an accuracy base for CysC measurement. However, a precise, accurate and sustainable LC-MS/MS method for CysC is still lacking. METHODS The developed LC-MS/MS method quantified CysC by detecting signature peptide (T3) obtained from tryptic digestion. Stable isotope labeled T3 peptide (SIL-T3) was spiked to control matrix effects and errors caused by liquid handling. The protein denaturation, reduction and alkylation procedures were combined into a single step with incubation time of 1 h, and the digestion lasted for 3.5 h. In the method validation, digestion time-course, imprecision, accuracy, matrix effect, interference, limit of quantification (LOQ), carryover, linearity, and the comparability to two routine immunoassays were evaluated. RESULTS No significant matrix effect or interference was observed with the CysC measurement. The LOQ was 0.21 mg/L; the within-run and total imprecision were 1.33-2.05 % and 2.18-3.90 % for three serum pools (1.18-5.34 mg/L). The LC-MS/MS method was calibrated by ERM-DA471/IFCC and showed good correlation with two immunoassays traceable to ERM-DA471/IFCC. However, significant bias was observed for immunoassays against the LC-MS/MS method. CONCLUSIONS The developed LC-MS/MS method is robust and simpler and holds the promise to provide an accuracy base for routine immunoassays, which will promote the standardization of CysC measurement.
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Affiliation(s)
- Li Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Xiaerbanu Nizhamuding
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Hao Zheng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Jie Zeng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Xinyi Yuan
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Zijia Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Weiyan Zhou
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Chao Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Tianjiao Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
| | - Chuanbao Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, P.R. China
- National Center of Gerontology, Beijing Engineering Research Center of Laboratory Medicine, Beijing, P.R. China
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4
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Ohno R, Mainka M, Kirchhoff R, Hartung NM, Schebb NH. Sterol Derivatives Specifically Increase Anti-Inflammatory Oxylipin Formation in M2-like Macrophages by LXR-Mediated Induction of 15-LOX. Molecules 2024; 29:1745. [PMID: 38675565 PMCID: PMC11052137 DOI: 10.3390/molecules29081745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/29/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
The understanding of the role of LXR in the regulation of macrophages during inflammation is emerging. Here, we show that LXR agonist T09 specifically increases 15-LOX abundance in primary human M2 macrophages. In time- and dose-dependent incubations with T09, an increase of 3-fold for ALOX15 and up to 15-fold for 15-LOX-derived oxylipins was observed. In addition, LXR activation has no or moderate effects on the abundance of macrophage marker proteins such as TLR2, TLR4, PPARγ, and IL-1RII, as well as surface markers (CD14, CD86, and CD163). Stimulation of M2-like macrophages with FXR and RXR agonists leads to moderate ALOX15 induction, probably due to side activity on LXR. Finally, desmosterol, 24(S),25-Ep cholesterol and 22(R)-OH cholesterol were identified as potent endogenous LXR ligands leading to an ALOX15 induction. LXR-mediated ALOX15 regulation is a new link between the two lipid mediator classes sterols, and oxylipins, possibly being an important tool in inflammatory regulation through anti-inflammatory oxylipins.
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Affiliation(s)
| | | | | | | | - Nils Helge Schebb
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119 Wuppertal, Germany
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5
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Fu Q, Vegesna M, Sundararaman N, Damoc E, Arrey TN, Pashkova A, Mengesha E, Debbas P, Joung S, Li D, Cheng S, Braun J, McGovern DPB, Murray C, Xuan Y, Eyk JEV. Paradigm shift in biomarker translation: a pipeline to generate clinical grade biomarker candidates from DIA-MS discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.586018. [PMID: 38562888 PMCID: PMC10983901 DOI: 10.1101/2024.03.20.586018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Clinical biomarker development has been stymied by inaccurate protein quantification from mass spectrometry (MS) discovery data and a prolonged validation process. To mitigate these issues, we created the Targeted Extraction Assessment of Quantification (TEAQ) software package. This innovative tool uses the discovery cohort analysis to select precursors, peptides, and proteins that adhere to established targeted assay criteria. TEAQ was applied to Data-Independent Acquisition MS data from plasma samples acquired on an Orbitrap™ Astral™ MS. Identified precursors were evaluated for linearity, specificity, repeatability, reproducibility, and intra-protein correlation from 11-point loading curves under three throughputs, to develop a resource for clinical-grade targeted assays. From a clinical cohort of individuals with inflammatory bowel disease (n=492), TEAQ successfully identified 1116 signature peptides for 327 quantifiable proteins from 1180 identified proteins. Embedding stringent selection criteria adaptable to targeted assay development into the analysis of discovery data will streamline the transition to validation and clinical studies.
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6
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Badgujar D, Paritala ST, Matre S, Sharma N. Enantiomeric purity of synthetic therapeutic peptides: A review. Chirality 2024; 36. [PMID: 38448043 DOI: 10.1002/chir.23652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Synthetic therapeutic peptides are a complex and popular class of pharmaceuticals. In recent years, peptides with proven therapeutic activity have gained significant interest in the market. The determination of synthetic peptide enantiomeric purity plays a critical role in the evaluation of the quality of the medicine. Since racemization is one of the most common side reactions occurring in AAs or peptides, enantiomeric impurities such as D-isomers can form during the peptide synthesis or can be introduced from the starting materials (e.g., AAs). The therapeutic effect of a synthetic or semi-synthetic bioactive peptide molecule depends on its AA enantiomeric purity and secondary/tertiary structure. Therefore, the enantiomeric purity determination for synthetic peptides is supportive for interpreting unwanted therapeutic effects and determining the quality of synthetic peptide therapeutics. However, enantiomeric purity analysis encounters formidable analytical challenges during chromatographic separation, as D/L isomers have identical physical-chemical properties except stereochemical configuration. To ensure peptides AA stereochemical configuration whether in the free or bound state, sensitive and reproducible quantitative analytical method is mandatory. In this regard, numerous analytical techniques were emerged for the quantification of D-isomeric impurities in synthetic peptides, but still, very few reports are available in the literature. Thus, the purpose of this paper is to provide an overview of the importance, regulatory requirements, and various analytical methods used for peptide enantiomeric purity determination. In addition, we discussed the available literature in terms of enantiomeric impurity detection, common hydrolysis procedural aspects, and different analytical strategies used for sample preparation.
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Affiliation(s)
- Devendra Badgujar
- National Institute of Pharmaceutical Education and Research-Ahmedabad, Ministry of Chemicals and Fertilizers, Government of India, Gandhinagar, Gujarat, India
| | - Sree Teja Paritala
- National Institute of Pharmaceutical Education and Research-Ahmedabad, Ministry of Chemicals and Fertilizers, Government of India, Gandhinagar, Gujarat, India
| | - Shubham Matre
- National Institute of Pharmaceutical Education and Research-Ahmedabad, Ministry of Chemicals and Fertilizers, Government of India, Gandhinagar, Gujarat, India
| | - Nitish Sharma
- National Institute of Pharmaceutical Education and Research-Ahmedabad, Ministry of Chemicals and Fertilizers, Government of India, Gandhinagar, Gujarat, India
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7
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Rebnegger C, Coltman BL, Kowarz V, Peña DA, Mentler A, Troyer C, Hann S, Schöny H, Koellensperger G, Mattanovich D, Gasser B. Protein production dynamics and physiological adaptation of recombinant Komagataella phaffii at near-zero growth rates. Microb Cell Fact 2024; 23:43. [PMID: 38331812 PMCID: PMC10851509 DOI: 10.1186/s12934-024-02314-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Specific productivity (qP) in yeast correlates with growth, typically peaking at intermediate or maximum specific growth rates (μ). Understanding the factors limiting productivity at extremely low μ might reveal decoupling strategies, but knowledge of production dynamics and physiology in such conditions is scarce. Retentostats, a type of continuous cultivation, enable the well-controlled transition to near-zero µ through the combined retention of biomass and limited substrate supply. Recombinant Komagataella phaffii (syn Pichia pastoris) secreting a bivalent single domain antibody (VHH) was cultivated in aerobic, glucose-limited retentostats to investigate recombinant protein production dynamics and broaden our understanding of relevant physiological adaptations at near-zero growth conditions. RESULTS By the end of the retentostat cultivation, doubling times of approx. two months were reached, corresponding to µ = 0.00047 h-1. Despite these extremely slow growth rates, the proportion of viable cells remained high, and de novo synthesis and secretion of the VHH were observed. The average qP at the end of the retentostat was estimated at 0.019 mg g-1 h-1. Transcriptomics indicated that genes involved in protein biosynthesis were only moderately downregulated towards zero growth, while secretory pathway genes were mostly regulated in a manner seemingly detrimental to protein secretion. Adaptation to near-zero growth conditions of recombinant K. phaffii resulted in significant changes in the total protein, RNA, DNA and lipid content, and lipidomics revealed a complex adaptation pattern regarding the lipid class composition. The higher abundance of storage lipids as well as storage carbohydrates indicates that the cells are preparing for long-term survival. CONCLUSIONS In conclusion, retentostat cultivation proved to be a valuable tool to identify potential engineering targets to decouple growth and protein production and gain important insights into the physiological adaptation of K. phaffii to near-zero growth conditions.
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Affiliation(s)
- Corinna Rebnegger
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Benjamin L Coltman
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Viktoria Kowarz
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - David A Peña
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Axel Mentler
- Department of Forest- and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Peter-Jordan-Straße 82, 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Harald Schöny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Straße 38, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Diethard Mattanovich
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
| | - Brigitte Gasser
- CD-Laboratory for Growth-Decoupled Protein Production in Yeast at Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology (IMMB), University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria.
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8
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Michaud SA, Pětrošová H, Sinclair NJ, Kinnear AL, Jackson AM, McGuire JC, Hardie DB, Bhowmick P, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Smith D, Mohammed Y, Schibli D, Sickmann A, Borchers CH. Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues. Commun Biol 2024; 7:6. [PMID: 38168632 PMCID: PMC10762018 DOI: 10.1038/s42003-023-05687-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Mouse is the mammalian model of choice to study human health and disease due to its size, ease of breeding and the natural occurrence of conditions mimicking human pathology. Here we design and validate multiple reaction monitoring mass spectrometry (MRM-MS) assays for quantitation of 2118 unique proteins in 20 murine tissues and organs. We provide open access to technical aspects of these assays to enable their implementation in other laboratories, and demonstrate their suitability for proteomic profiling in mice by measuring normal protein abundances in tissues from three mouse strains: C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. Sex- and strain-specific differences in protein abundances are identified and described, and the measured values are freely accessible via our MouseQuaPro database: http://mousequapro.proteincentre.com . Together, this large library of quantitative MRM-MS assays established in mice and the measured baseline protein abundances represent an important resource for research involving mouse models.
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Affiliation(s)
- Sarah A Michaud
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada.
| | - Helena Pětrošová
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Nicholas J Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Andrea L Kinnear
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Angela M Jackson
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Jamie C McGuire
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Pallab Bhowmick
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Milan Ganguly
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann M Flenniken
- The Center for Phenogenomics, Toronto, ON, Canada
- Sinai Health Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Derek Smith
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - David Schibli
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Department of Pathology, McGill University, Montreal, QC, Canada.
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9
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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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10
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Macur K, Schissel A, Yu F, Lei S, Morsey B, Fox HS, Ciborowski P. Change of histone H3 lysine 14 acetylation stoichiometry in human monocyte derived macrophages as determined by MS-based absolute targeted quantitative proteomic approach: HIV infection and methamphetamine exposure. Clin Proteomics 2023; 20:48. [PMID: 37880620 PMCID: PMC10599040 DOI: 10.1186/s12014-023-09438-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Histones posttranslational modification represent an epigenetic mechanism that regulate gene expression and other cellular processes. Quantitative mass spectrometry used for the absolute quantification of such modifications provides further insight into cellular responses to extracellular insults such as infections or toxins. Methamphetamine (Meth), a drug of abuse, is affecting the overall function of the immune system. In this report, we developed, validated and applied a targeted, MS-based quantification assay to measure changes in histone H3 lysine 14 acetylation (H3K14Ac) during exposure of human primary macrophages to HIV-1 infection and/or Meth. METHODS The quantification assay was developed and validated to determine H3K14Ac stoichiometry in histones that were isolated from the nuclei of control (CIC) and exposed to Meth before (CIM) or/and after (MIM) HIV-infection human monocyte-derived macrophages (hMDM) of six donors. It was based on LC-MS/MS measurement using multiple reaction monitoring (MRM) acquisition of the unmodified and acetylated form of lysine K14 of histone H3 9KSTGGKAPR17 peptides and the corresponding stable isotope labeled (SIL) heavy peptide standards of the same sequences. The histone samples were propionylated (Poy) pre- and post- trypsin digestion so that the sequences of the monitored peptides were: K[Poy]STGGK[1Ac]APR, K[Poy]STGGK[1Ac]APR-heavy, K[Poy]STGGK[Poy]APR and K[Poy]STGGK[Poy]APR-heavy. The absolute amounts of the acetylated and unmodified peptides were determined by comparing to the abundances of their SIL standards, that were added to the samples in the known concentrations, and, then used for calculation of H3K14Ac stoichiometry in CIC, CIM and MIM hMDM. RESULTS The assay was characterized by LLOD of 0.106 fmol/µL and 0.204 fmol/µL for unmodified and acetylated H3 9KSTGGKAPR17 peptides, respectively. The LLOQ was 0.5 fmol/µL and the linear range of the assay was from 0.5 to 2500 fmol/µL. The absolute abundances of the quantified peptides varied between the donors and conditions, and so did the H3K14Ac stoichiometry. This was rather attributed to the samples nature itself, as the variability of their triplicate measurements was low. CONCLUSIONS The developed LC-MS/MS assay enabled absolute quantification of H3K14Ac in exposed to Meth HIV-infected hMDM. It can be further applied determination of this PTM stoichiometry in other studies on human primary macrophages.
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Affiliation(s)
- Katarzyna Macur
- Core Facility Laboratories, Intercollegiate Faculty of Biotechnology UG & MUG, University of Gdańsk, Gdańsk, Poland.
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Andrew Schissel
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Fang Yu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shulei Lei
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Brenda Morsey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
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11
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Sleumer B, Kema IP, van de Merbel NC. Quantitative bioanalysis of proteins by digestion and LC-MS/MS: the use of multiple signature peptides. Bioanalysis 2023; 15:1203-1216. [PMID: 37724471 DOI: 10.4155/bio-2023-0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023] Open
Abstract
The use of multiple signature peptides for the quantification of proteins by digestion and LC-MS/MS is reviewed and evaluated here. A distinction is made based on the purpose of the use of multiple peptides: confirmation of the protein concentration, discrimination between different protein forms or species and in vivo biotransformation. Most reports that describe methods with at least two peptides use these for confirmation, but it is not always mentioned how the peptides are used and how possible differences in concentration between the peptides are handled. Differences in concentration are often reported in the case of monitoring different protein forms or in vivo biotransformation, and this offers insight into the biological fate of the protein.
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Affiliation(s)
- Bas Sleumer
- ICON Bioanalytical Laboratories, Amerikaweg 18, 9407 TK, Assen, The Netherlands
- Department of Analytical Biochemistry, University of Groningen, A Deusinglaan 1, 9700 AV Groningen, The Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, EA61, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Ido P Kema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, EA61, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Nico C van de Merbel
- ICON Bioanalytical Laboratories, Amerikaweg 18, 9407 TK, Assen, The Netherlands
- Department of Analytical Biochemistry, University of Groningen, A Deusinglaan 1, 9700 AV Groningen, The Netherlands
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12
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Woessmann J, Petrosius V, Üresin N, Kotol D, Aragon-Fernandez P, Hober A, auf dem Keller U, Edfors F, Schoof EM. Assessing the Role of Trypsin in Quantitative Plasma and Single-Cell Proteomics toward Clinical Application. Anal Chem 2023; 95:13649-13658. [PMID: 37639361 PMCID: PMC10500548 DOI: 10.1021/acs.analchem.3c02543] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Mass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large-scale biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the most widely applied protease in proteomics due to its characteristics. With ever-larger cohort sizes and possible future clinical application of mass spectrometry-based proteomics, the technical impact of trypsin becomes increasingly relevant. To assess possible biases introduced by trypsin digestion, we evaluated the impact of eight commercially available trypsins in a variety of bottom-up proteomics experiments and across a range of protease concentrations and storage times. To investigate the universal impact of these technical attributes, we included bulk HeLa cell lysate, human plasma, and single HEK293 cells, which were analyzed over a range of selected reaction monitoring (SRM), data-independent acquisition (DIA), and data-dependent acquisition (DDA) instrument methods on three LC-MS instruments. The quantification methods employed encompassed both label-free approaches and absolute quantification utilizing spike-in heavy-labeled recombinant protein fragment standards. Based on this extensive data set, we report variations between commercial trypsins, their source, and their concentration. Furthermore, we provide suggestions on the handling of trypsin in large-scale studies.
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Affiliation(s)
- Jakob Woessmann
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
- Science
for Life Laboratory, KTH—Royal Institute
of Technology, SE-171 65 Solna, Sweden
- Department
of Protein Science, KTH—Royal Institute
of Technology, SE-106 91 Stockholm, Sweden
| | - Valdemaras Petrosius
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nil Üresin
- The
Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech
Research and Innovation Centre (BRIC), University
of Copenhagen, 2200 Copenhagen, Denmark
| | - David Kotol
- Science
for Life Laboratory, KTH—Royal Institute
of Technology, SE-171 65 Solna, Sweden
- Department
of Protein Science, KTH—Royal Institute
of Technology, SE-106 91 Stockholm, Sweden
| | - Pedro Aragon-Fernandez
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andreas Hober
- Science
for Life Laboratory, KTH—Royal Institute
of Technology, SE-171 65 Solna, Sweden
- Department
of Protein Science, KTH—Royal Institute
of Technology, SE-106 91 Stockholm, Sweden
| | - Ulrich auf dem Keller
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Fredrik Edfors
- Science
for Life Laboratory, KTH—Royal Institute
of Technology, SE-171 65 Solna, Sweden
- Department
of Protein Science, KTH—Royal Institute
of Technology, SE-106 91 Stockholm, Sweden
| | - Erwin M. Schoof
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
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13
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Maurer J, Grouzmann E, Eugster PJ. Tutorial review for peptide assays: An ounce of pre-analytics is worth a pound of cure. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1229:123904. [PMID: 37832388 DOI: 10.1016/j.jchromb.2023.123904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
The recent increase in peptidomimetic-based medications and the growing interest in peptide hormones has brought new attention to the quantification of peptides for diagnostic purposes. Indeed, the circulating concentrations of peptide hormones in the blood provide a snapshot of the state of the body and could eventually lead to detecting a particular health condition. Although extremely useful, the quantification of such molecules, preferably by liquid chromatography coupled to mass spectrometry, might be quite tricky. First, peptides are subjected to hydrolysis, oxidation, and other post-translational modifications, and, most importantly, they are substrates of specific and nonspecific proteases in biological matrixes. All these events might continue after sampling, changing the peptide hormone concentrations. Second, because they include positively and negatively charged groups and hydrophilic and hydrophobic residues, they interact with their environment; these interactions might lead to a local change in the measured concentrations. A phenomenon such as nonspecific adsorption to lab glassware or materials has often a tremendous effect on the concentration and needs to be controlled with particular care. Finally, the circulating levels of peptides might be low (pico- or femtomolar range), increasing the impact of the aforementioned effects and inducing the need for highly sensitive instruments and well-optimized methods. Thus, despite the extreme diversity of these peptides and their matrixes, there is a common challenge for all the assays: the need to keep concentrations unchanged from sampling to analysis. While significant efforts are often placed on optimizing the analysis, few studies consider in depth the impact of pre-analytical steps on the results. By working through practical examples, this solution-oriented tutorial review addresses typical pre-analytical challenges encountered during the development of a peptide assay from the standpoint of a clinical laboratory. We provide tips and tricks to avoid pitfalls as well as strategies to guide all new developments. Our ultimate goal is to increase pre-analytical awareness to ensure that newly developed peptide assays produce robust and accurate results.
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Affiliation(s)
- Jonathan Maurer
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Eric Grouzmann
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe J Eugster
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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14
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Lundeen RA, Kennedy JJ, Murillo OD, Ivey RG, Zhao L, Schoenherr RM, Hoofnagle AN, Wang P, Whiteaker JR, Paulovich AG. Monitoring Both Extended and Tryptic Forms of Stable Isotope-Labeled Standard Peptides Provides an Internal Quality Control of Proteolytic Digestion in Targeted Mass Spectrometry-Based Assays. Mol Cell Proteomics 2023; 22:100621. [PMID: 37478973 PMCID: PMC10458721 DOI: 10.1016/j.mcpro.2023.100621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted mass spectrometry (MS)-based proteomic assays, such as multiplexed multiple reaction monitoring (MRM)-MS assays, enable sensitive and specific quantification of proteotypic peptides as stoichiometric surrogates for proteins. Efforts are underway to expand the use of MRM-MS assays in clinical environments, which requires a reliable strategy to monitor proteolytic digestion efficiency within individual samples. Towards this goal, extended stable isotope-labeled standard (SIS) peptides (hE), which incorporate native proteolytic cleavage sites, can be spiked into protein lysates prior to proteolytic (trypsin) digestion, and release of the tryptic SIS peptide (hT) can be monitored. However, hT measurements alone cannot monitor the extent of digestion and may be confounded by matrix effects specific to individual patient samples; therefore, they are not sufficient to monitor sample-to-sample digestion variability. We hypothesized that measuring undigested hE, along with its paired hT, would improve detection of digestion issues compared to only measuring hT. We tested the ratio of the SIS pair measurements, or hE/hT, as a quality control (QC) metric of trypsin digestion for two MRM assays: a direct-MRM (398 targets) and an immuno-MRM (126 targets requiring immunoaffinity peptide enrichment) assay, with extended SIS peptides observable for 54% (216) and 62% (78) of the targets, respectively. We evaluated the quantitative bias for each target in a series of experiments that adversely affected proteolytic digestion (e.g., variable digestion times, pH, and temperature). We identified a subset of SIS pairs (36 for the direct-MRM, 7 for the immuno-MRM assay) for which the hE/hT ratio reliably detected inefficient digestion that resulted in decreased assay sensitivity and unreliable endogenous quantification. The hE/hT ratio was more responsive to a decrease in digestion efficiency than a metric based on hT measurements alone. For clinical-grade MRM-MS assays, this study describes a ready-to-use QC panel and also provides a road map for designing custom QC panels.
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Affiliation(s)
- Rachel A Lundeen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Regine M Schoenherr
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
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15
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Shi M, McHugh KJ. Strategies for overcoming protein and peptide instability in biodegradable drug delivery systems. Adv Drug Deliv Rev 2023; 199:114904. [PMID: 37263542 PMCID: PMC10526705 DOI: 10.1016/j.addr.2023.114904] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023]
Abstract
The global pharmaceutical market has recently shifted its focus from small molecule drugs to peptide, protein, and nucleic acid drugs, which now comprise a majority of the top-selling pharmaceutical products on the market. Although these biologics often offer improved drug specificity, new mechanisms of action, and/or enhanced efficacy, they also present new challenges, including an increased potential for degradation and a need for frequent administration via more invasive administration routes, which can limit patient access, patient adherence, and ultimately the clinical impact of these drugs. Controlled-release systems have the potential to mitigate these challenges by offering superior control over in vivo drug levels, localizing these drugs to tissues of interest (e.g., tumors), and reducing administration frequency. Unfortunately, adapting controlled-release devices to release biologics has proven difficult due to the poor stability of biologics. In this review, we summarize the current state of controlled-release peptides and proteins, discuss existing techniques used to stabilize these drugs through encapsulation, storage, and in vivo release, and provide perspective on the most promising opportunities for the clinical translation of controlled-release peptides and proteins.
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Affiliation(s)
- Miusi Shi
- Department of Bioengineering, Rice University, Houston, TX 77030, USA; The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine, Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, PR China
| | - Kevin J McHugh
- Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Chemistry, Rice University, Houston, TX 77030, USA.
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16
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Xu K, Sun H, Wang K, Quan Y, Qiao Z, Hu Y, Li C. The Quantification of Spike Proteins in the Inactivated SARS-CoV-2 Vaccines of the Prototype, Delta, and Omicron Variants by LC-MS. Vaccines (Basel) 2023; 11:vaccines11051002. [PMID: 37243106 DOI: 10.3390/vaccines11051002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Developing variant vaccines or multivalent vaccines is a feasible way to address the epidemic as the SARS-CoV-2 variants of concern (VOCs) posed an increased risk to global public health. The spike protein of the SARS-CoV-2 virus was usually used as the main antigen in many types of vaccines to produce neutralizing antibodies against the virus. However, the spike (S) proteins of different variants were only differentiated by a few amino acids, making it difficult to obtain specific antibodies that can distinguish different VOCs, thereby challenging the accurate distinction and quantification of the variants using immunological methods such as ELISA. Here, we established a method based on LC-MS to quantify the S proteins in inactivated monovalent vaccines or trivalent vaccines (prototype, Delta, and Omicron strains). By analyzing the S protein sequences of the prototype, Delta, and Omicron strains, we identified peptides that were different and specific among the three strains and synthesized them as references. The synthetic peptides were isotopically labeled as internal targets. Quantitative analysis was performed by calculating the ratio between the reference and internal target. The verification results have shown that the method we established had good specificity, accuracy, and precision. This method can not only accurately quantify the inactivated monovalent vaccine but also could be applied to each strain in inactivated trivalent SARS-CoV-2 vaccines. Hence, the LC-MS method established in this study can be applied to the quality control of monovalent and multivalent SARS-CoV-2 variation vaccines. By enabling more accurate quantification, it will help to improve the protection of the vaccine to some extent.
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Affiliation(s)
- Kangwei Xu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Huang Sun
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Kaiqin Wang
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Yaru Quan
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Zhizhong Qiao
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Yaling Hu
- Sinovac Life Sciences Co., Ltd., No. 21, Tianfu St., Daxing Biomedicine Industrial Base of Zhongguancun Science Park, Daxing District, Beijing 100050, China
| | - Changgui Li
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
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17
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Barker AD, Alba MM, Mallick P, Agus DB, Lee JSH. An Inflection Point in Cancer Protein Biomarkers: What Was and What's Next. Mol Cell Proteomics 2023:100569. [PMID: 37196763 PMCID: PMC10388583 DOI: 10.1016/j.mcpro.2023.100569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Biomarkers remain the highest value proposition in cancer medicine today - especially protein biomarkers. Yet despite decades of evolving regulatory frameworks to facilitate the review of emerging technologies, biomarkers have been mostly about promise with very little to show for improvements in human health. Cancer is an emergent property of a complex system and deconvoluting the integrative and dynamic nature of the overall system through biomarkers is a daunting proposition. The last two decades have seen an explosion of multi-omics profiling and a range of advanced technologies for precision medicine, including the emergence of liquid biopsy, exciting advances in single cell analysis, artificial intelligence (machine and deep learning) for data analysis and many other advanced technologies that promise to transform biomarker discovery. Combining multiple omics modalities to acquire a more comprehensive landscape of the disease state, we are increasingly developing biomarkers to support therapy selection and patient monitoring. Furthering precision medicine, especially in oncology, necessitates moving away from the lens of reductionist thinking towards viewing and understanding that complex diseases are, in fact, complex adaptive systems. As such, we believe it is necessary to re-define biomarkers as representations of biological system states at different hierarchical levels of biological order. This definition could include traditional molecular, histologic, radiographic, or physiological characteristics, as well as emerging classes of digital markers and complex algorithms. To succeed in the future, we must move past purely observational individual studies and instead start building a mechanistic framework to enable integrative analysis of new studies within the context of prior studies. Identifying information in complex systems and applying theoretical constructs, such as information theory, to study cancer as a disease of dysregulated communication could prove to be "game changing" for the clinical outcome of cancer patients.
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Affiliation(s)
- Anna D Barker
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Complex Adaptive Systems Initiative and School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Mario M Alba
- Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, CA; Department of Radiology, Stanford University, Stanford, CA
| | - David B Agus
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA; Viterbi School of Engineering, University of Southern California, Los Angeles, CA
| | - Jerry S H Lee
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA; Viterbi School of Engineering, University of Southern California, Los Angeles, CA
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18
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Li W, Keller AA. Optimization of Targeted Plant Proteomics Using Liquid Chromatography with Tandem Mass Spectrometry (LC-MS/MS). ACS AGRICULTURAL SCIENCE & TECHNOLOGY 2023; 3:421-431. [PMID: 37206883 PMCID: PMC10189723 DOI: 10.1021/acsagscitech.3c00017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/21/2023]
Abstract
This study was conducted to optimize a targeted plant proteomics approach from signature peptide selection and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analytical method development and optimization to sample preparation method optimization. Three typical protein extraction and precipitation methods, including trichloroacetic acid (TCA)/acetone method, phenol method, and TCA/acetone/phenol method, and two digestion methods, including trypsin digestion and LysC/trypsin digestion, were evaluated for selected proteins related to the impact of engineered nanomaterials (ENMs) on wheat (Triticum aestivum) plant growth. In addition, we compared two plant tissue homogenization methods: grinding freeze-dried tissue and fresh tissue into a fine powder using a mortar and pestle aided with liquid nitrogen. Wheat plants were grown under a 16 h photoperiod (light intensity 150 μmol·m-2·s-1) for 4 weeks at 22 °C with a relative humidity of 60% and were watered daily to maintain a 70-90% water content in the soil. Processed samples were analyzed with an optimized LC-MS/MS method. The concentration of selected signature peptides for the wheat proteins of interest indicated that the phenol extraction method using fresh plant tissue, coupled with trypsin digestion, was the best sample preparation method for the targeted proteomics study. Overall, the optimized approach yielded the highest total peptide concentration (68,831 ng/g, 2.4 times the lowest concentration) as well as higher signature peptide concentrations for most peptides (19 out of 28). In addition, three of the signature peptides could only be detected using the optimized approach. This study provides a workflow for optimizing targeted proteomics studies.
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19
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Whiteaker JR, Zhao L, Schoenherr RM, Huang D, Lundeen RA, Voytovich U, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Perry CD, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Chowdhury S, Vandermeer J, Smith SD, Gopal AK, Ramchurren N, Fling SP, Wang P, Paulovich AG. A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials. Front Oncol 2023; 13:1168710. [PMID: 37205196 PMCID: PMC10185886 DOI: 10.3389/fonc.2023.1168710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/10/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction Immunotherapy is an effective treatment for a subset of cancer patients, and expanding the benefits of immunotherapy to all cancer patients will require predictive biomarkers of response and immune-related adverse events (irAEs). To support correlative studies in immunotherapy clinical trials, we are developing highly validated assays for quantifying immunomodulatory proteins in human biospecimens. Methods Here, we developed a panel of novel monoclonal antibodies and incorporated them into a novel, multiplexed, immuno-multiple reaction monitoring mass spectrometry (MRM-MS)-based proteomic assay targeting 49 proteotypic peptides representing 43 immunomodulatory proteins. Results and discussion The multiplex assay was validated in human tissue and plasma matrices, where the linearity of quantification was >3 orders of magnitude with median interday CVs of 8.7% (tissue) and 10.1% (plasma). Proof-of-principle demonstration of the assay was conducted in plasma samples collected in clinical trials from lymphoma patients receiving an immune checkpoint inhibitor. We provide the assays and novel monoclonal antibodies as a publicly available resource for the biomedical community.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Dongqing Huang
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Rachel A. Lundeen
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Oscar D. Murillo
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Travis D. Lorentzen
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Tessa W. Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Rhonda R. Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joseph G. Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joshua J. Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Candice D. Perry
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Christopher W. Richardson
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Sandra S. Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen M. Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jackie Vandermeer
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Stephen D. Smith
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Ajay K. Gopal
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Nirasha Ramchurren
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Steven P. Fling
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
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20
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Bijttebier S, Rodrigues Martins D, Mertens L, Grauwen K, Bruinzeel W, Willems R, Bartolomé-Nebreda JM, Theunis C, Bretteville A, Ebneth A, Dillen L. IP-LC-MSMS Enables Identification of Three Tau O-GlcNAcylation Sites as O-GlcNAcase Inhibition Pharmacodynamic Readout in Transgenic Mice Overexpressing Human Tau. J Proteome Res 2023; 22:1309-1321. [PMID: 36888912 DOI: 10.1021/acs.jproteome.2c00822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
O-β-linked N-acetylglucosaminylation (O-GlcNAcylation) modulates tau phosphorylation and aggregation: the pharmacological increase of tau O-GlcNAcylation upon treatment with inhibitors of O-GlcNAc hydrolase (OGA) constitutes a potential strategy to tackle neurodegenerative diseases. Analysis of tau O-GlcNAcylation could potentially be used as a pharmacodynamic biomarker both in preclinical and clinical studies. The goal of the current study was to confirm tau O-GlcNAcylation at S400 as a pharmacodynamic readout of OGA inhibition in P301S transgenic mice overexpressing human tau and treated with the OGA inhibitor Thiamet G and to explore if additional O-GlcNAcylation sites on tau could be identified. As a first step, an immunoprecipitation-liquid chromatography-mass spectrometry (IP-LC-MS) methodology was developed to monitor changes in O-GlcNAcylation around S400 of tau in mouse brain homogenate (BH) extracts. Second, additional O-GlcNAc sites were identified in in-house produced recombinant O-GlcNAcylated human tau at relatively high concentrations, thereby facilitating collection of informative LC-MS data for identification of low-concentration O-GlcNAc-tryptic tau peptides in human transgenic mouse BH extracts. This strategy enabled, for the first time, identification of three low abundant N-terminal and mid-domain O-GlcNAc sites of tau (at S208, S191, and S184 or S185) in human transgenic mouse BH. Data are openly available at data.mendeley.com (doi: 10.17632/jp57yk9469.1; doi: 10.17632/8n5j45dnd8.1; doi: 10.17632/h5vdrx4n3d.1).
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Affiliation(s)
- Sebastiaan Bijttebier
- Bioanalytical Discovery & Development Sciences, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Liesbeth Mertens
- R&D Neurosciences, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Karolien Grauwen
- R&D Neurosciences, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Wouter Bruinzeel
- R&D Structural & Protein Sciences, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Roland Willems
- R&D Neurosciences, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Clara Theunis
- R&D Neurosciences, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Andreas Ebneth
- R&D Neurosciences, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Lieve Dillen
- Bioanalytical Discovery & Development Sciences, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
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21
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Chouhan S, Sawant M, Weimholt C, Luo J, Sprung RW, Terrado M, Mueller DM, Earp HS, Mahajan NP. TNK2/ACK1-mediated phosphorylation of ATP5F1A (ATP synthase F1 subunit alpha) selectively augments survival of prostate cancer while engendering mitochondrial vulnerability. Autophagy 2023; 19:1000-1025. [PMID: 35895804 PMCID: PMC9980697 DOI: 10.1080/15548627.2022.2103961] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/02/2022] Open
Abstract
The challenge of rapid macromolecular synthesis enforces the energy-hungry cancer cell mitochondria to switch their metabolic phenotypes, accomplished by activation of oncogenic tyrosine kinases. Precisely how kinase activity is directly exploited by cancer cell mitochondria to meet high-energy demand, remains to be deciphered. Here we show that a non-receptor tyrosine kinase, TNK2/ACK1 (tyrosine kinase non receptor 2), phosphorylated ATP5F1A (ATP synthase F1 subunit alpha) at Tyr243 and Tyr246 (Tyr200 and 203 in the mature protein, respectively) that not only increased the stability of complex V, but also increased mitochondrial energy output in cancer cells. Further, phospho-ATP5F1A (p-Y-ATP5F1A) prevented its binding to its physiological inhibitor, ATP5IF1 (ATP synthase inhibitory factor subunit 1), causing sustained mitochondrial activity to promote cancer cell growth. TNK2 inhibitor, (R)-9b reversed this process and induced mitophagy-based autophagy to mitigate prostate tumor growth while sparing normal prostate cells. Further, depletion of p-Y-ATP5F1A was needed for (R)-9b-mediated mitophagic response and tumor growth. Moreover, Tnk2 transgenic mice displayed increased p-Y-ATP5F1A and loss of mitophagy and exhibited formation of prostatic intraepithelial neoplasia (PINs). Consistent with these data, a marked increase in p-Y-ATP5F1A was seen as prostate cancer progressed to the malignant stage. Overall, this study uncovered the molecular intricacy of tyrosine kinase-mediated mitochondrial energy regulation as a distinct cancer cell mitochondrial vulnerability and provided evidence that TNK2 inhibitors can act as "mitocans" to induce cancer-specific mitophagy.Abbreviations: ATP5F1A: ATP synthase F1 subunit alpha; ATP5IF1: ATP synthase inhibitory factor subunit 1; CRPC: castration-resistant prostate cancer; DNM1L: dynamin 1 like; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; Mdivi-1: mitochondrial division inhibitor 1; Mut-ATP5F1A: Y243,246A mutant of ATP5F1A; OXPHOS: oxidative phosphorylation; PC: prostate cancer; PINK1: PTEN induced kinase 1; p-Y-ATP5F1A: phosphorylated tyrosine 243 and 246 on ATP5F1A; TNK2/ACK1: tyrosine kinase non receptor 2; Ub: ubiquitin; WT: wild type.
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Affiliation(s)
- Surbhi Chouhan
- Department of Surgery, Cancer Research Building, St. Louis, MO, USA
- Division of Urologic Surgery Washington University, St. Louis, MO, USA
| | - Mithila Sawant
- Department of Surgery, Cancer Research Building, St. Louis, MO, USA
- Division of Urologic Surgery Washington University, St. Louis, MO, USA
| | - Cody Weimholt
- Department of Pathology & Immunology Washington University, St. Louis, MO, USA
| | - Jingqin Luo
- Division of Public Health Sciences, Washington University, St. Louis, MO, USA
| | - Robert W. Sprung
- Department of Surgery, Cancer Research Building, St. Louis, MO, USA
| | - Mailyn Terrado
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University, North Chicago, IL, USA
| | - David M. Mueller
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University, North Chicago, IL, USA
| | - H. Shelton Earp
- Lineberger Comprehensive Cancer Center, Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Nupam P. Mahajan
- Department of Surgery, Cancer Research Building, St. Louis, MO, USA
- Division of Urologic Surgery Washington University, St. Louis, MO, USA
- Siteman Cancer Center Washington University, St. Louis, MO, USA
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22
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Impact of VALID Act implementation on mass spectrometry-based clinical proteomic laboratory developed tests. J Mass Spectrom Adv Clin Lab 2023; 28:30-34. [PMID: 36865788 PMCID: PMC9971545 DOI: 10.1016/j.jmsacl.2023.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Mass spectrometry (MS)-based clinical proteomic Laboratory Developed Tests (LDTs) for the measurement of protein biomarkers related to endocrinology, cardiovascular disease, cancer, and Alzheimer's disease are gaining traction in clinical laboratories due to their value in supporting diagnostic and treatment decisions for patients. Under the current regulatory landscape, MS-based clinical proteomic LDTs are regulated by Clinical Laboratory Improvement Amendments (CLIA) under the auspices of the Centers for Medicaid and Medicare Services (CMS). However, should the Verifying Accurate Leading-Edge In Vitro Clinical Test Development (VALID) Act pass, it will grant the FDA greater authority to oversee diagnostic tests, including LDTs. This could impede clinical laboratories' ability to develop new MS-based proteomic LDTs to support existing and emerging patient care needs. Therefore, this review discusses the currently available MS-based proteomic LDTs and their current regulatory landscape in the context of the potential impacts imposed by the passage of the VALID Act.
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23
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Pauletti BA, Granato DC, M Carnielli C, Câmara GA, Normando AGC, Telles GP, Leme AFP. Typic: A Practical and Robust Tool to Rank Proteotypic Peptides for Targeted Proteomics. J Proteome Res 2023; 22:539-545. [PMID: 36480281 DOI: 10.1021/acs.jproteome.2c00585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The selection of a suitable proteotypic peptide remains a challenge for designing a targeted quantitative proteomics assay. Although the criteria are well-established in the literature, the selection of these peptides is often performed in a subjective and time-consuming manner. Here, we have developed a practical and semiautomated workflow implemented in an open-source program named Typic. Typic is designed to run in a command line and a graphical interface to help selecting a list of proteotypic peptides for targeted quantitation. The tool combines the input data and downloads additional data from public repositories to produce a file per protein as output. Each output file includes relevant information to the selection of proteotypic peptides organized in a table, a colored ranking of peptides according to their potential value as targets for quantitation and auxiliary plots to assist users in the task of proteotypic peptides selection. Taken together, Typic leads to a practical and straightforward data extraction from multiple data sets, allowing the identification of most suitable proteotypic peptides based on established criteria, in an unbiased and standardized manner, ultimately leading to a more robust targeted proteomics assay.
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Affiliation(s)
- Bianca A Pauletti
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Daniela C Granato
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Carolina M Carnielli
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Guilherme A Câmara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Ana Gabriela C Normando
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
| | - Guilherme P Telles
- Instituto de Computação, Universidade Estadual de Campinas (UNICAMP), Campinas, 13083-852 São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 São Paulo, Brazil
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24
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Kilpatrick LE, Bouillon R, Davis WC, Henderson CM, Hoofnagle AN, Pauwels S, Vanderschueren D, Waelkens E, Wildiers H, Yen JH, Phinney KW. The influence of proteoforms: assessing the accuracy of total vitamin D-binding protein quantification by proteolysis and LC-MS/MS. Clin Chem Lab Med 2023; 61:78-85. [PMID: 36279170 DOI: 10.1515/cclm-2022-0642] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/26/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Vitamin D-binding protein (VDBP), a serum transport protein for 25-hydroxyvitamin D [25(OH)D], has three common proteoforms which have co-localized amino acid variations and glycosylation. A monoclonal immunoassay was found to differentially detect VDBP proteoforms and methods using liquid chromatography-tandem mass spectrometry (LC-MS/MS) might be able to overcome this limitation. Previously developed multiple reaction monitoring LC-MS/MS methods for total VDBP quantification represent an opportunity to probe the potential effects of proteoforms on proteolysis, instrument response and quantification accuracy. METHODS VDBP was purified from homozygous human donors and quantified using proteolysis or acid hydrolysis and LC-MS/MS. An interlaboratory comparison was performed using pooled human plasma [Standard Reference Material® 1950 (SRM 1950) Metabolites in Frozen Human Plasma] and analyses with different LC-MS/MS methods in two laboratories. RESULTS Several shared peptides from purified proteoforms were found to give reproducible concentrations [≤2.7% coefficient of variation (CV)] and linear instrument responses (R2≥0.9971) when added to human serum. Total VDBP concentrations from proteolysis or amino acid analysis (AAA) of purified proteoforms had ≤1.92% CV. SRM 1950, containing multiple proteoforms, quantified in two laboratories resulted in total VDBP concentrations with 7.05% CV. CONCLUSIONS VDBP proteoforms were not found to cause bias during quantification by LC-MS/MS, thus demonstrating that a family of proteins can be accurately quantified using shared peptides. A reference value was assigned for total VDBP in SRM 1950, which may be used to standardize methods and improve the accuracy of VDBP quantification in research and clinical samples.
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Affiliation(s)
- Lisa E Kilpatrick
- Material Measurement Laboratory, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Roger Bouillon
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - W Clay Davis
- Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC, USA
| | - Clark M Henderson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Seagen, Inc., Bothell, WA, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Steven Pauwels
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Dirk Vanderschueren
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Hans Wildiers
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - James H Yen
- Statistical Engineering Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Karen W Phinney
- Material Measurement Laboratory, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
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25
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Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023; 28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.
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26
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Ponce S, Zhang H. Developing quantitative assays for six urinary glycoproteins using parallel reaction monitoring, data-independent acquisition, and TMT-based data-dependent acquisition. Proteomics 2023; 23:e2200072. [PMID: 36592098 DOI: 10.1002/pmic.202200072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023]
Abstract
Quantitative approaches encompassing parallel reaction monitoring (PRM), data-independent acquisition (DIA), and data-dependent acquisition (DDA) are commonly used to investigate protein expression profiles. However, analytical performances of assays developed using PRM, DIA, and Tandem Mass Tag (TMT)-based DDA for quantitative proteomics have yet not been investigated. Here, we developed assays for glycopeptides identified from six glycoproteins, including Leucine-rich alpha-2-glycoprotein (LRG1), Prostaglandin-H2 D-isomerase (PTGDS), Aminopeptidase N (ANPEP), CD63 antigen (CD63), Clusterin (CLU), and Prostatic acid phosphatase (ACPP), using PRM, DDA, and DIA and evaluated the analytical performances of each assay using the different acquisition modes. We also compared assays in each acquisition mode on three different orbitrap instruments: Thermo Fisher Q Exactive, Exploris 480, and Lumos. We found that DIA showed the largest linear range, highest sensitivity, and most reproducibility. We then applied our developed DIA assays to urine samples from non-aggressive (n = 48) and aggressive (n = 35) prostate cancer patients. In conclusion, we developed assays for the six glycoproteins, evaluated the analytical performances of each assay in DIA, PRM, and PRM acquisition modes on three types of mass spectrometry instruments, and chose the DIA assays for the quantitative analysis of urine samples from patients with aggressive and non-aggressive prostate cancer.
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Affiliation(s)
- Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hui Zhang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
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27
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Gómez-Guerrero N, González-López N, Zapata-Velásquez JD, Martínez-Ramírez JA, Rivera-Monroy ZJ, García-Castañeda JE. Synthetic Peptides in Doping Control: A Powerful Tool for an Analytical Challenge. ACS OMEGA 2022; 7:38193-38206. [PMID: 36340120 PMCID: PMC9631397 DOI: 10.1021/acsomega.2c05296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Peptides are very diverse molecules that can participate in a wide variety of biological processes. In this way, peptides are attractive for doping, since these molecules can activate or trigger biological processes that can improve the sports performance of athletes. Peptide molecules are found in the official World Anti-Doping Agency lists, mainly in sections S2, S4, and S5. In most cases, these molecules have a very short half-life in the body and/or are identical to natural molecules in the body, making it difficult to analyze them as performance-enhancing drugs. This article reviews the role of peptides in doping, with special emphasis on the peptides used as reference materials, the pretreatment of samples in biological matrices, the instrumentation, and the validation of analytical methodologies for the analysis of peptides used in doping. The growing need to characterize and quantify these molecules, especially in complex biological matrices, has generated the need to search for robust strategies that allow for obtaining sensitive and conclusive results. In this sense, strategies such as solid phase peptide synthesis (SPPS), seeking to obtain specific peptides, metabolites, or isotopically labeled analogs, is a key tool for adequate quantification of different peptide molecules in biological matrices. This, together with the use of optimal methodologies for sample pretreatment (e.g., SPE or protein precipitation), and for subsequent analysis by high-resolution techniques (mainly hyphenated LC-HRMS techniques), have become the preferred instrumentation to meet the analytical challenge involved in the analysis of peptides in complex matrices.
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Affiliation(s)
- Néstor
Alejandro Gómez-Guerrero
- Chemistry
Department, Universidad Nacional de Colombia, Bogotá, Carrera 45 No 26-85,
Building 451, 11321 Bogotá, Colombia
- Doping
Control Laboratory, Ministerio del Deporte,
Bogotá, Carrera
68 No 55-65, 111071 Bogotá, Colombia
| | - Nicolás
Mateo González-López
- Pharmacy
Department, Universidad Nacional de Colombia, Bogotá, Carrera 45 No 26-85,
Building 450, 11321 Bogotá, Colombia
| | - Juan Diego Zapata-Velásquez
- Pharmacy
Department, Universidad Nacional de Colombia, Bogotá, Carrera 45 No 26-85,
Building 450, 11321 Bogotá, Colombia
| | - Jorge Ariel Martínez-Ramírez
- Pharmacy
Department, Universidad Nacional de Colombia, Bogotá, Carrera 45 No 26-85,
Building 450, 11321 Bogotá, Colombia
| | - Zuly Jenny Rivera-Monroy
- Chemistry
Department, Universidad Nacional de Colombia, Bogotá, Carrera 45 No 26-85,
Building 451, 11321 Bogotá, Colombia
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28
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Yilmaz O, Jensen AM, Harboe T, Møgster M, Jensen RM, Mjaavatten O, Birkeland E, Spriet E, Sandven L, Furmanek T, Berven FS, Wargelius A, Norberg B. Quantitative proteome profiling reveals molecular hallmarks of egg quality in Atlantic halibut: impairments of transcription and protein folding impede protein and energy homeostasis during early development. BMC Genomics 2022; 23:635. [PMID: 36071374 PMCID: PMC9450261 DOI: 10.1186/s12864-022-08859-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Background Tandem mass tag spectrometry (TMT labeling-LC-MS/MS) was utilized to examine the global proteomes of Atlantic halibut eggs at the 1-cell-stage post fertilization. Comparisons were made between eggs judged to be of good quality (GQ) versus poor quality (BQ) as evidenced by their subsequent rates of survival for 12 days. Altered abundance of selected proteins in BQ eggs was confirmed by parallel reaction monitoring spectrometry (PRM-LC-MS/MS). Correspondence of protein levels to expression of related gene transcripts was examined via qPCR. Potential mitochondrial differences between GQ and BQ eggs were assessed by transmission electron microscopy (TEM) and measurements of mitochondrial DNA (mtDNA) levels. Results A total of 115 proteins were found to be differentially abundant between GQ and BQ eggs. Frequency distributions of these proteins indicated higher protein folding activity in GQ eggs compared to higher transcription and protein degradation activities in BQ eggs. BQ eggs were also significantly enriched with proteins related to mitochondrial structure and biogenesis. Quantitative differences in abundance of several proteins with parallel differences in their transcript levels were confirmed in egg samples obtained over three consecutive reproductive seasons. The observed disparities in global proteome profiles suggest impairment of protein and energy homeostasis related to unfolded protein response and mitochondrial stress in BQ eggs. TEM revealed BQ eggs to contain significantly higher numbers of mitochondria, but differences in corresponding genomic mtDNA (mt-nd5 and mt-atp6) levels were not significant. Mitochondria from BQ eggs were significantly smaller with a more irregular shape and a higher number of cristae than those from GQ eggs. Conclusion The results of this study indicate that BQ Atlantic halibut eggs are impaired at both transcription and translation levels leading to endoplasmic reticulum and mitochondrial disorders. Observation of these irregularities over three consecutive reproductive seasons in BQ eggs from females of diverse background, age and reproductive experience indicates that they are a hallmark of poor egg quality. Additional research is needed to discover when in oogenesis and under what circumstances these defects may arise. The prevalence of this suite of markers in BQ eggs of diverse vertebrate species also begs investigation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08859-0.
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Affiliation(s)
- Ozlem Yilmaz
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway.
| | | | - Torstein Harboe
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
| | - Margareth Møgster
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
| | | | - Olav Mjaavatten
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Even Birkeland
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Endy Spriet
- Department of Biomedicine, The Molecular Imaging Center (MIC), University of Bergen, 5009, Bergen, Norway
| | - Linda Sandven
- Department of Biomedicine, The Molecular Imaging Center (MIC), University of Bergen, 5009, Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, The Proteomics Facility of the University of Bergen (PROBE), 5009, Bergen, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Birgitta Norberg
- Institute of Marine Research, Austevoll Research Station, 5392, Storebø, Norway
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29
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Kim JY, Kim J, Lim YS, Gwak GY, Yeo I, Kim Y, Lee J, Shin D, Lee JH, Kim Y. Proteome Multimarker Panel for the Early Detection of Hepatocellular Carcinoma: Multicenter Derivation, Validation, and Comparison. ACS OMEGA 2022; 7:29934-29943. [PMID: 36061641 PMCID: PMC9434733 DOI: 10.1021/acsomega.2c02926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Conventional methods for the surveillance of hepatocellular carcinoma (HCC) by imaging, with and without serum tumor markers, are suboptimal with regard to accuracy. We aimed to develop and validate a reliable serum biomarker panel for the early detection of HCC using a proteomic technique. This multicenter case-control study comprised 727 patients with HCC and patients with risk factors but no HCC. We developed a multiple reaction monitoring-mass spectrometry (MRM-MS) multimarker panel using 17 proteins from the sera of 398 patients. Area under the receiver operating characteristics curve (AUROC) values of this MRM-MS panel with and without α-fetoprotein (AFP) and protein induced by vitamin K absence or antagonist-II (PIVKA-II) were compared. The combination and standalone MRM-MS panels had higher AUROC values than AFP in the training (0.940 and 0.929 vs 0.775, both P < 0.05), test (0.894 and 0.893 vs 0.593, both P < 0.05), and confirmation sets (0.961 and 0.937 vs 0.806, both P < 0.05) in detecting small single HCC. The combination and standalone MRM-MS panels had significantly higher AUROC values than the GALAD score (0.945 and 0.931 vs 0.829, both P < 0.05). Our proteome 17-protein multimarker panel distinguished HCC patients from high-risk controls and had high accuracy in the early detection of HCC.
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Affiliation(s)
- Ju Yeon Kim
- Department
of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jaenyeon Kim
- Interdisciplinary
Program of Bioengineering, Graduate School,
Seoul National University, Seoul 08826, Republic of Korea
| | - Young-Suk Lim
- Department
of Gastroenterology, Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 44610, Republic of Korea
| | - Geum-Youn Gwak
- Department
of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic
of Korea
| | - Injoon Yeo
- Interdisciplinary
Program of Bioengineering, Graduate School,
Seoul National University, Seoul 08826, Republic of Korea
| | - Yoseop Kim
- Interdisciplinary
Program of Bioengineering, Graduate School,
Seoul National University, Seoul 08826, Republic of Korea
| | - Jihyeon Lee
- Department
of Biomedical Sciences, Seoul National University
College of Medicine, Seoul 03080, Republic of Korea
| | - Dongyoon Shin
- Department
of Biomedical Sciences, Seoul National University
College of Medicine, Seoul 03080, Republic of Korea
| | - Jeong-Hoon Lee
- Department
of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Youngsoo Kim
- Interdisciplinary
Program of Bioengineering, Graduate School,
Seoul National University, Seoul 08826, Republic of Korea
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30
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Lee SY, Lee H, Yun SH, Park EC, Seo G, Kim HY, Jun S, Kim NH, Tark D, Lee JY, Lee CS, Kim SI. Proteomics-based diagnostic peptide discovery for severe fever with thrombocytopenia syndrome virus in patients. Clin Proteomics 2022; 19:28. [PMID: 35842602 PMCID: PMC9287713 DOI: 10.1186/s12014-022-09366-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Severe fever with thrombocytopenia syndrome (SFTS) virus is an emerging infectious virus which causes severe hemorrhage, thrombocytopenia, and leukopenia, with a high fatality rate. Since there is no approved therapeutics or vaccines for SFTS, early diagnosis is essential to manage this infectious disease. METHODS Here, we tried to detect SFTS virus in serum samples from SFTS patients by proteomic analysis. Firstly, in order to obtain the reference MS/MS spectral data of SFTS virus, medium from infected Vero cell culture was used for shotgun proteomic analysis. Then, tryptic peptides in sera from SFTS patients were confirmed by comparative analysis with the reference MS/MS spectral data of SFTS virus. RESULTS Proteomic analysis of culture medium successfully discovered tryptic peptides from all the five antigen proteins of SFTS virus. The comparative spectral analysis of sera of SFTS patients revealed that the N-terminal tryptic peptide of the nucleocapsid (N) protein is the major epitope of SFTS virus detected in the patient samples. The prevalence of the peptides was strongly correlated with the viral load in the clinical samples. CONCLUSIONS Proteomic analysis of SFTS patient samples revealed that nucleocapsid (N) protein is the major antigen proteins in sera of SFTS patients and N-terminal tryptic peptide of the N protein might be a useful proteomic target for direct detection of SFTS virus. These findings suggest that proteomic analysis could be an alternative tool for detection of pathogens in clinical samples and diagnosis of infectious diseases.
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Affiliation(s)
- Sang-Yeop Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea.,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea
| | - Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea.,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea.,Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Sung Ho Yun
- Center for Research Equipment, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Edmond Changkyun Park
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea.,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea.,Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Giwan Seo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea.,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea
| | - Hye-Yeon Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea.,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea
| | - Sangmi Jun
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea.,Center for Research Equipment, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Nam Hoon Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea
| | - Dongseob Tark
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk, 54531, Republic of Korea
| | - Ju Yeon Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Chang-Seop Lee
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju, 54986, Republic of Korea. .,Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, 54907, Republic of Korea.
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea. .,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Republic of Korea. .,Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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31
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Nix C, Cobraiville G, Gou MJ, Fillet M. Potential of Single Pulse and Multiplexed Drift-Tube Ion Mobility Spectrometry Coupled to Micropillar Array Column for Proteomics Studies. Int J Mol Sci 2022; 23:ijms23147497. [PMID: 35886845 PMCID: PMC9319919 DOI: 10.3390/ijms23147497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/02/2022] [Accepted: 07/03/2022] [Indexed: 02/04/2023] Open
Abstract
Proteomics is one of the most significant methodologies to better understand the molecular pathways involved in diseases and to improve their diagnosis, treatment and follow-up. The investigation of the proteome of complex organisms is challenging from an analytical point of view, because of the large number of proteins present in a wide range of concentrations. In this study, nanofluidic chromatography, using a micropillar array column, was coupled to drift-tube ion mobility and time-of-flight mass spectrometry to identify as many proteins as possible in a protein digest standard of HeLa cells. Several chromatographic parameters were optimized. The high interest of drift-tube ion mobility to increase the number of identifications and to separate isobaric coeluting peptides was demonstrated. Multiplexed drift-tube ion mobility spectrometry was also investigated, to increase the sensitivity in proteomics studies. This innovative proteomics platform will be useful for analyzing patient samples to better understand unresolved disorders.
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32
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Li P, Cong Y, Zhang W, Wang L, Ren L, Li X, Yang S, Zhang Z, Li G, Liu L. Simultaneous quantification of apolipoproteins A-I, E, and J in human plasma by LC-MS/MS for clinical application to diabetes mellitus complicated with cardiovascular disease. RSC Adv 2022; 12:16763-16771. [PMID: 35754896 PMCID: PMC9170378 DOI: 10.1039/d2ra02840a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/29/2022] [Indexed: 11/25/2022] Open
Abstract
Apolipoproteins (Apos) play an important role in regulating plasma lipid concentration. Complex disorders of Apos are highly related with diabetes mellitus, cardiovascular and other diseases. Direct measures of lipoprotein fractions for risk assessment suffer from inaccuracy in the dyslipidemia and pathological states. Therefore, a reliable precise assay will be of high clinical utility. LC-MS/MS methods with multiple reaction monitoring modes have proven suitable for multiplexed quantification. We aimed to develop a simple, cost-effective and amenable LC-MS/MS assay for quantification of ApoA-I, ApoE and ApoJ in human plasma. Standards were constructed from substitute matrix and proteotypic peptides for external calibration and corresponding stable isotope labeled peptides were added as internal standards to remove matrix effects. Analytical validation of the assay included the assessment of linearity, accuracy (RE: −3.02% to 5.32%), intra-assay precision (RSD: 2.50% to 6.56%), inter-assay precision (RSD: 0.78% to 6.68%), spiking recovery rate (accuracy: 87.17% to 112.71%), matrix effect (accuracy: 88.03% to 114.87%), and reproducibility and repeatability of sample preparation (RSD: 1.95% to 7.26%). The performance of proteotypic peptides ApoA-I, ApoE and ApoJ was sufficient for triplex quantitation within a linear range from 16.26 to 1626.41 pmol mL−1, 1.03 to 103.35 pmol mL−1 and 0.86 to 86.46 pmol mL−1 respectively. For all quantified peptides, the determination coefficient (R2) was >0.997. Besides, the validated LC-MS/MS method has been successfully applied to the quantification of plasma samples in diabetes mellitus and cardiovascular diseases. We anticipate that this assay may provide an alternative method for future clinical applications. Simultaneous quantification of apolipoproteins A-I, E, and J in human plasma by LC-MS/MS.![]()
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Affiliation(s)
- Pengfei Li
- Pharmacy Department of Beijing Chao-Yang Hospital, Capital Medical University No. 8 Gongti South Road, Chaoyang District Beijing China
| | - Yuting Cong
- Shanghai AB Sciex Analytical Instrument Trading Co. Ltd 518 North Fuquan Road, Changning District Shanghai China
| | - Wen Zhang
- Pharmacy Department of Beijing Chao-Yang Hospital, Capital Medical University No. 8 Gongti South Road, Chaoyang District Beijing China
| | - Lefeng Wang
- Heart Center of Beijing Chao-Yang Hospital, Capital Medical University No. 8 Gongti South Road, Chaoyang District Beijing China
| | - Lulu Ren
- Pharmacy Department of Beijing Chao-Yang Hospital, Capital Medical University No. 8 Gongti South Road, Chaoyang District Beijing China
| | - Xin Li
- Heart Center of Beijing Chao-Yang Hospital, Capital Medical University No. 8 Gongti South Road, Chaoyang District Beijing China
| | - Song Yang
- Pharmacy Department of Beijing Chao-Yang Hospital, Capital Medical University No. 8 Gongti South Road, Chaoyang District Beijing China
| | - Zhiyong Zhang
- Heart Center of Beijing Chao-Yang Hospital, Capital Medical University No. 8 Gongti South Road, Chaoyang District Beijing China
| | - Guoqing Li
- Shanghai AB Sciex Analytical Instrument Trading Co. Ltd 518 North Fuquan Road, Changning District Shanghai China
| | - Lihong Liu
- Pharmacy Department of Beijing Chao-Yang Hospital, Capital Medical University No. 8 Gongti South Road, Chaoyang District Beijing China
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33
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Fernández-Metzler C, Ackermann B, Garofolo F, Arnold ME, DeSilva B, Gu H, Laterza O, Mao Y, Rose M, Vazvaei-Smith F, Steenwyk R. Biomarker Assay Validation by Mass Spectrometry. AAPS J 2022; 24:66. [PMID: 35534647 DOI: 10.1208/s12248-022-00707-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022] Open
Abstract
Decades of discussion and publication have gone into the guidance from the scientific community and the regulatory agencies on the use and validation of pharmacokinetic and toxicokinetic assays by chromatographic and ligand binding assays for the measurement of drugs and metabolites. These assay validations are well described in the FDA Guidance on Bioanalytical Methods Validation (BMV, 2018). While the BMV included biomarker assay validation, the focus was on understanding the challenges posed in validating biomarker assays and the importance of having reliable biomarker assays when used for regulatory submissions, rather than definition of the appropriate experiments to be performed. Different from PK bioanalysis, analysis of biomarkers can be challenging due to the presence of target analyte(s) in the control matrices used for calibrator and quality control sample preparation, and greater difficulty in procuring appropriate reference standards representative of the endogenous molecule. Several papers have been published offering recommendations for biomarker assay validation. The situational nature of biomarker applications necessitates fit-for-purpose (FFP) assay validation. A unifying theme for FFP analysis is that method validation requirements be consistent with the proposed context of use (COU) for any given biomarker. This communication provides specific recommendations for biomarker assay validation (BAV) by LC-MS, for both small and large molecule biomarkers. The consensus recommendations include creation of a validation plan that contains definition of the COU of the assay, use of the PK assay validation elements that support the COU, and definition of assay validation elements adapted to fit biomarker assays and the acceptance criteria for both.
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Affiliation(s)
| | - Brad Ackermann
- Eli Lilly & Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Fabio Garofolo
- BRI - a Frontage Company, 8898 Heather St, Vancouver, British Columbia, V6P 3S8, Canada
| | - Mark E Arnold
- Labcorp Drug Development, 221 Tulip Tree Drive, Westampton, NJ, 08060-5511, USA
| | - Binodh DeSilva
- Bristol-Myers Squibb Co., Route 206 & Province Line Road, Princeton, NJ, 08543, USA
| | - Huidong Gu
- Bristol-Myers Squibb Co., Route 206 & Province Line Road, Princeton, NJ, 08543, USA
| | - Omar Laterza
- Merck and Co Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | - Yan Mao
- Boehringer-Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Mark Rose
- Gossamer Bio Inc., 3013 Science Park Road, Suite 200, San Diego, CA, 92121, USA
| | | | - Rick Steenwyk
- Pfizer-Retired, 8739 N Homestead Circle, Irons, MI, 49644, USA
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34
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Edfors F, Iglesias MJ, Butler LM, Odeberg J. Proteomics in thrombosis research. Res Pract Thromb Haemost 2022; 6:e12706. [PMID: 35494505 PMCID: PMC9039028 DOI: 10.1002/rth2.12706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
A State of the Art lecture titled “Proteomics in Thrombosis Research” was presented at the ISTH Congress in 2021. In clinical practice, there is a need for improved plasma biomarker‐based tools for diagnosis and risk prediction of venous thromboembolism (VTE). Analysis of blood, to identify plasma proteins with potential utility for such tools, could enable an individualized approach to treatment and prevention. Technological advances to study the plasma proteome on a large scale allows broad screening for the identification of novel plasma biomarkers, both by targeted and nontargeted proteomics methods. However, assay limitations need to be considered when interpreting results, with orthogonal validation required before conclusions are drawn. Here, we review and provide perspectives on the application of affinity‐ and mass spectrometry‐based methods for the identification and analysis of plasma protein biomarkers, with potential application in the field of VTE. We also provide a future perspective on discovery strategies and emerging technologies for targeted proteomics in thrombosis research. Finally, we summarize relevant new data on this topic, presented during the 2021 ISTH Congress.
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Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
| | - Maria Jesus Iglesias
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
| | - Lynn M. Butler
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Clinical Chemistry and Blood Coagulation Research Department of Molecular Medicine and Surgery Karolinska Institute Stockholm Sweden
- Clinical Chemistry Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
- Department of Clinical Medicine The Arctic University of Norway Tromsø Norway
| | - Jacob Odeberg
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Department of Clinical Medicine The Arctic University of Norway Tromsø Norway
- Division of Internal Medicine University Hospital of North Norway Tromsø Norway
- Coagulation Unit Department of Hematology Karolinska University Hospital Stockholm Sweden
- Department of Medicine Solna Karolinska Institute Stockholm Sweden
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35
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Berardi G, Frey-Law L, Sluka KA, Bayman EO, Coffey CS, Ecklund D, Vance CGT, Dailey DL, Burns J, Buvanendran A, McCarthy RJ, Jacobs J, Zhou XJ, Wixson R, Balach T, Brummett CM, Clauw D, Colquhoun D, Harte SE, Harris RE, Williams DA, Chang AC, Waljee J, Fisch KM, Jepsen K, Laurent LC, Olivier M, Langefeld CD, Howard TD, Fiehn O, Jacobs JM, Dakup P, Qian WJ, Swensen AC, Lokshin A, Lindquist M, Caffo BS, Crainiceanu C, Zeger S, Kahn A, Wager T, Taub M, Ford J, Sutherland SP, Wandner LD. Multi-Site Observational Study to Assess Biomarkers for Susceptibility or Resilience to Chronic Pain: The Acute to Chronic Pain Signatures (A2CPS) Study Protocol. Front Med (Lausanne) 2022; 9:849214. [PMID: 35547202 PMCID: PMC9082267 DOI: 10.3389/fmed.2022.849214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors and molecular mechanisms that contribute to the development of chronic pain. The Acute to Chronic Pain Signatures (A2CPS) Program aims to characterize the predictive nature of biomarkers (brain imaging, high-throughput molecular screening techniques, or "omics," quantitative sensory testing, patient-reported outcome assessments and functional assessments) to identify individuals who will develop chronic pain following surgical intervention. The A2CPS is a multisite observational study investigating biomarkers and collective biosignatures (a combination of several individual biomarkers) that predict susceptibility or resilience to the development of chronic pain following knee arthroplasty and thoracic surgery. This manuscript provides an overview of data collection methods and procedures designed to standardize data collection across multiple clinical sites and institutions. Pain-related biomarkers are evaluated before surgery and up to 3 months after surgery for use as predictors of patient reported outcomes 6 months after surgery. The dataset from this prospective observational study will be available for researchers internal and external to the A2CPS Consortium to advance understanding of the transition from acute to chronic postsurgical pain.
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Affiliation(s)
- Giovanni Berardi
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Laura Frey-Law
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Kathleen A. Sluka
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Emine O. Bayman
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Christopher S. Coffey
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Dixie Ecklund
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Carol G. T. Vance
- Department of Physical Therapy and Rehabilitation Science, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Dana L. Dailey
- Department of Physical Therapy, St. Ambrose University, Davenport, IA, United States
| | - John Burns
- Department of Psychiatry, Rush University Medical Center, Chicago, IL, United States
| | - Asokumar Buvanendran
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, United States
| | - Robert J. McCarthy
- Department of Anesthesiology, Rush University Medical Center, Chicago, IL, United States
| | - Joshua Jacobs
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, United States
| | - Xiaohong Joe Zhou
- Departments of Radiology, Neurosurgery, and Bioengineering, University of Illinois College of Medicine at Chicago, Chicago, IL, United States
| | - Richard Wixson
- NorthShore Orthopaedic and Spine Institute, NorthShore University HealthSystem, Skokie, IL, United States
| | - Tessa Balach
- Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago, Chicago, IL, United States
| | - Chad M. Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Clauw
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, United States
| | - Douglas Colquhoun
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
| | - Steven E. Harte
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
| | - Richard E. Harris
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
| | - David A. Williams
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Medicine (Rheumatology), University of Michigan, Ann Arbor, MI, United States
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, United States
- Department of Psychology, University of Michigan, Ann Arbor, MI, United States
| | - Andrew C. Chang
- Section of Thoracic Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Jennifer Waljee
- Section of Plastic and Reconstructive Surgery, University of Michigan, Ann Arbor, MI, United States
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Kristen Jepsen
- Institute of Genomic Medicine Genomics Center, University of California, San Diego, La Jolla, CA, United States
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Michael Olivier
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Jon M. Jacobs
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Panshak Dakup
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam C. Swensen
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Anna Lokshin
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Martin Lindquist
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Brian S. Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ciprian Crainiceanu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Scott Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ari Kahn
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, United States
| | - Tor Wager
- Presidential Cluster in Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, United States
| | - Margaret Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - James Ford
- Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Stephani P. Sutherland
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura D. Wandner
- National Institute of Neurological Disorders and Stroke, The National Institutes of Health, Bethesda, MD, United States
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36
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Assignment of a Reference Value of Total Cow’s Milk Protein Content in Baked Cookies Used in an Interlaboratory Comparison. Foods 2022; 11:foods11060869. [PMID: 35327290 PMCID: PMC8956096 DOI: 10.3390/foods11060869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 02/04/2023] Open
Abstract
Interlaboratory comparisons (ILC) in the food allergens field mainly rely on the use of consensus values per applied methodology or even per type of an ELISA test kit. Results suggest good reproducibility; however, possible biases may not be recognized since metrological traceability to an independent reference is lacking. The work presented here utilizes isotope dilution mass spectrometry (IDMS) to assign a reference value of the total cow’s milk protein (TCMP) content in a baked cookie and its associated uncertainty. TCMP consists of several individual proteins, of which five (representing 92%) served us as markers for TCMP. Per marker, one to four proteotypic peptides were selected for the quantification. These were synthesized, and the mass fractions of respective reference solutions were determined with peptide-impurity-corrected amino acid analysis to establish traceability to SI units. Stable isotope labelled (“heavy”) analogues of the proteotypic peptides were also synthesized and blended with extracts of the test material or the reference solutions for IDMS. Through careful measurement design minimizing biases, well-defined model equations were developed, allowing appropriate estimation of the associated uncertainty. The determined reference value of 11.8 ± 1.1 mg TCMP/kg cookie was used for scoring of a novel ILC.
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Lee H, Kim SI. Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. Int J Mol Sci 2022; 23:ijms23042187. [PMID: 35216306 PMCID: PMC8878692 DOI: 10.3390/ijms23042187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
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Affiliation(s)
- Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence:
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Goy RW, Shrestha HK, Colman RJ, Dukes NJ, Ziegler TE, Kapoor A. Development and Validation of an LC-MS/MS Based Quantitative Assay for Marmoset Insulin in Serum. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1195:123150. [PMID: 35247678 PMCID: PMC8958664 DOI: 10.1016/j.jchromb.2022.123150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/07/2022] [Accepted: 01/31/2022] [Indexed: 10/19/2022]
Abstract
Insulin is a peptide hormone that is secreted by the β cells of the pancreas and is essential to the metabolism of carbohydrates, fats, and proteins in the body. The marmoset insulin peptide is not homologous with human insulin and therefore commonly available assays do not work for this species. Due to the increasing popularity of marmoset research, a simple, specific assay for the quantitation of marmoset insulin is needed. This study aimed to develop and validate a bottom-up proteomic workflow with trypsin digestion and analysis using LC coupled with triple quadrupole mass spectrometry (LC-MS/MS). Marmoset serum proteins were subjected to denaturation, reduction, and enzymatic cleavage to extract a unique, 7 amino acid peptide for quantitation of marmoset insulin. Resolution of the peptide was achieved by LC-MS/MS using electrospray ionization operating in positive mode. Calibration was achieved by aliquot dilution of fully synthetic marmoset insulin tryptic peptide into macaque serum. A stable-isotope labeled (13C, 15N) synthetic marmoset insulin tryptic peptide was used as internal standard. The assay was fully validated according to bioanalytical method validation guidelines for linearity, precision, and dilution linearity using purified marmoset insulin. The limit of detection was 15.49 pmol/L and the limit of quantitation was 140.78 pmol/L. Biological validation was achieved by comparison of samples previously run by radioimmunoassay and measurement of the marmoset insulin response to glucose via an oral glucose tolerance test (OGTT). The physiological range of marmoset insulin was shown to be 84.5 to 1222 pmol/L. In summary, this paper presents a simple, reproducible method to measure marmoset insulin in serum using LC-MS/MS.
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Reverter-Branchat G, Eugster PJ, Kuenzli C, Rindlisbacher B, Stauffer T, Nakas CT, Herzig D, Grouzmann E, Bally L. Multiplexed Assay to Quantify the PP-Fold Family of Peptides in Human Plasma Using Microflow Liquid Chromatography-Tandem Mass Spectrometry. Clin Chem 2022; 68:584-594. [PMID: 35015868 DOI: 10.1093/clinchem/hvab229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/29/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Peptide Tyr-Tyr (PYY1-36), pancreatic polypeptide (PP1-36) and neuropeptide Y (NPY1-36) constitute the PP-fold family of peptides that is involved in metabolic regulation. Very low plasma concentrations and cleavage into active 3-36 fragments challenge bioanalytical assays used for the quantification of these peptides. METHODS We developed a multiplexed isotopic dilution assay to quantify PYY1-36, PP1-36, and NPY1-36 and their dipeptidyl peptidase-4 (DPP4)-derived metabolites PYY3-36, PP3-36 and NPY3-36. All peptides were immunocaptured from plasma using a monoclonal antibody and quantified by micro-ultra-HPLC-MS/MS. Blood samples from healthy volunteers were collected fasting and 30 min after nutrient stimulation. Method comparison was performed with commercial immunoassays. RESULTS Linearity was shown in the measured intervals (r2 > 0.99). The lower limit of quantification (LLOQ) with a CV at 20% was 1.5 pM for PYY1-36 and PYY3-36, 3.0 pM for PP1-36 and PP3-36, 0.8 pM for NPY1-36 and 0.5 pM for NPY3-36. In all cases, intra- and inter-assay bias and imprecision were <21%. Pre-analytical stability required addition of a protease inhibitor cocktail. Physiological concentrations of PYY3-36, NPY3-36, PP1-36 and PP3-36 were above the LLOQ in 43% to 100% of the samples. PYY1-36 and NPY1-36 were above the LLOQ in 9% and 0% of the samples, respectively. Immunoassays showed higher concentrations of measurands and poor agreement when compared with micro-UHPLC-MS/MS. CONCLUSIONS The assay allowed for specific multiplexed analysis of the PP-fold family of peptides and their DPP4-cleaved fragments in a single sample, thereby offering new perspectives to study the role and therapeutic potential of these essential peptide hormones in health and metabolic disease.
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Affiliation(s)
- Gemma Reverter-Branchat
- Department of Diabetes, Endocrinology, Nutritional Medicine and Metabolism, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Philippe J Eugster
- Laboratoire des Catécholamines et Peptides, Service de Pharmacologie Clinique, University Hospital of Lausanne, Lausanne, Switzerland
| | | | | | | | - Christos T Nakas
- Laboratory of Biometry, School of Agriculture, University of Thessaly, Nea Ionia Magnesia, Greece.,University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - David Herzig
- Department of Diabetes, Endocrinology, Nutritional Medicine and Metabolism, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Eric Grouzmann
- Laboratoire des Catécholamines et Peptides, Service de Pharmacologie Clinique, University Hospital of Lausanne, Lausanne, Switzerland
| | - Lia Bally
- Department of Diabetes, Endocrinology, Nutritional Medicine and Metabolism, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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Francotte A, Esson R, Abachin E, Vanhamme M, Dobly A, Carpick B, Uhlrich S, Dierick JF, Vanhee C. Development and validation of a targeted LC-MS/MS quantitation method to monitor cell culture expression of tetanus neurotoxin during vaccine production. Talanta 2022; 236:122883. [PMID: 34635263 DOI: 10.1016/j.talanta.2021.122883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022]
Abstract
The tetanus neurotoxin (TeNT) is one of the most toxic proteins known to man, which prior to the use of the vaccine against the TeNT producing bacteria Clostridium tetani, resulted in a 20% mortality rate upon infection. The clinical detrimental effects of tetanus have decreased immensely since the introduction of global vaccination programs, which depend on sustainable vaccine production. One of the major critical points in the manufacturing of these vaccines is the stable and reproducible production of high levels of toxin by the bacterial seed strains. In order to minimize time loss, the amount of TeNT is often monitored during and at the end of the bacterial culturing. The different methods that are currently available to assess the amount of TeNT in the bacterial medium suffer from variability, lack of sensitivity, and/or require specific antibodies. In accordance with the consistency approach and the three Rs (3Rs), both aiming to reduce the use of animals for testing, in-process monitoring of TeNT production could benefit from animal and antibody-free analytical tools. In this paper, we describe the development and validation of a new and reliable antibody free targeted LC-MS/MS method that is able to identify and quantify the amount of TeNT present in the bacterial medium during the different production time points up to the harvesting of the TeNT just prior to further upstream purification and detoxification. The quantitation method, validated according to ICH guidelines and by the application of the total error approach, was utilized to assess the amount of TeNT present in the cell culture medium of two TeNT production batches during different steps in the vaccine production process prior to the generation of the toxoid. The amount of TeNT generated under different physical stress conditions applied during bacterial culture was also monitored.
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Affiliation(s)
- Antoine Francotte
- Department of Expertise and Service Provision, Quality of Vaccines and Blood Products, Sciensano, 14 rue Juliette Wytsman, 1050, Brussels, Belgium; Department of Chemical and Physical Health Risks, Medicines and Health Care Products, Sciensano, 14 rue Juliette Wytsman, 1050, Brussels, Belgium
| | - Raphael Esson
- Sanofi Pasteur, 1541 Avenue Marcel Mérieux, 69280, Marcy l'Etoile, France
| | - Eric Abachin
- Sanofi Pasteur, 1541 Avenue Marcel Mérieux, 69280, Marcy l'Etoile, France
| | - Melissa Vanhamme
- Department of Chemical and Physical Health Risks, Medicines and Health Care Products, Sciensano, 14 rue Juliette Wytsman, 1050, Brussels, Belgium
| | - Alexandre Dobly
- Department of Expertise and Service Provision, Quality of Vaccines and Blood Products, Sciensano, 14 rue Juliette Wytsman, 1050, Brussels, Belgium
| | - Bruce Carpick
- Sanofi Pasteur, 1755 Steeles Ave West, Toronto, Ontario, Canada
| | - Sylvie Uhlrich
- Sanofi Pasteur, 1541 Avenue Marcel Mérieux, 69280, Marcy l'Etoile, France
| | | | - Celine Vanhee
- Department of Chemical and Physical Health Risks, Medicines and Health Care Products, Sciensano, 14 rue Juliette Wytsman, 1050, Brussels, Belgium.
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Sobsey CA, Froehlich B, Batist G, Borchers CH. Immuno-MALDI-MS for Accurate Quantitation of Targeted Peptides from Volume-Restricted Samples. Methods Mol Biol 2022; 2515:203-225. [PMID: 35776354 DOI: 10.1007/978-1-0716-2409-8_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The immuno-MALDI-MS method can be used to quantify low-abundance proteins from clinical samples that offer only a limited amount of material for analysis. An internal standard, in the form of a stable isotope-labeled peptide, is used to ensure reproducible and absolute quantitation. The protocol described here was optimized for the quantitation of AKT1 and AKT2, but we offer instructions on how to adapt the method to target other proteins. The described workflow is compatible with automation via a liquid handling robot for high-throughput applications.
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Affiliation(s)
- Constance A Sobsey
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Bjoern Froehlich
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Gerald Batist
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC, Canada
- Exactis Innovation, Montreal, QC, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC, Canada.
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Gangnus T, Burckhardt BB. Reliable measurement of plasma kinin peptides: Importance of preanalytical variables. Res Pract Thromb Haemost 2022; 6:e12646. [PMID: 35036825 PMCID: PMC8753134 DOI: 10.1002/rth2.12646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The kallikrein-kinin system is involved in many (patho)physiological processes and kinin peptides are considered potential clinical biomarkers. Variance in blood specimen collection and processing, artificial ex vivo bradykinin formation, and rapid degradation of kinins have contributed to divergence in published plasma levels, therefore limiting their significance. Thus, reliable preanalytical settings are highly required. OBJECTIVES This study aimed to develop and evaluate a standardized preanalytical procedure for reliable kinin quantification. The procedure was based on identification of the most impactful variables on ex vivo plasma level alterations. METHODS Suitable protease inhibitors and blood specimen collection and handling conditions were systematically investigated. Their influence on plasma levels of seven kinins was monitored using an established in-house liquid chromatography-tandem mass spectrometry platform. RESULTS In nonstandardized settings, ex vivo rise of bradykinin was found to already occur 30 seconds after blood sampling with high interindividual variation. The screening of 17 protease inhibitors resulted in a customized seven-component protease inhibitor, which efficiently stabilized ex vivo kinin levels. The reliability of kinin levels was substantially jeopardized by prolonged rest time until centrifugation, phlebotomy methodology (eg, straight needles, catheters), vacuum sampling technique, or any time delays during venipuncture. The subsequently developed standardized procedure was applied to healthy volunteers and proved it significantly limited interday and interindividual kinin level variability. CONCLUSION The developed procedure for blood specimen collection and handling is feasible in clinical settings and allows for determination of reliable kinin levels. It may contribute to further elucidating the role of the kallikrein-kinin system in diseases like angioedema, sepsis, or coronavirus disease 2019.
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Affiliation(s)
- Tanja Gangnus
- Institute of Clinical Pharmacy and PharmacotherapyHeinrich‐Heine UniversityDusseldorfGermany
| | - Bjoern B. Burckhardt
- Institute of Clinical Pharmacy and PharmacotherapyHeinrich‐Heine UniversityDusseldorfGermany
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Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG. Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens. Front Immunol 2021; 12:765898. [PMID: 34858420 PMCID: PMC8632241 DOI: 10.3389/fimmu.2021.765898] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022] Open
Abstract
Immunotherapies are revolutionizing cancer care, producing durable responses and potentially cures in a subset of patients. However, response rates are low for most tumors, grade 3/4 toxicities are not uncommon, and our current understanding of tumor immunobiology is incomplete. While hundreds of immunomodulatory proteins in the tumor microenvironment shape the anti-tumor response, few of them can be reliably quantified. To address this need, we developed a multiplex panel of targeted proteomic assays targeting 52 peptides representing 46 proteins using peptide immunoaffinity enrichment coupled to multiple reaction monitoring-mass spectrometry. We validated the assays in tissue and plasma matrices, where performance figures of merit showed over 3 orders of dynamic range and median inter-day CVs of 5.2% (tissue) and 21% (plasma). A feasibility study in clinical biospecimens showed detection of 48/52 peptides in frozen tissue and 38/52 peptides in plasma. The assays are publicly available as a resource for the research community.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Rachel A. Lundeen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Aura Burian
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Dongqing Huang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Tao Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Oscar D. Murillo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Travis D. Lorentzen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | | | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Tessa W. Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Rhonda R. Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joseph G. Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joshua J. Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Jan A. Kaczmarczyk
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Christopher W. Richardson
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Sandra S. Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen M. Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Karen E. Murray
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
| | - Nhan Do
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Mary Brophy
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Stephen W. Wilz
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- Pathology and Laboratory Medicine Service, Program, Veteran’s Administration (VA) Boston Healthcare System, Jamaica Plain, MA, United States
| | - Hongbo Yu
- Pathology and Laboratory Medicine Service, Program, Veteran’s Administration (VA) Boston Healthcare System, Jamaica Plain, MA, United States
- Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Samuel Ajjarapu
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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Fernández AS, Rodríguez-González P, Álvarez L, García M, Iglesias HG, García Alonso JI. Multiple heart-cutting two dimensional liquid chromatography and isotope dilution tandem mass spectrometry for the absolute quantification of proteins in human serum. Anal Chim Acta 2021; 1184:339022. [PMID: 34625263 DOI: 10.1016/j.aca.2021.339022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/28/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
We evaluate here the combination of two-dimensional liquid chromatography (2D-LC) in the multiple heart cutting mode and isotope dilution tandem mass spectrometry for the direct analysis of tryptic digests of serum samples. As a proof of concept, we attempt the quantification of proteotypic peptides of Apolipoprotein AIV (APOA4), Complement C3 (C3) and Vitronectin (VTN) which have been previously identified as potential candidate biomarkers of glaucoma. Using this 2D-LC strategy, analyte enrichment steps are avoided and the sample preparation involved after enzymatic digestion amounted to a simple centrifugation, evaporation of the supernatant and reconstitution in the 1D mobile phase. A mobile phase not compatible with the ESI source (10 mM KH2PO4 at pH 2.7) was used in the first dimension as it provided a satisfactory chromatographic resolution of the peptides and a high buffering capacity avoiding changes in retention times when analyzing complex matrices like human serum. We also demonstrate that using coeluting labelled analogues of the target peptides, protein concentrations were not affected by slight retention time shifts affecting the amount of target peptides transferred to the second dimension. Satisfactory results were obtained when analyzing fortified serum samples (recoveries from 98 to 113%). Precisions in the range of 1-9% RSD were obtained when replicating the analysis of a pooled serum sample. The comparative analysis of serum samples from n = 94 control subjects and n = 91 patients diagnosed with primary open-angle glaucoma did not show significant differences in the APOA4, VTN and C3 concentrations in contrast with previous studies using immunoassays.
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Affiliation(s)
- Amanda Suárez Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Calle Julián Clavería 8, 33006, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, University of Oviedo, Calle Julián Clavería 8, 33006, Oviedo, Spain.
| | - Lydia Álvarez
- Instituto Universitario Fernández-Vega (Fundación de Investigación Oftalmológica, Universidad de Oviedo), 33012, Oviedo, Spain
| | - Montserrat García
- Instituto Universitario Fernández-Vega (Fundación de Investigación Oftalmológica, Universidad de Oviedo), 33012, Oviedo, Spain; Instituto Oftalmológico Fernández-Vega, Avda. Dres. Fernández-Vega, 34, 33012, Oviedo, Spain
| | - Héctor González Iglesias
- Instituto Universitario Fernández-Vega (Fundación de Investigación Oftalmológica, Universidad de Oviedo), 33012, Oviedo, Spain; Instituto Oftalmológico Fernández-Vega, Avda. Dres. Fernández-Vega, 34, 33012, Oviedo, Spain
| | - J Ignacio García Alonso
- Department of Physical and Analytical Chemistry, University of Oviedo, Calle Julián Clavería 8, 33006, Oviedo, Spain
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Mangalaparthi KK, Chavan S, Madugundu AK, Renuse S, Vanderboom PM, Maus AD, Kemp J, Kipp BR, Grebe SK, Singh RJ, Pandey A. A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples. Clin Proteomics 2021; 18:25. [PMID: 34686148 PMCID: PMC8532087 DOI: 10.1186/s12014-021-09331-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/01/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2, a novel human coronavirus, has created a global disease burden infecting > 100 million humans in just over a year. RT-PCR is currently the predominant method of diagnosing this viral infection although a variety of tests to detect viral antigens have also been developed. In this study, we adopted a SISCAPA-based enrichment approach using anti-peptide antibodies generated against peptides from the nucleocapsid protein of SARS-CoV-2. We developed a targeted workflow in which nasopharyngeal swab samples were digested followed by enrichment of viral peptides using the anti-peptide antibodies and targeted parallel reaction monitoring (PRM) analysis using a high-resolution mass spectrometer. This workflow was applied to 41 RT-PCR-confirmed clinical SARS-CoV-2 positive nasopharyngeal swab samples and 30 negative samples. The workflow employed was highly specific as none of the target peptides were detected in negative samples. Further, the detected peptides showed a positive correlation with the viral loads as measured by RT-PCR Ct values. The SISCAPA-based platform described in the current study can serve as an alternative method for SARS-CoV-2 viral detection and can also be applied for detecting other microbial pathogens directly from clinical samples.
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Affiliation(s)
- Kiran K Mangalaparthi
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sandip Chavan
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Anil K Madugundu
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA.,Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka, India
| | - Santosh Renuse
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Patrick M Vanderboom
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Anthony D Maus
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jennifer Kemp
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Stefan K Grebe
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Medicine, Division of Endocrinology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Ravinder J Singh
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA. .,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka, India. .,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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van Bentum M, Selbach M. An Introduction to Advanced Targeted Acquisition Methods. Mol Cell Proteomics 2021; 20:100165. [PMID: 34673283 PMCID: PMC8600983 DOI: 10.1016/j.mcpro.2021.100165] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 01/13/2023] Open
Abstract
Targeted proteomics via selected reaction monitoring (SRM) or parallel reaction monitoring (PRM) enables fast and sensitive detection of a preselected set of target peptides. However, the number of peptides that can be monitored in conventional targeting methods is usually rather small. Recently, a series of methods has been described that employ intelligent acquisition strategies to increase the efficiency of mass spectrometers to detect target peptides. These methods are based on one of two strategies. First, retention time adjustment-based methods enable intelligent scheduling of target peptide retention times. These include Picky, iRT, as well as spike-in free real-time adjustment methods such as MaxQuant.Live. Second, in spike-in triggered acquisition methods such as SureQuant, Pseudo-PRM, TOMAHAQ, and Scout-MRM, targeted scans are initiated by abundant labeled synthetic peptides added to samples before the run. Both strategies enable the mass spectrometer to better focus data acquisition time on target peptides. This either enables more sensitive detection or a higher number of targets per run. Here, we provide an overview of available advanced targeting methods and highlight their intrinsic strengths and weaknesses and compatibility with specific experimental setups. Our goal is to provide a basic introduction to advanced targeting methods for people starting to work in this field.
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Affiliation(s)
- Mirjam van Bentum
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Targeting Ovarian Carcinoma with TSP-1:CD47 Antagonist TAX2 Activates Anti-Tumor Immunity. Cancers (Basel) 2021; 13:cancers13195019. [PMID: 34638503 PMCID: PMC8508526 DOI: 10.3390/cancers13195019] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 11/17/2022] Open
Abstract
TAX2 peptide is a cyclic peptide that acts as an orthosteric antagonist for thrombospondin-1 (TSP-1) interaction with CD47. TAX2 was first described for its anti-angiogenic activities and showed anti-cancer efficacy in numerous preclinical models. Here, we aimed at providing an extensive molecular characterization of TAX2 mode of action, while evaluating its potential in ovarian cancer therapy. Multidisciplinary approaches were used to qualify a TAX2 drug candidate in terms of stability, solubility and potency. Then, efficacy studies, together with benchmark experiments, were performed in relevant mouse models of ovarian carcinoma. TAX2 peptide appears to be stable and soluble in clinically relevant solvents, while displaying a favorable safety profile. Moreover, clinical data mining allowed for the identification of TSP-1 as a relevant pharmacological target in ovarian cancer. In mice, TAX2 therapy inhibits ovarian tumor growth and metastatic dissemination, while activating anti-cancer adaptive immunity. Interestingly, TAX2 also synergizes when administered in combination with anti-PD-1 immune checkpoint inhibitiors. Altogether, our data expose TAX2 as an optimized candidate with advanced preclinical characterization. Using relevant syngeneic ovarian carcinoma models, we highlighted TAX2's ability to convert poorly immunogenic tumors into ones displaying effective anti-tumor T-cell immunity.
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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Sabbah N, Wolf P, Piedvache C, Trabado S, Verdelet T, Cornu C, Souberbielle JC, Chanson P. Reference values for IGF-I serum concentration in an adult population: use of the VARIETE cohort for two new immunoassays. Endocr Connect 2021; 10:1027-1034. [PMID: 34343107 PMCID: PMC8428081 DOI: 10.1530/ec-21-0175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 08/03/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Measurement of IGF-I is important in the management of patients with growth hormone disorders. Here we aim to establish normative data for two new IGF-I assay kits based on a large random sample of the French general adult population. SUBJECTS AND METHODS We measured IGF-I in 911 healthy adults (18-90 years) with two immunoassays (ROCHE Elecsys® and IMMULITE-2000 calibrated against the new IS 02/2547). We compared the data with those of the six immunoassays (iSYS, LIAISON XL, IMMULITE-2000 calibrated against the first IS 87/518, IGF-I RIACT, Mediagnost ELISA, and Mediagnost RIA) that we reported previously. The pairwise concordance among the eight assays was assessed with Bland-Altman plots for both the IGF-1 raw data and the standard deviation scores (SDS), as well as with the percentage of observed agreement and the weighted Kappa coefficient for categorizing IGF-I SDS (ClinicalTrials.gov Identifier: NCT01831648). RESULTS The normative data included the range of values (2.5-97.5 percentiles) given by the two new IGF-I assays according to age group and sex. A formula for the SDS calculation is provided. As for the previous six assays, the lower limits of the reference intervals of the two new assays were similar, but the upper limits varied markedly. The pairwise concordances were only moderate (kappa 0.57). CONCLUSIONS Data obtained for these two new IGF-I immunoassays confirm that despite being obtained in the same large healthy population, the reference intervals of the eight commercial IGF-1 assay kits showed noteworthy differences. The agreement among the various methods was moderate to good.
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Affiliation(s)
- Nadia Sabbah
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Service d’Endocrinologie et des Maladies de la Reproduction, Centre de Référence des Maladies Rares de l’Hypophyse, Le Kremlin-Bicêtre, France
- Hôpital de Cayenne, Service d’Endocrinologie et des Maladies Métaboliques, Cayenne, Guyane Française
| | - Peter Wolf
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Service d’Endocrinologie et des Maladies de la Reproduction, Centre de Référence des Maladies Rares de l’Hypophyse, Le Kremlin-Bicêtre, France
- Division of Endocrinology and Metabolism, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Céline Piedvache
- Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Unité de Recherche Clinique, Le Kremlin-Bicêtre, France
| | - Séverine Trabado
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Le Kremlin-Bicêtre, France
| | - Tristan Verdelet
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Service d’Endocrinologie et des Maladies de la Reproduction, Centre de Référence des Maladies Rares de l’Hypophyse, Le Kremlin-Bicêtre, France
| | - Catherine Cornu
- Centre d’Investigation Clinique, INSERM CIC1407/UMR5558, Hospices Civils de Lyon, Bron, France
| | - Jean-Claude Souberbielle
- Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Service d’Explorations Fonctionnelles, Paris, France
| | - Philippe Chanson
- Université Paris-Saclay, Inserm, Physiologie et Physiopathologie Endocriniennes, Assistance Publique-Hôpitaux de Paris, Hôpital de Bicêtre, Service d’Endocrinologie et des Maladies de la Reproduction, Centre de Référence des Maladies Rares de l’Hypophyse, Le Kremlin-Bicêtre, France
- Correspondence should be addressed to P Chanson:
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Xiong W, Parker CH, Boo CC, Fiedler KL. Comparison of allergen quantification strategies for egg, milk, and peanut in food using targeted LC-MS/MS. Anal Bioanal Chem 2021; 413:5755-5766. [PMID: 34341840 DOI: 10.1007/s00216-021-03550-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/24/2022]
Abstract
Methods for the detection and quantification of food allergens in complex matrices are necessary to ensure compliance with labeling regulations and assess the effectiveness of food allergen preventive controls. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as an orthogonal technique in complement to immunochemical-based assays. However, the absence of established guidelines for MS-based quantification of allergens in food has limited harmonization among the method development community. In this study, different quantification strategies were evaluated using a previously developed multiplexed LC-MS/MS method for the detection of egg, milk, and peanut. Peptide performance criteria (retention time, signal-to-noise ratio, and ion ratio tolerance) were established and quantification approaches using varying calibrants, internal standards, background matrices, and calibration curve preparation schemes were systematically evaluated to refine the previous method for routine laboratory use. A matrix-matched calibration curve using allergen ingredients as calibrants and stable isotope-labeled peptides as internal standards provided the most accurate quantitative results. The strategy was further verified with commercially available reference materials and allowed for the confident detection and quantification of food allergens. This work highlights the need for transparency in calibration strategy and peptide performance requirements for effective evaluation of mass spectrometric methods for the quantification of food allergens.
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Affiliation(s)
- Weili Xiong
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740-3835, USA.,Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, 20740, USA
| | - Christine H Parker
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740-3835, USA
| | - Chelsea C Boo
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740-3835, USA.,Dynamic Omics, Antibody Discovery and Protein Engineering (ADPE), R&D, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Katherine L Fiedler
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740-3835, USA.
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