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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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Calvete JJ, Lomonte B, Saviola AJ, Calderón Celis F, Ruiz Encinar J. Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives. MASS SPECTROMETRY REVIEWS 2023. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.
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Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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3
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Sato K, Jinno S, Nakamura Y, Eto S, Inagaki M. Absolute quantification of bovine lactadherin to screen the anti-rotavirus activity of dairy ingredients. J Dairy Sci 2023; 106:2261-2270. [PMID: 36870836 DOI: 10.3168/jds.2022-22401] [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: 06/13/2022] [Accepted: 11/12/2022] [Indexed: 03/06/2023]
Abstract
The anti-rotavirus components in breast milk and infant formulas play an important role in the prevention of rotavirus infection. The present study examined whether the levels of phospholipids and bovine lactadherin, which are the major components and proteins of the milk fat globule membrane complex, are useful indices of the anti-rotavirus activity of dairy ingredients used in infant formulas. We compared the anti-rotavirus activity of 2 types of dairy ingredients enriched in the milk fat globule membrane complex: high-fat whey protein concentrate (high-fat WPC) and butter milk powder (BMP), using 50% inhibition concentration (IC50) and linear inhibition activity to determine levels of solid contents, total proteins, phospholipids, and bovine lactadherin. Here, we developed a quantification method using full-length isotope-labeled proteins to measure bovine lactadherin levels in these dairy ingredients. The evaluation of anti-rotavirus activity showed that the difference in IC50 was the smallest when the 2 dairy ingredients were compared at the bovine lactadherin level, among other indices in this study. Additionally, no significant difference was observed between the inhibition linearity of 2 dairy ingredients when evaluating only bovine lactadherin levels. These results indicated that the level of bovine lactadherin was more strongly associated with anti-rotavirus activity than the level of phospholipids. Our results suggest that bovine lactadherin levels can be used to estimate the anti-rotavirus activity of dairy ingredients and can be a criterion used in selecting ingredients for infant formulas.
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Affiliation(s)
- Keigo Sato
- Food Microbiology and Function Research Laboratory, Meiji Co. Ltd. 1-29-1 Nanakui, Hachioji, Tokyo 192-0919, Japan.
| | - Shinji Jinno
- Food Microbiology and Function Research Laboratory, Meiji Co. Ltd. 1-29-1 Nanakui, Hachioji, Tokyo 192-0919, Japan
| | - Yoshitaka Nakamura
- Food Microbiology and Function Research Laboratory, Meiji Co. Ltd. 1-29-1 Nanakui, Hachioji, Tokyo 192-0919, Japan
| | - Shinichi Eto
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
| | - Mizuho Inagaki
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
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4
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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Wang X, Shi J, Zhu HJ. Targeted Absolute Protein Quantification Using SILAC Internal Standard and Full-Length Protein Calibrators (TAQSI). Methods Mol Biol 2023; 2603:269-283. [PMID: 36370287 DOI: 10.1007/978-1-0716-2863-8_22] [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] [Indexed: 06/16/2023]
Abstract
Mass spectrometry (MS)-based proteomics has been increasingly used for targeted absolute protein quantifications in both basic and clinical research. There is a great need to overcome some pitfalls of current MS-based targeted absolute protein quantification methods, such as high inter-assay variability and high cost associated with the use of synthesized isotopic peptides/proteins. Here we describe a targeted absolute protein quantification method utilizing SILAC internal standards and unlabeled full-length protein calibrators (TAQSI). The method has proven accurate, precise, reproducible, and cost-effective. Notably, the method is resistant to the variabilities caused by protein extraction and digestion. Moreover, it avoids measurement errors due to nonsynonymous mutations. This versatile method can be used for determining the absolute expressions of numerous proteins in various biological samples. As a proof-of-concept, this method was successfully applied to absolutely quantitate the protein expressions of carboxylesterase 1 (CES1) in human liver tissues.
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Affiliation(s)
- Xinwen Wang
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Jian Shi
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA.
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6
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Targeted Proteomics Analysis of Staphylococcal Superantigenic Toxins in Menstrual Fluid from Women with Menstrual Toxic Shock Syndrome (mTSS). Toxins (Basel) 2022; 14:toxins14120886. [PMID: 36548783 PMCID: PMC9788610 DOI: 10.3390/toxins14120886] [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: 10/23/2022] [Revised: 11/23/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Menstrual toxic shock syndrome (mTSS) is a rare life-threatening febrile illness that occurs in women using intravaginal menstrual protection. It is caused by toxic shock syndrome toxin 1 (TSST-1) produced by Staphylococcus aureus, triggering a sudden onset of rash and hypotension, subsequently leading to multiple organ failure. Detecting TSST-1 and S. aureus virulence factors in menstrual fluid could accelerate the diagnosis and improve therapeutic management of mTSS. However, menstrual fluid is a highly complex matrix, making detection of bacterial toxins challenging. Here, we present a mass-spectrometry-based proteomics workflow for the targeted, quantitative analysis of four S. aureus superantigenic toxins in menstrual fluids (TSST-1, SEA, SEC, and SED). This method was applied to characterize toxin levels in menstrual fluids collected from patients with mTSS and healthy women. Toxins were detectable in samples from patients with mTSS and one healthy donor at concentrations ranging from 0 to 0.46 µg/mL for TSST-1, and 0 to 1.07 µg/mL for SEC. SEA and SED were never detected in clinical specimens, even though many S. aureus strains were positive for the corresponding genes. The method presented here could be used to explore toxin production in vivo in users of intravaginal devices to improve the diagnosis, understanding, and prevention of mTSS.
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Ahire D, Kruger L, Sharma S, Mettu VS, Basit A, Prasad B. Quantitative Proteomics in Translational Absorption, Distribution, Metabolism, and Excretion and Precision Medicine. Pharmacol Rev 2022; 74:769-796. [PMID: 35738681 DOI: 10.1124/pharmrev.121.000449] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A reliable translation of in vitro and preclinical data on drug absorption, distribution, metabolism, and excretion (ADME) to humans is important for safe and effective drug development. Precision medicine that is expected to provide the right clinical dose for the right patient at the right time requires a comprehensive understanding of population factors affecting drug disposition and response. Characterization of drug-metabolizing enzymes and transporters for the protein abundance and their interindividual as well as differential tissue and cross-species variabilities is important for translational ADME and precision medicine. This review first provides a brief overview of quantitative proteomics principles including liquid chromatography-tandem mass spectrometry tools, data acquisition approaches, proteomics sample preparation techniques, and quality controls for ensuring rigor and reproducibility in protein quantification data. Then, potential applications of quantitative proteomics in the translation of in vitro and preclinical data as well as prediction of interindividual variability are discussed in detail with tabulated examples. The applications of quantitative proteomics data in physiologically based pharmacokinetic modeling for ADME prediction are discussed with representative case examples. Finally, various considerations for reliable quantitative proteomics analysis for translational ADME and precision medicine and the future directions are discussed. SIGNIFICANCE STATEMENT: Quantitative proteomics analysis of drug-metabolizing enzymes and transporters in humans and preclinical species provides key physiological information that assists in the translation of in vitro and preclinical data to humans. This review provides the principles and applications of quantitative proteomics in characterizing in vitro, ex vivo, and preclinical models for translational research and interindividual variability prediction. Integration of these data into physiologically based pharmacokinetic modeling is proving to be critical for safe, effective, timely, and cost-effective drug development.
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Affiliation(s)
- Deepak Ahire
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Laken Kruger
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Sheena Sharma
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Vijaya Saradhi Mettu
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Abdul Basit
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington
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8
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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: 0] [Impact Index Per Article: 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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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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10
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Cao Z, Yu LR. Mass Spectrometry-Based Proteomics for Biomarker Discovery. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2486:3-17. [PMID: 35437715 DOI: 10.1007/978-1-0716-2265-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and toxicity of drugs. Mass spectrometry is the core technology for quantitative proteomics, providing the capabilities of identification and quantitation of thousands of proteins. The technology has been applied to biomarker discovery and understanding the mechanisms of drug action. Both stable isotope labeling of proteins or peptides and label-free approaches have been incorporated with multidimensional LC separation and tandem mass spectrometry (LC-MS/MS) to increase the coverage and depth of proteome analysis. A protocol of such an approach exemplified by dimethyl labeling in combination with 2D-LC-MS/MS is described. With further development of novel proteomic tools and increase in sample throughput, the full spectrum of mass spectrometry-based proteomic research will greatly advance systems medicine.
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Affiliation(s)
- Zhijun Cao
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
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Abstract
Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model acetogen Clostridium autoethanogenum grown autotrophically on three gas mixtures (CO, CO+H2, or CO+CO2+H2). We detect the prioritization of proteome allocation for C1 fixation and the significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are likely relevant in vivo for CO oxidation, H2 metabolism, and ethanol production. The integration of proteomic and metabolic flux data demonstrated that enzymes catalyze high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied by changing enzyme catalytic rates rather than concentrations. IMPORTANCE Acetogen bacteria are important for maintaining biosustainability as they can recycle gaseous C1 waste feedstocks (e.g., industrial waste gases and syngas from gasified biomass or municipal solid waste) into fuels and chemicals. Notably, the acetogen Clostridium autoethanogenum is being used as a cell factory in industrial-scale gas fermentation. Here, we perform reliable absolute proteome quantification for the first time in an acetogen. This is important as our work advances both rational metabolic engineering of acetogen cell factories and accurate in silico reconstruction of their phenotypes. Furthermore, this absolute proteomics data set serves as a reference toward a better systems-level understanding of the ancient metabolism of acetogens.
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12
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Vreeke GJ, Lubbers W, Vincken JP, Wierenga PA. A method to identify and quantify the complete peptide composition in protein hydrolysates. Anal Chim Acta 2022; 1201:339616. [DOI: 10.1016/j.aca.2022.339616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/19/2022] [Accepted: 02/14/2022] [Indexed: 11/26/2022]
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Multiplex Detection of 24 Staphylococcal Enterotoxins in Culture Supernatant Using Liquid Chromatography Coupled to High-Resolution Mass Spectrometry. Toxins (Basel) 2022; 14:toxins14040249. [PMID: 35448858 PMCID: PMC9031063 DOI: 10.3390/toxins14040249] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/04/2023] Open
Abstract
Staphylococcal food poisoning outbreaks are caused by the ingestion of food contaminated with staphylococcal enterotoxins (SEs). Among the 27 SEs described in the literature to date, only a few can be detected using immuno-enzymatic-based methods that are strongly dependent on the availability of antibodies. Liquid chromatography, coupled to high-resolution mass spectrometry (LC-HRMS), has, therefore, been put forward as a relevant complementary method, but only for the detection of a limited number of enterotoxins. In this work, LC-HRMS was developed for the detection and quantification of 24 SEs. A database of 93 specific signature peptides and LC-HRMS parameters was optimized using sequences from 24 SEs, including their 162 variants. A label-free quantification protocol was established to overcome the absence of calibration standards. The LC-HRMS method showed high performance in terms of specificity, sensitivity, and accuracy when applied to 49 enterotoxin-producing strains. SE concentrations measured depended on both SE type and the coagulase-positive staphylococci (CPS) strain. This study indicates that LC-MS is a relevant alternative and complementary tool to ELISA methods. The advantages of LC-MS clearly lie in both the multiplex analysis of a large number of SEs, and the automated analysis of a high number of samples.
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14
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Lemke N, El-Khatib AH, Tchipilov T, Jakubowski N, Weller MG, Vogl J. Procedure providing SI-traceable results for the calibration of protein standards by sulfur determination and its application on tau. Anal Bioanal Chem 2022; 414:4441-4455. [PMID: 35316347 PMCID: PMC9142460 DOI: 10.1007/s00216-022-03974-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 11/20/2022]
Abstract
Quantitative proteomics is a growing research area and one of the most important tools in the life sciences. Well-characterized and quantified protein standards are needed to achieve accurate and reliable results. However, only a limited number of sufficiently characterized protein standards are currently available. To fill this gap, a method for traceable protein quantification using sulfur isotope dilution inductively coupled plasma mass spectrometry (ICP-MS) was developed in this study. Gel filtration and membrane filtration were tested for the separation of non-protein-bound sulfur in the protein solution. Membrane filtration demonstrated a better performance due to the lower workload and the very low sulfur blanks of 11 ng, making it well suited for high-purity proteins such as NIST SRM 927, a bovine serum albumin (BSA). The method development was accomplished with NIST SRM 927e and a commercial avidin. The quantified mass fraction of NIST SRM 927e agreed very well with the certified value and showed similar uncertainties (3.6%) as established methods while requiring less sample preparation and no species-specific standards. Finally, the developed procedure was applied to the tau protein, which is a biomarker for a group of neurodegenerative diseases denoted “tauopathies” including, e.g., Alzheimer’s disease and frontotemporal dementia. For the absolute quantification of tau in the brain of transgenic mice overexpressing human tau, a well-defined calibration standard was needed. Therefore, a pure tau solution was quantified, yielding a protein mass fraction of (0.328 ± 0.036) g/kg, which was confirmed by amino acid analysis.
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Affiliation(s)
- Nora Lemke
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Hessische Str. 3-4, 10115, Berlin, Germany
| | - Ahmed H El-Khatib
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany.,Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Teodor Tchipilov
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | | | - Michael G Weller
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany
| | - Jochen Vogl
- , Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Straße 11, 12489, Berlin, Germany.
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15
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Huynh HH, Delatour V, Derbez-Morin M, Liu Q, Boeuf A, Vinh J. Candidate High-Resolution Mass Spectrometry-Based Reference Method for the Quantification of Procalcitonin in Human Serum Using a Characterized Recombinant Protein as a Primary Calibrator. Anal Chem 2022; 94:4146-4154. [PMID: 35235744 PMCID: PMC8928150 DOI: 10.1021/acs.analchem.1c03061] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Procalcitonin
(PCT) is a widely used biomarker for rapid sepsis
diagnosis and antibiotic stewardship. Variability of results in commercial
assays has highlighted the need for standardization of PCT measurements.
An antibody-free candidate reference measurement procedure (RMP) based
on the isotope dilution mass spectrometry and protein calibration
approach was developed and validated to quantify PCT in human serum.
The method allows quantification of PCT from 0.25 to 13.74 μg/L
(R > 0.998) with extension up to 132 μg/L
after
dilution of samples with PCT concentration above 13.74 μg/L.
Intraday bias was between −3.3 and +5.7%, and interday bias
was between −3.0 and −0.7%. Intraday precision was below
5.1%, and interday precision was below 4.0%. The candidate RMP was
successfully applied to the absolute quantification of PCT in five
frozen human serum pools. A recombinant PCT used as a primary calibrator
was characterized by high-resolution mass spectrometry and amino acid
analysis to establish traceability of the results to the SI units.
This candidate RMP is fit to assign target values to secondary certified
reference materials (CRMs) for further use in external quality assessment
schemes to monitor the accuracy and comparability of the commercially
available immunoassay results and to confirm the need for improving
the harmonization of PCT assays. The candidate RMP will also be used
to evaluate whether the correlation between the candidate RMP and
immunoassays is sufficiently high. Overall, this candidate RMP will
support reliable sepsis diagnosis and guide treatment decisions, patient
monitoring, and outcomes.
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Affiliation(s)
- Huu-Hien Huynh
- Department of Biomedical and Organic Chemistry, Laboratoire National de Métrologie et d'Essais (LNE), 75724 Paris, France.,Biological Mass Spectrometry and Proteomics, SMBP, PDC UMR 8249 CNRS, ESPCI Paris, Université PSL, 75005 Paris, France
| | - Vincent Delatour
- Department of Biomedical and Organic Chemistry, Laboratoire National de Métrologie et d'Essais (LNE), 75724 Paris, France
| | - Maxence Derbez-Morin
- Department of Biomedical and Organic Chemistry, Laboratoire National de Métrologie et d'Essais (LNE), 75724 Paris, France.,CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Qinde Liu
- Chemical Metrology Division, Applied Sciences Group, Health Sciences Authority, 117528 Singapore
| | - Amandine Boeuf
- Department of Biomedical and Organic Chemistry, Laboratoire National de Métrologie et d'Essais (LNE), 75724 Paris, France
| | - Joëlle Vinh
- Biological Mass Spectrometry and Proteomics, SMBP, PDC UMR 8249 CNRS, ESPCI Paris, Université PSL, 75005 Paris, France
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16
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Sakaguchi Y, Kinumi T, Takatsu A. A Dual Functional-Group Derivatization Liquid Chromatography–Tandem Mass Spectrometry Method: Application for Quantification of Human Insulin. Chromatographia 2022. [DOI: 10.1007/s10337-022-04136-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes 2022; 10:proteomes10010002. [PMID: 35076627 PMCID: PMC8788469 DOI: 10.3390/proteomes10010002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
In proteomics, it is essential to quantify proteins in absolute terms if we wish to compare results among studies and integrate high-throughput biological data into genome-scale metabolic models. While labeling target peptides with stable isotopes allow protein abundance to be accurately quantified, the utility of this technique is constrained by the low number of quantifiable proteins that it yields. Recently, label-free shotgun proteomics has become the “gold standard” for carrying out global assessments of biological samples containing thousands of proteins. However, this tool must be further improved if we wish to accurately quantify absolute levels of proteins. Here, we used different label-free quantification techniques to estimate absolute protein abundance in the model yeast Saccharomyces cerevisiae. More specifically, we evaluated the performance of seven different quantification methods, based either on spectral counting (SC) or extracted-ion chromatogram (XIC), which were applied to samples from five different proteome backgrounds. We also compared the accuracy and reproducibility of two strategies for transforming relative abundance into absolute abundance: a UPS2-based strategy and the total protein approach (TPA). This study mentions technical challenges related to UPS2 use and proposes ways of addressing them, including utilizing a smaller, more highly optimized amount of UPS2. Overall, three SC-based methods (PAI, SAF, and NSAF) yielded the best results because they struck a good balance between experimental performance and protein quantification.
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18
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Thyroglobulin and thyroid cancer. Cancer Biomark 2022. [DOI: 10.1016/b978-0-12-824302-2.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Li T, Hentschel A, Ahrends R. Analytical comparison of absolute quantification strategies to investigate the Insulin signaling pathway in fat cells. Proteomics 2021; 22:e2100136. [PMID: 34964541 DOI: 10.1002/pmic.202100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
So far, mass spectrometry based targeted proteomics is the most sensitive approach to answer and address specific biological questions in an accurate and quantitative fashion. However, the data analysis design used for such quantification varies in the field leading to discrepancies in the reported values. In this study, different quantification strategies based on calibration curves were evaluated and compared. The best accuracy and coefficient of variation was achieved by ratio to ratio calibration curves. We applied the ratio to ratio quantification approach to analyze very low abundant insulin signaling proteins such as PIK3RA (0.10-0.93 fmol/μg), AKT1 (0.1-0.39 fmol/μg) and the Insulin receptor (0.22 -2.62 fmol/μg) in a fat cell model and demonstrated the adaptation of this pathway at different states of insulin sensitivity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tingting Li
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany.,Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, Vienna, 1090, Austria
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20
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Increased carvone production in Escherichia coli by balancing limonene conversion enzyme expression via targeted quantification concatamer proteome analysis. Sci Rep 2021; 11:22126. [PMID: 34764337 PMCID: PMC8586248 DOI: 10.1038/s41598-021-01469-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 10/27/2021] [Indexed: 11/25/2022] Open
Abstract
(−)-Carvone is a monoterpenoid with a spearmint flavor. A sustainable biotechnological production process for (−)-carvone is desirable. Although all enzymes in (−)-carvone biosynthesis have been functionally expressed in Escherichia coli independently, the yield was low in previous studies. When cytochrome P450 limonene-6-hydroxylase (P450)/cytochrome P450 reductase (CPR) and carveol dehydrogenase (CDH) were expressed in a single strain, by-product formation (dihydrocarveol and dihydrocarvone) was detected. We hypothesized that P450 and CDH expression levels differ in E. coli. Thus, two strains independently expressing P450/CPR and CDH were mixed with different ratios, confirming increased carvone production and decreased by-product formation when CDH input was reduced. The optimum ratio of enzyme expression to maximize (−)-carvone production was determined using the proteome analysis quantification concatamer (QconCAT) method. Thereafter, a single strain expressing both P450/CPR and CDH was constructed to imitate the optimum expression ratio. The upgraded strain showed a 15-fold improvement compared to the initial strain, showing a 44 ± 6.3 mg/L (−)-carvone production from 100 mg/L (−)-limonene. Our study showed the usefulness of the QconCAT proteome analysis method for strain development in the industrial biotechnology field.
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21
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Pailleux F, Maes P, Jaquinod M, Barthelon J, Darnaud M, Lacoste C, Vandenbrouck Y, Gilquin B, Louwagie M, Hesse AM, Kraut A, Garin J, Leroy V, Zarski JP, Bruley C, Couté Y, Samuel D, Ichai P, Faivre J, Brun V. Mass Spectrometry-Based Proteomics Reveal Alcohol Dehydrogenase 1B as a Blood Biomarker Candidate to Monitor Acetaminophen-Induced Liver Injury. Int J Mol Sci 2021; 22:ijms222011071. [PMID: 34681731 PMCID: PMC8540689 DOI: 10.3390/ijms222011071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 12/18/2022] Open
Abstract
Acute liver injury (ALI) is a severe disorder resulting from excessive hepatocyte cell death, and frequently caused by acetaminophen intoxication. Clinical management of ALI progression is hampered by the dearth of blood biomarkers available. In this study, a bioinformatics workflow was developed to screen omics databases and identify potential biomarkers for hepatocyte cell death. Then, discovery proteomics was harnessed to select from among these candidates those that were specifically detected in the blood of acetaminophen-induced ALI patients. Among these candidates, the isoenzyme alcohol dehydrogenase 1B (ADH1B) was massively leaked into the blood. To evaluate ADH1B, we developed a targeted proteomics assay and quantified ADH1B in serum samples collected at different times from 17 patients admitted for acetaminophen-induced ALI. Serum ADH1B concentrations increased markedly during the acute phase of the disease, and dropped to undetectable levels during recovery. In contrast to alanine aminotransferase activity, the rapid drop in circulating ADH1B concentrations was followed by an improvement in the international normalized ratio (INR) within 10–48 h, and was associated with favorable outcomes. In conclusion, the combination of omics data exploration and proteomics revealed ADH1B as a new blood biomarker candidate that could be useful for the monitoring of acetaminophen-induced ALI.
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Affiliation(s)
- Floriane Pailleux
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Pauline Maes
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Michel Jaquinod
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Justine Barthelon
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
- Clinique Universitaire d’Hépato-gastroentérologie, Centre Hospitalier Universitaire Grenoble, 38000 Grenoble, France; (V.L.); (J.-P.Z.)
| | - Marion Darnaud
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Claire Lacoste
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Yves Vandenbrouck
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Benoît Gilquin
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
- Univ. Grenoble Alpes, CEA, LETI, Clinatec, 38000 Grenoble, France
| | - Mathilde Louwagie
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Anne-Marie Hesse
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Alexandra Kraut
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Jérôme Garin
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Vincent Leroy
- Clinique Universitaire d’Hépato-gastroentérologie, Centre Hospitalier Universitaire Grenoble, 38000 Grenoble, France; (V.L.); (J.-P.Z.)
- Institute for Advanced Biosciences, Université Grenoble Alpes, CNRS, INSERM U1209, 38000 Grenoble, France
| | - Jean-Pierre Zarski
- Clinique Universitaire d’Hépato-gastroentérologie, Centre Hospitalier Universitaire Grenoble, 38000 Grenoble, France; (V.L.); (J.-P.Z.)
- Institute for Advanced Biosciences, Université Grenoble Alpes, CNRS, INSERM U1209, 38000 Grenoble, France
| | - Christophe Bruley
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
| | - Didier Samuel
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Philippe Ichai
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Jamila Faivre
- Hepatobiliary Centre, Paul-Brousse University Hospital, INSERM U1193, 94800 Villejuif, France; (M.D.); (C.L.); (D.S.); (P.I.)
- Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Pôle de Biologie Médicale, Paul-Brousse University Hospital, 94800 Villejuif, France
- Correspondence: (J.F.); (V.B.)
| | - Virginie Brun
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France; (F.P.); (P.M.); (M.J.); (J.B.); (Y.V.); (B.G.); (M.L.); (A.-M.H.); (A.K.); (J.G.); (C.B.); (Y.C.)
- Univ. Grenoble Alpes, CEA, LETI, Clinatec, 38000 Grenoble, France
- Correspondence: (J.F.); (V.B.)
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22
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Wheeler JX, Thelwell C, Rigsby P, Whiting G. Quantitation of thrombin-activatable fibrinolysis inhibitor in human plasma by isotope dilution mass spectrometry. Anal Biochem 2021; 638:114413. [PMID: 34644544 DOI: 10.1016/j.ab.2021.114413] [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: 06/11/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022]
Abstract
Measurement of Thrombin-activatable fibrinolysis inhibitor (TAFI) in human plasma is dependent on reproducible assays. To date, standards for measuring TAFI are frequently calibrated relative to pooled normal human plasma and arbitrarily assigned a potency of 100% TAFI, despite variation in TAFI concentrations between plasma pools. Alternatively, TAFI calibrators can be assigned a value in SI units but the approach used for value assignment is not consistent and furthermore, if purified TAFI is used to determine TAFI concentration in plasma, may be adversely affected by matrix effects. A TAFI plasma standard in mass units with traceability to the SI unit of mass is desirable. We report here the establishment of a quantitative mass spectrometry method for TAFI in plasma. Traceability is obtained by reference to calibrators that consist of blank plasma spiked with a defined amount of purified TAFI, value assigned by amino acid analysis. The calibrators are run alongside the samples, using the same preparation steps and conditions; an acetonitrile assisted tryptic digestion and multi-dimensional liquid chromatography (LC) separation followed by SRM-MS analysis. We measured the TAFI quantitatively in human plasma with reproducibility, reliability and precision, and demonstrated the applicability of this approach for value assigning a common reference standard.
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Affiliation(s)
- Jun X Wheeler
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Craig Thelwell
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Peter Rigsby
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK
| | - Gail Whiting
- National Institute for Biological Standards and Control, South Mimms, Potters Bar, EN6 3QG, UK.
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23
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Wenzel C, Drozdzik M, Oswald S. Mass spectrometry-based targeted proteomics method for the quantification of clinically relevant drug metabolizing enzymes in human specimens. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1180:122891. [PMID: 34390906 DOI: 10.1016/j.jchromb.2021.122891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/06/2021] [Accepted: 07/30/2021] [Indexed: 01/15/2023]
Abstract
Biotransformation by phase I and II metabolizing enzymes represents the major determinant for the oral bioavailability of many drugs. To estimate the pharmacokinetics, data on protein abundance of hepatic and extrahepatic tissues, such as the small intestine, are required. Targeted proteomics assays are nowadays state-of-the-art for absolute protein quantification and several methods for quantification of drug metabolizing enzymes have been published. However, some enzymes remain still uncovered by the analytical spectra of those methods. Therefore, we developed and validated a quantification assay for two carboxylesterases (CES-1, CES-2), 17 cytochrome P450 enzymes (CYP) (CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C18, CYP2C19, CYP2D6, CYP2E1, CYP2J2, CYP3A4, CYP3A5, CYP3A7, CYP4F2, CYP4F12, CYP4A11) and five UDP-glucuronosyltransferases (UGTs) (UGT1A1, UGT1A3, UGT2B7, UGT2B15, UGT2B17). Protein quantification was performed by analyzing proteospecific surrogate peptides after tryptic digestion with stable isotope-labelled standards. Chromatographic separation was performed on a Kinetex® 2.6 µm C18 100 Å core-shell column (100 × 2.1 mm) with a gradient elution using 0.1% formic acid and acetonitrile containing 0.1% formic acid with a flow rate of 200 µl/min. Three mass transitions were simultaneously monitored with a scheduled multiple reaction monitoring (sMRM) method for each analyte and standard. The method was partly validated according to current bioanalytical guidelines and met the criteria regarding linearity (0.1-25 nmol/L), within-day and between-day accuracy and precision as well as multiple stability criteria. Finally, the developed method was successfully applied to determine the abundance of the aforementioned enzymes in human intestinal und liver microsomes. Our work offers a new fit for purpose method for the absolute quantification of CES, CYPs and UGTs in various human tissues and can be used for the acquisition of data for physiologically based pharmacokinetic modelling.
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Affiliation(s)
- Christoph Wenzel
- Department of Pharmacology, Center of Drug Absorption and Transport, University Medicine Greifswald, Greifswald, Germany
| | - Marek Drozdzik
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin, Poland
| | - Stefan Oswald
- Institute of Pharmacology and Toxicology, Rostock University Medical Center, Rostock, Germany.
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24
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Liang L, Xia J, Liu C, Liu S. [Highly toxic type Ⅱ ribosome-inactivating proteins ricin and abrin and their detection methods: a review]. Se Pu 2021; 39:260-270. [PMID: 34227307 PMCID: PMC9403808 DOI: 10.3724/sp.j.1123.2020.10001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Ⅱ型核糖体失活蛋白(RIPs)是一类重要的蛋白毒素,该类毒素大都具有一对二硫键连接的A-B链结构特征,B链具有半乳糖结合特性,能够与真核细胞膜表面受体特异性结合,将具有N-糖苷酶活性的A链导入细胞,与核糖体特定位点发生脱嘌呤作用使核糖体失活,最终通过抑制蛋白质合成而展现出细胞毒性。Ⅱ型RIPs毒素毒性极强,来源于植物的蓖麻毒素(ricin)和相思子毒素(abrin)的毒性分别是神经性毒剂维埃克斯(Vx)的385倍和2885倍。同时,该类毒素来源广泛、易于制备、稳定性好,成为一类潜在化生恐怖战剂,受到国内外广泛关注,其中蓖麻毒素作为唯一的蛋白毒素被收录于禁止化学武器公约禁控清单。近年来发生的多次蓖麻毒素邮件恐怖事件,进一步促进了有关Ⅱ型RIPs毒素的准确、灵敏、快速的检测鉴定技术的发展。剧毒性Ⅱ型RIPs毒素的检测鉴定方法主要涉及免疫分析法为代表的特异性识别和生物质谱分析为主的定性定量检测方法,以及基于脱嘌呤反应活性和细胞毒性的毒素活性检测方法。基于抗原-抗体作用的免疫检测法及基于寡核苷酸适配体的特异性识别检测法具有速度快、灵敏度高的优势,但对于复杂样品中高度同源蛋白的检测,易产生假阳性结果。随着生物质谱技术的快速发展,电喷雾离化(ESI)或基质辅助激光解吸离化(MALDI)等技术广泛应用于蛋白质的准确鉴定,不仅能够提供蛋白毒素的准确分子量和结构序列信息,而且能够实现准确定量。酶解质谱法是应用最为广泛的检测鉴定方法,通过酶解肽指纹谱分析,实现蛋白毒素的准确鉴定;对于复杂样品中蛋白毒素的分析,通过多种蛋白酶酶解策略获得丰富的特异性肽段标志物,然后进行肽段标志物的靶向质谱分析从而获得准确的定性及定量信息,方法有效提升了Ⅱ型RIPs毒素鉴定的准确度和灵敏度。免疫分析法和生物质谱法能够准确鉴定Ⅱ型RIPs毒素,但无法识别毒素是否还保持毒性。对于Ⅱ型RIPs毒素的活性分析,主要包括基于N-糖苷酶活性的脱嘌呤反应测定法和细胞毒性测定法,两种方法均可实现毒素毒性的简便、快速、灵敏的分析检测,是Ⅱ型RIPs毒素检测方法的有效补充。由于该类毒素的高度敏感性,国际禁止化学武器组织(OPCW)对相关样品中Ⅱ型RIPs毒素的分析提出了唯一性鉴定的技术要求。该文引用了Ⅱ型RIPs毒素及其检测方法相关的70篇文献,综述了以上Ⅱ型RIPs毒素的结构性质、中毒机理及典型剧毒性Ⅱ型RIPs毒素检测方法的研究进展,对不同检测方法的特点和应用潜力进行了总结,并结合OPCW对Ⅱ型RIPs毒素唯一性鉴定的技术需求,展望了未来Ⅱ型RIPs毒素检测技术研究的发展趋势。
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Affiliation(s)
- Longhui Liang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Junmei Xia
- The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Changcai Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
| | - Shilei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.,The Laboratory of Analytical Chemistry, Research Institute of Chemical Defence, Beijing 102205, China
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25
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McDonald Z, Taylor P, Liyasova M, Liu Q, Ma B. Mass Spectrometry Provides a Highly Sensitive Noninvasive Means of Sequencing and Tracking M-Protein in the Blood of Multiple Myeloma Patients. J Proteome Res 2021; 20:4176-4185. [PMID: 34242034 DOI: 10.1021/acs.jproteome.0c01022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The amino acid sequence of the M-protein for multiple myeloma is unique compared to the polyclonal antibodies in patients' blood. This uniqueness is exploited to develop an ultrasensitive M-protein detection method utilizing mass spectrometry (MS). The method involves the de novo amino acid sequencing of the full-length M-protein, and a targeted MS/MS assay to detect and quantify the unique M-protein sequence in serum samples. Healthy control serum spiked with NISTmAb and serial samples from an MM patient were used to demonstrate the ability of the platform to sequence and monitor a target M-protein. The de novo NISTmAb protein sequence obtained matched the published sequence, confirming the ability of the platform to accurately sequence a target M-protein in serum. NISTmAb was quantified down to 0.0002 g/dL in serum, a level hundreds of times more sensitive than conventional blood-based tests such as SPEP and IFE. The M-protein in the patient sample could be quantified throughout complete remission, demonstrating the utility of the assay to track M-protein considerably beyond the sensitivities of current blood-based tests. Notably, the assay detected a 2-fold rise in M-protein levels 10 months before any changes were detected by conventional IFE. The MS-based assay is highly sensitive, noninvasive, and requires only a small amount of serum, less than 100 μL. Sequencing data is deposited into PRIDE with identifier PXD022784, and quantification data can be found in Panorama Public with identifier PXD022980.
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Affiliation(s)
- Zac McDonald
- Rapid Novor, Inc., Kitchener, Ontario N2G 4X8, Canada
| | - Paul Taylor
- Rapid Novor, Inc., Kitchener, Ontario N2G 4X8, Canada
| | | | - Qixin Liu
- Rapid Novor, Inc., Kitchener, Ontario N2G 4X8, Canada
| | - Bin Ma
- University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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26
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Benesova E, Vidova V, Spacil Z. A comparative study of synthetic winged peptides for absolute protein quantification. Sci Rep 2021; 11:10880. [PMID: 34035340 PMCID: PMC8149832 DOI: 10.1038/s41598-021-90087-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/06/2021] [Indexed: 11/09/2022] Open
Abstract
A proper internal standard choice is critical for accurate, precise, and reproducible mass spectrometry-based proteomics assays. Synthetic isotopically labeled (SIL) proteins are currently considered the gold standard. However, they are costly and challenging to obtain. An alternative approach uses SIL peptides or SIL "winged" peptides extended at C- or/and N-terminus with an amino acid sequence or a tag cleaved during enzymatic proteolysis. However, a consensus on the design of a winged peptide for absolute quantification is missing. In this study, we used human serum albumin as a model system to compare the quantitative performance of reference SIL protein with four different designs of SIL winged peptides: (i) commercially available SIL peptides with a proprietary trypsin cleavable tag at C-terminus, (ii) SIL peptides extended with five amino acid residues at C-terminus, (iii) SIL peptides extended with three and (iv) with five amino acid residues at both C- and N-termini. Our results demonstrate properties of various SIL extended peptides designs, e.g., water solubility and efficiency of trypsin enzymatic cleavage with primary influence on quantitative performance. SIL winged peptides extended with three amino acids at both C- and N-termini demonstrated optimal quantitative performance, equivalent to the SIL protein.
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Affiliation(s)
- Eliska Benesova
- Faculty of Science, Masaryk University, RECETOX, Kamenice 753/5, Pavilion D29, 625 00, Brno, Czech Republic
| | - Veronika Vidova
- Faculty of Science, Masaryk University, RECETOX, Kamenice 753/5, Pavilion D29, 625 00, Brno, Czech Republic
| | - Zdenek Spacil
- Faculty of Science, Masaryk University, RECETOX, Kamenice 753/5, Pavilion D29, 625 00, Brno, Czech Republic.
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27
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Abstract
PURPOSE OF REVIEW Erythropoiesis is a hierarchical process by which hematopoietic stem cells give rise to red blood cells through gradual cell fate restriction and maturation. Deciphering this process requires the establishment of dynamic gene regulatory networks (GRNs) that predict the response of hematopoietic cells to signals from the environment. Although GRNs have historically been derived from transcriptomic data, recent proteomic studies have revealed a major role for posttranscriptional mechanisms in regulating gene expression during erythropoiesis. These new findings highlight the need to integrate proteomic data into GRNs for a refined understanding of erythropoiesis. RECENT FINDINGS Here, we review recent proteomic studies that have furthered our understanding of erythropoiesis with a focus on quantitative mass spectrometry approaches to measure the abundance of transcription factors and cofactors during differentiation. Furthermore, we highlight challenges that remain in integrating transcriptomic, proteomic, and other omics data into a predictive model of erythropoiesis, and discuss the future prospect of single-cell proteomics. SUMMARY Recent proteomic studies have considerably expanded our knowledge of erythropoiesis beyond the traditional transcriptomic-centric perspective. These findings have both opened up new avenues of research to increase our understanding of erythroid differentiation, while at the same time presenting new challenges in integrating multiple layers of information into a comprehensive gene regulatory model.
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Affiliation(s)
- Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada
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28
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Quantification of major royal jelly proteins using ultra performance liquid chromatography tandem triple quadrupole mass spectrometry and application in honey authenticity. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103801] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Smit NPM, Ruhaak LR, Romijn FPHTM, Pieterse MM, van der Burgt YEM, Cobbaert CM. The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:636-647. [PMID: 33522792 PMCID: PMC7944566 DOI: 10.1021/jasms.0c00379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/22/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
Protein mass spectrometry (MS) is an enabling technology that is ideally suited for precision diagnostics. In contrast to immunoassays with indirect readouts, MS quantifications are multiplexed and include identification of proteoforms in a direct manner. Although widely used for routine measurements of drugs and metabolites, the number of clinical MS-based protein applications is limited. In this paper, we share our experience and aim to take away the concerns that have kept laboratory medicine from implementing quantitative protein MS. To ensure added value of new medical tests and guarantee accurate test results, five key elements of test evaluation have been established by a working group within the European Federation for Clinical Chemistry and Laboratory Medicine. Moreover, it is emphasized to identify clinical gaps in the contemporary clinical pathways before test development is started. We demonstrate that quantitative protein MS tests that provide an additional layer of clinical information have robust performance and meet long-term desirable analytical performance specifications as exemplified by our own experience. Yet, the adoption of quantitative protein MS tests into medical laboratories is seriously hampered due to its complexity, lack of robotization and high initial investment costs. Successful and widespread implementation in medical laboratories requires uptake and automation of this next generation protein technology by the In-Vitro Diagnostics industry. Also, training curricula of lab workers and lab specialists should include education on enabling technologies for transitioning to precision medicine by quantitative protein MS tests.
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Affiliation(s)
- Nico P. M. Smit
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L. Renee Ruhaak
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P. H. T. M. Romijn
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Mervin M. Pieterse
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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30
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Rozanova S, Barkovits K, Nikolov M, Schmidt C, Urlaub H, Marcus K. Quantitative Mass Spectrometry-Based Proteomics: An Overview. Methods Mol Biol 2021; 2228:85-116. [PMID: 33950486 DOI: 10.1007/978-1-0716-1024-4_8] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent decades, mass spectrometry has moved more than ever before into the front line of protein-centered research. After being established at the qualitative level, the more challenging question of quantification of proteins and peptides using mass spectrometry has become a focus for further development. In this chapter, we discuss and review actual strategies and problems of the methods for the quantitative analysis of peptides, proteins, and finally proteomes by mass spectrometry. The common themes, the differences, and the potential pitfalls of the main approaches are presented in order to provide a survey of the emerging field of quantitative, mass spectrometry-based proteomics.
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Affiliation(s)
- Svitlana Rozanova
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Katalin Barkovits
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany
| | - Miroslav Nikolov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.,Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany.,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, Bochum, Germany. .,Medical Proteome Analysis, Center for protein diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.
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31
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Cardozo KHM, Lebkuchen A, Okai GG, Schuch RA, Viana LG, Olive AN, Lazari CDS, Fraga AM, Granato CFH, Pintão MCT, Carvalho VM. Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nat Commun 2020; 11:6201. [PMID: 33273458 PMCID: PMC7713649 DOI: 10.1038/s41467-020-19925-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.
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Affiliation(s)
| | - Adriana Lebkuchen
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | | | | | - Luciana Godoy Viana
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | - Aline Nogueira Olive
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | | | - Ana Maria Fraga
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
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32
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Adrait A, Dumonceau JM, Delhaye M, Annessi-Ramseyer I, Frossard JL, Couté Y, Farina A. Liquid Biopsy of Bile based on Targeted Mass Spectrometry for the Diagnosis of Malignant Biliary Strictures. Clin Transl Sci 2020; 14:148-152. [PMID: 33048472 PMCID: PMC7877827 DOI: 10.1111/cts.12890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Bile holds biomarkers of malignant biliary strictures (MBS) but is unsuited for automated analyzers used in routine diagnostic laboratories. Selected reaction monitoring (SRM) is a flexible high‐throughput analytical approach based on targeted mass spectrometry (MS) already implemented in clinical settings. We tested the hypothesis that SRM could be used to quantify cancer biomarkers in human bile. An SRM‐based assay was developed to simultaneously quantify up to 37 peptides from 13 bile proteins in a developmental cohort of 15 patients (MBS, n = 8; benign biliary stricture or obstruction (BBS), n = 7). The most reliable biomarkers were then absolutely quantified by SRM in a verification cohort of 67 patients (MBS, n = 37; BBS, n = 30). The diagnostic performances of single and combined biomarkers were assessed. In the developmental cohort, SRM‐based analysis revealed six protein biomarkers with significantly higher peptide ratios (endogenous vs. standard) in bile from MBS vs. BBS. In the verification cohort, five of these biomarkers proved good diagnostic ability (individual receiver operating characteristic‐area under the receiver operating characteristic curve (ROC‐AUC) up to 0.889, accuracies from 67.8% to 83.1%). Combining bile biomarkers and serum CA19‐9 in 2 panels allowed differentiating MBS from BBS with up to 0.929 ROC‐AUC and 89.8% accuracy. In this study, a newly developed SRM‐based assay proved able to simultaneously quantify multiple biomarkers in bile samples. The combination of bile biomarkers with serum CA19‐9 was highly accurate for the diagnosis of MBS. Liquid biopsy of bile based on targeted MS is eligible to support MBS diagnosis in clinical practice.
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Affiliation(s)
- Annie Adrait
- University Grenoble Alpes, CEA, Inserm, IRIG, BGE, Grenoble, France
| | | | - Myriam Delhaye
- Department of Gastroenterology, Hepatopancreatology and GI Oncology, Erasme University Hospital, Brussels, Belgium
| | | | - Jean-Louis Frossard
- Department of Medicine, Geneva University, Geneva, Switzerland.,Division of Gastroenterology, Geneva University Hospitals, Geneva, Switzerland
| | - Yohann Couté
- University Grenoble Alpes, CEA, Inserm, IRIG, BGE, Grenoble, France
| | - Annarita Farina
- Department of Medicine, Geneva University, Geneva, Switzerland.,Division of Gastroenterology, Geneva University Hospitals, Geneva, Switzerland
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Han SH, Kim JS, Lee Y, Choi H, Kim JW, Na DL, Yang EG, Yu MH, Hwang D, Lee C, Mook-Jung I. Both Targeted Mass Spectrometry and Flow Sorting Analysis Methods Detected the Decreased Serum Apolipoprotein E Level in Alzheimer's Disease Patients. Mol Cell Proteomics 2020; 13:407-19. [PMID: 33498128 DOI: 10.1074/mcp.m113.028639] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apolipoprotein E (ApoE) polymorphism has been appreciated as a valuable predictor of Alzheimer disease (AD), and the associated ε4 allele has been recognized as an indicator of susceptibility to this disease. However, serum ApoE levels have been a controversial issue in AD, due to the great variability regarding the different target detection methods, ethnicity, and the geographic variations of cohorts. The aim of this study was to validate serum ApoE levels in relation to AD, particularly using two distinct detection methods, liquid chromatography-selected reaction monitoring (SRM) mass spectrometry and microsphere-based fluorescence-activated cell sorting (FACS) analysis, to overcome experimental variations. Also, comparison of serum ApoE levels was performed between the level of protein detection by FACS and peptide level by SRM in both control and AD patients. Results from the two detection methods were cross-confirmed and validated. Both methods produced fairly consistent results, showing a significant decrease of serum ApoE levels in AD patients relative to those of a control cohort (43 control versus 45 AD, p < 0.0001). Significant correlation has been revealed between results from FACS and SRM (p < 0.0001) even though lower serum ApoE concentration values were measured in protein by FACS analysis than in peptide-level detections by SRM. Correlation study suggested that a decrease of the serum ApoE level in AD is related to the mini-mental state exam score in both results from different experimental methods, but it failed to show consistent correlation with age, gender, or clinical dementia rating.
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Affiliation(s)
- Sun-Ho Han
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, 28 Yungun-dong, Jongro-gu, Seoul 110-799, Korea
| | - Jun Seok Kim
- BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea
| | - Youngju Lee
- BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea
| | - Heesun Choi
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, 28 Yungun-dong, Jongro-gu, Seoul 110-799, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, 135-710, Korea
| | - Duk Lyul Na
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University, School of Medicine, 50 Ilwon-dong, Kangnam-Ku, Seoul, 135-710, Korea
| | - Eun Gyeong Yang
- BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea
| | - Myeong-Hee Yu
- BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea
| | - Daehee Hwang
- I-Bio Program & Department of Chemical Engineering, POSTECH, Pohang, Korea
| | - Cheolju Lee
- BRI, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Korea;.
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, Seoul National University, College of Medicine, 28 Yungun-dong, Jongro-gu, Seoul 110-799, Korea;.
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Geisslitz S, Longin CFH, Koehler P, Scherf KA. Comparative quantitative LC-MS/MS analysis of 13 amylase/trypsin inhibitors in ancient and modern Triticum species. Sci Rep 2020; 10:14570. [PMID: 32883982 PMCID: PMC7471314 DOI: 10.1038/s41598-020-71413-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/10/2020] [Indexed: 12/16/2022] Open
Abstract
Amylase/trypsin inhibitors (ATIs) are major wheat allergens and they are also implicated in causing non-celiac gluten sensitivity and worsening other inflammatory conditions. With only few studies on ATI contents in different Triticum species available so far, we developed a targeted liquid chromatography-tandem mass spectrometry (LC–MS/MS) method based on stable isotope dilution assays to quantitate the 13 most important ATIs in a well-defined sample set of eight cultivars of common wheat and durum wheat (modern species), as well as spelt, emmer and einkorn (ancient species) grown at three locations in Germany, respectively. Only few ATIs with low contents were detected in einkorn. In contrast, spelt had the highest total ATI contents. Emmer and common wheat had similar total ATI contents, with durum wheat having lower contents than common wheat. Due to the lack of correlation, it was not possible to estimate ATI contents based on crude protein contents. The wheat species had a higher influence on ATI contents than the growing location and the heritability of this trait was high. Despite comparatively low intra-species variability, some cultivars were identified that may be promising candidates for breeding for naturally low ATI contents.
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Affiliation(s)
- Sabrina Geisslitz
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany.,Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20 a, 76131, Karlsruhe, Germany
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - Peter Koehler
- biotask AG, Schelztorstrasse 54-56, 73728, Esslingen am Neckar, Germany
| | - Katharina Anne Scherf
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany. .,Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20 a, 76131, Karlsruhe, Germany.
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Hoshi Y, Uchida Y, Kuroda T, Tachikawa M, Couraud PO, Suzuki T, Terasaki T. Distinct roles of ezrin, radixin and moesin in maintaining the plasma membrane localizations and functions of human blood-brain barrier transporters. J Cereb Blood Flow Metab 2020; 40:1533-1545. [PMID: 31409174 PMCID: PMC7308513 DOI: 10.1177/0271678x19868880] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The purpose of this study was to clarify the roles of ERM proteins (ezrin/radixin/moesin) in the regulation of membrane localization and transport activity of transporters at the human blood-brain barrier (BBB). Ezrin or moesin knockdown in a human in vitro BBB model cell line (hCMEC/D3) reduced both BCRP and GLUT1 protein expression levels on the plasma membrane. Radixin knockdown reduced not only BCRP and GLUT1, but also P-gp membrane expression. These results indicate that P-gp, BCRP and GLUT1 proteins are maintained on the plasma membrane via different ERM proteins. Furthermore, moesin knockdown caused the largest decrease of P-gp and BCRP efflux activity among the ERM proteins, whereas GLUT1 influx activity was similarly reduced by knockdown of each ERM protein. To investigate how moesin knockdown reduced P-gp efflux activity without loss of P-gp from the plasma membrane, we examined the role of PKCβI. PKCβI increased P-gp phosphorylation and reduced P-gp efflux activity. Radixin and moesin proteins were detected in isolated human brain capillaries, and their protein abundances were within a 3-fold range, compared with those in hCMEC/D3 cell line. These findings may mean that ezrin, radixin and moesin maintain the functions of different transporters in different ways at the human BBB.
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Affiliation(s)
- Yutaro Hoshi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yasuo Uchida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Takashi Kuroda
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Masanori Tachikawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | | | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tetsuya Terasaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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Rajkovic A, Jovanovic J, Monteiro S, Decleer M, Andjelkovic M, Foubert A, Beloglazova N, Tsilla V, Sas B, Madder A, De Saeger S, Uyttendaele M. Detection of toxins involved in foodborne diseases caused by Gram‐positive bacteria. Compr Rev Food Sci Food Saf 2020; 19:1605-1657. [DOI: 10.1111/1541-4337.12571] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Andreja Rajkovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Jelena Jovanovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Silvia Monteiro
- Laboratorio Analises, Instituto Superior TecnicoUniversidade de Lisboa Lisbon Portugal
| | - Marlies Decleer
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Mirjana Andjelkovic
- Operational Directorate Food, Medicines and Consumer SafetyService for Chemical Residues and Contaminants Brussels Belgium
| | - Astrid Foubert
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Natalia Beloglazova
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
- Nanotechnology Education and Research CenterSouth Ural State University Chelyabinsk Russia
| | - Varvara Tsilla
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Benedikt Sas
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Annemieke Madder
- Laboratorium for Organic and Biomimetic Chemistry, Department of Organic and Macromolecular ChemistryGhent University Ghent Belgium
| | - Sarah De Saeger
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Mieke Uyttendaele
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
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Van Gool A, Corrales F, Čolović M, Krstić D, Oliver-Martos B, Martínez-Cáceres E, Jakasa I, Gajski G, Brun V, Kyriacou K, Burzynska-Pedziwiatr I, Wozniak LA, Nierkens S, Pascual García C, Katrlik J, Bojic-Trbojevic Z, Vacek J, Llorente A, Antohe F, Suica V, Suarez G, t'Kindt R, Martin P, Penque D, Martins IL, Bodoki E, Iacob BC, Aydindogan E, Timur S, Allinson J, Sutton C, Luider T, Wittfooth S, Sammar M. Analytical techniques for multiplex analysis of protein biomarkers. Expert Rev Proteomics 2020; 17:257-273. [PMID: 32427033 DOI: 10.1080/14789450.2020.1763174] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The importance of biomarkers for pharmaceutical drug development and clinical diagnostics is more significant than ever in the current shift toward personalized medicine. Biomarkers have taken a central position either as companion markers to support drug development and patient selection, or as indicators aiming to detect the earliest perturbations indicative of disease, minimizing therapeutic intervention or even enabling disease reversal. Protein biomarkers are of particular interest given their central role in biochemical pathways. Hence, capabilities to analyze multiple protein biomarkers in one assay are highly interesting for biomedical research. AREAS COVERED We here review multiple methods that are suitable for robust, high throughput, standardized, and affordable analysis of protein biomarkers in a multiplex format. We describe innovative developments in immunoassays, the vanguard of methods in clinical laboratories, and mass spectrometry, increasingly implemented for protein biomarker analysis. Moreover, emerging techniques are discussed with potentially improved protein capture, separation, and detection that will further boost multiplex analyses. EXPERT COMMENTARY The development of clinically applied multiplex protein biomarker assays is essential as multi-protein signatures provide more comprehensive information about biological systems than single biomarkers, leading to improved insights in mechanisms of disease, diagnostics, and the effect of personalized medicine.
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Affiliation(s)
- Alain Van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Fernado Corrales
- Functional Proteomics Laboratory, Centro Nacional De Biotecnología , Madrid, Spain
| | - Mirjana Čolović
- Department of Physical Chemistry, "Vinča" Institute of Nuclear Sciences, University of Belgrade , Belgrade, Serbia
| | - Danijela Krstić
- Institute of Medical Chemistry, Faculty of Medicine, University of Belgrade , Belgrade, Serbia
| | - Begona Oliver-Martos
- Neuroimmunology and Neuroinflammation Group. Instituto De Investigación Biomédica De Málaga-IBIMA. UGC Neurociencias, Hospital Regional Universitario De Málaga , Malaga, Spain
| | - Eva Martínez-Cáceres
- Immunology Division, LCMN, Germans Trias I Pujol University Hospital and Research Institute, Campus Can Ruti, Badalona, and Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma De Barcelona , Cerdanyola Del Vallès, Spain
| | - Ivone Jakasa
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb , Zagreb, Croatia
| | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health , Zagreb, Croatia
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm, IRIG, BGE , Grenoble, France
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Biology, The Cyprus School of Molecular Medicine/The Cyprus Institute of Neurology and Genetics , Nicosia, Cyprus
| | - Izabela Burzynska-Pedziwiatr
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Lucyna Alicja Wozniak
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Stephan Nierkens
- Center for Translational Immunology, University Medical Center Utrecht & Princess Máxima Center for Pediatric Oncology , Utrecht, The Netherlands
| | - César Pascual García
- Materials Research and Technology Department, Luxembourg Institute of Science and Technology (LIST) , Belvaux, Luxembourg
| | - Jaroslav Katrlik
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences , Bratislava, Slovakia
| | - Zanka Bojic-Trbojevic
- Laboratory for Biology of Reproduction, Institute for the Application of Nuclear Energy - INEP, University of Belgrade , Belgrade, Serbia
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital , Oslo, Norway
| | - Felicia Antohe
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Viorel Suica
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Guillaume Suarez
- Center for Primary Care and Public Health (Unisanté), University of Lausanne , Lausanne, Switzerland
| | - Ruben t'Kindt
- Research Institute for Chromatography (RIC) , Kortrijk, Belgium
| | - Petra Martin
- Department of Medical Oncology, Midland Regional Hospital Tullamore/St. James's Hospital , Dublin, Ireland
| | - Deborah Penque
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ines Lanca Martins
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ede Bodoki
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Bogdan-Cezar Iacob
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Eda Aydindogan
- Department of Chemistry, Graduate School of Sciences and Engineering, Koç University , Istanbul, Turkey
| | - Suna Timur
- Institute of Natural Sciences, Department of Biochemistry, Ege University , Izmir, Turkey
| | | | | | - Theo Luider
- Department of Neurology, Erasmus MC , Rotterdam, The Netherlands
| | | | - Marei Sammar
- Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College , Karmiel, Israel
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Simultaneous quantification of major capsid protein of human papillomavirus 16 and human papillomavirus 18 in multivalent human papillomavirus vaccines by liquid chromatography-tandem mass spectrometry. J Chromatogr A 2020; 1619:460962. [DOI: 10.1016/j.chroma.2020.460962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 01/29/2023]
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A novel mass spectrometry method for the absolute quantification of several cytochrome P450 and uridine 5'-diphospho-glucuronosyltransferase enzymes in the human liver. Anal Bioanal Chem 2020; 412:1729-1740. [PMID: 32030490 DOI: 10.1007/s00216-020-02445-7] [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: 10/09/2019] [Revised: 12/22/2019] [Accepted: 01/21/2020] [Indexed: 10/25/2022]
Abstract
Cytochrome P450 (CYP450) and 5'-diphosphate glucuronosyltransferases (UGT) are the two major families of drug-metabolizing enzymes in the human liver microsome (HLM). As a result of their frequent abundance fluctuation among populations, the accurate quantification of these enzymes in different individuals is important for designing patient-specific dosage regimens in the framework of precision medicine. The preparation and quantification of internal standards is an essential step for the quantitative analysis of enzymes. However, the commonly employed stable isotope labeling-based strategy (QconCAT) suffers from requiring very expensive isotopic reagents, tedious experimental procedures, and long labeling times. Furthermore, arginine-to-proline conversion during metabolic isotopic labeling compromises the quantification accuracy. Therefore, we present a new strategy that replaces stable isotope-labeled amino acids with lanthanide labeling for the preparation and quantification of QconCAT internal standard peptides, which leads to a threefold reduction in the reagent costs and a fivefold reduction in the time consumed. The absolute amount of trypsin-digested QconCAT peptides can be obtained by lanthanide labeling and inductively coupled plasma-optical emission spectrometry (ICP-OES) analysis with a high quantification accuracy (%RE < 20%). By taking advantage of the highly selective and facile ICP-OES procedure and multiplexed large-scale absolute target protein quantification using biological mass spectrometry, this strategy was successfully used for the absolute quantification of drug-metabolizing enzymes. We obtained good linearity (correlation coefficient > 0.95) over concentrations spanning 2.5 orders of magnitude with improved sensitivity (limit of quantification = 2 fmol) in nine HLM samples, indicating the potential of this method for large-scale absolute target protein quantification in clinical samples. Graphical abstract.
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40
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Matthiesen R, Carvalho AS. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry. Methods Mol Biol 2020; 2051:161-197. [PMID: 31552629 DOI: 10.1007/978-1-4939-9744-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.
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Affiliation(s)
- Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal.
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Abstract
Mass spectrometry, a technology to determine the mass of ionized molecules and biomolecules, is increasingly applied for the global identification and quantification of proteins. Proteomics applies mass spectrometry in many applications, and each application requires consideration of analytical choices, instrumental limitations and data processing steps. These depend on the aim of the study and means of conducting it. Choosing the right combination of sample preparation, MS instrumentation, and data processing allows exploration of different aspects of the proteome. This chapter gives an outline for some of these commonly used setups and some of the key concepts, many of which later chapters discuss in greater depth. Understanding and handling mass spectrometry data is a multifaceted task that requires many user decisions to obtain the most comprehensive information from an MS experiment. Later chapters in this book deal in-depth with various aspects of the process and how different tools addresses the many analytical challenges. This chapter revises the basic concept in mass spectrometry (MS)-based proteomics.
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Affiliation(s)
- Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal.
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Huang YS, Lin YM, Chen H, Wu CH, Syu CH, Huang TE, Do QT, Chen SH. Targeting Endogenous Adduction Level of Serum Albumin by Parallel Reaction Monitoring via Standard Additions and Intact Protein Measurement: Biological Dosimetry of Catechol Estrogens. Anal Chem 2019; 91:15922-15931. [DOI: 10.1021/acs.analchem.9b04425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yu-Shan Huang
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Yu-Min Lin
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Hsin Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Chih-Hsing Wu
- Department of Family Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Chong-Hua Syu
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Ting-En Huang
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Quynh-Trang Do
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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Anjo SI, Simões I, Castanheira P, Grãos M, Manadas B. Use of recombinant proteins as a simple and robust normalization method for untargeted proteomics screening: exhaustive performance assessment. Talanta 2019; 205:120163. [DOI: 10.1016/j.talanta.2019.120163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 01/13/2023]
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Merkley ED, Burnum-Johnson KE, Anderson LN, Jenson SC, Wahl KL. Uniformly 15N-Labeled Recombinant Ricin A-Chain as an Internal Retention Time Standard for Increased Confidence in Forensic Identification of Ricin by Untargeted Nanoflow Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem 2019; 91:13372-13376. [PMID: 31596564 DOI: 10.1021/acs.analchem.9b03389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ricin, a toxic protein from the castor plant, is of forensic and biosecurity interest because of its high toxicity and common occurrence in crimes and attempted crimes. Qualitative methods to detect ricin are therefore needed. Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics methods are well suited because of their high specificity. Specificity in LC-MS/MS comes from both the LC and MS components. However, modern untargeted proteomics methods often use nanoflow LC, which has less reproducible retention times than standard-flow LC, making it challenging to use retention time as a point of identification in a forensic assay. We address this challenge by using retention times relative to a standard, namely, the uniformly 15N-labeled ricin A-chain produced recombinantly in a bacterial expression system. This material, added as an internal standard prior to trypsin digestion, produces a stable-isotope-labeled standard for every ricin tryptic peptide in the sample. We show that the MS signals for 15N and natural isotopic abundance ricin peptides are distinct, with mass shifts that correspond to the numbers of nitrogen atoms in each peptide or fragment. We also show that, as expected, labeled and unlabeled peptides coelute, with relative retention time differences of less than 0.2%.
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Affiliation(s)
- Eric D Merkley
- Chemical and Biological Signature Sciences Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kristin E Burnum-Johnson
- Integrative Omics Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Lindsey N Anderson
- Biological Systems Science Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Sarah C Jenson
- Chemical and Biological Signature Sciences Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Karen L Wahl
- Integrative Omics Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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Heaven MR, Wilson L, Barnes S, Brenner M. Relative stabilities of wild-type and mutant glial fibrillary acidic protein in patients with Alexander disease. J Biol Chem 2019; 294:15604-15612. [PMID: 31484723 DOI: 10.1074/jbc.ra119.009777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/24/2019] [Indexed: 01/13/2023] Open
Abstract
Alexander disease (AxD) is an often fatal astrogliopathy caused by dominant gain-of-function missense mutations in the glial fibrillary acidic protein (GFAP) gene. The mechanism by which the mutations produce the AxD phenotype is not known. However, the observation that features of AxD are displayed by mice that express elevated levels of GFAP from a human WT GFAP transgene has contributed to the notion that the mutations produce AxD by increasing accumulation of total GFAP above some toxic threshold rather than the mutant GFAP being inherently toxic. A possible mechanism for accumulation of GFAP in AxD patients is that the mutated GFAP variants are more stable than the WT, an attribution abetted by observations that GFAP complexes containing GFAP variants are more resistant to solvent extraction. Here we tested this hypothesis by determining the relative levels of WT and mutant GFAP in three individuals with AxD, each of whom carried a common but different GFAP mutation (R79C, R239H, or R416W). Mass spectrometry analysis identified a peptide specific to the mutant or WT GFAP in each patient, and we quantified this peptide by comparing its signal to that of an added [15N]GFAP standard. In all three individuals, the level of mutant GFAP was less than that of the WT. This finding suggests that AxD onset is due to an intrinsic toxicity of the mutant GFAP instead of it acting indirectly by being more stable than WT GFAP and thereby increasing the total GFAP level.
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Affiliation(s)
- Michael R Heaven
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Landon Wilson
- Department of Pharmacology and Toxicology, Targeted Metabolomics and Proteomics Laboratory, University of Alabama, Birmingham, Alabama 35294
| | - Stephen Barnes
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294.,Department of Pharmacology and Toxicology, Targeted Metabolomics and Proteomics Laboratory, University of Alabama, Birmingham, Alabama 35294
| | - Michael Brenner
- Department of Neurobiology, University of Alabama, Birmingham, Alabama 35294
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Development and validation of an absolute protein assay for the simultaneous quantification of fourteen CYP450s in human microsomes by HPLC-MS/MS-based targeted proteomics. J Pharm Biomed Anal 2019; 173:96-107. [DOI: 10.1016/j.jpba.2019.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 01/05/2023]
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Determination of Cetuximab in Plasma by Liquid Chromatography-High-Resolution Mass Spectrometry Orbitrap With a Stable Labeled 13C,15N-Cetuximab Internal Standard. Ther Drug Monit 2019; 41:467-475. [PMID: 31306393 DOI: 10.1097/ftd.0000000000000613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Cetuximab (CTX) is a chimeric IgG1 Kappa monoclonal antibody used to treat head and neck cancer and colorectal cancer. Previous clinical studies indicated that the pharmacokinetics of CTX influences patient survival. Thus, individualizing CTX treatment by measuring trough levels of the drug in plasma could have a major impact on clinical efficacy. METHODS To measure these levels, a full-length stable isotope-labeled CTX standard was used in a generic, rapid, and high-throughput sample preparation protocol based on IgG capture followed by trypsin digestion, on-line solid-phase extraction cleanup, and liquid chromatography-high resolution mass spectrometry (LC-HRMS). RESULTS The optimized method displayed good analytical performance and was linear over a range from 5 to 150 mcg/mL. The within-run and between-run imprecision of the assay were equal to or less than 10%, for 6 replicates at 3 different concentrations and for runs performed on 5 separate days. The plasma CTX concentrations in 19 patients were also determined. CONCLUSIONS The results showed that quantification of mAb in clinical samples does not strictly require a tandem mass spectrometry system, and LC-HRMS is also relevant in this context. This first study implementing a quantitative LC-HRMS assay with a specific stable isotope-labeled mAb internal standard paves the way for more robust clinical monitoring of anticancer mAbs.
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Kontostathi G, Makridakis M, Zoidakis J, Vlahou A. Applications of multiple reaction monitoring targeted proteomics assays in human plasma. Expert Rev Mol Diagn 2019; 19:499-515. [PMID: 31057016 DOI: 10.1080/14737159.2019.1615448] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Multiple (or selected) reaction monitoring-mass spectrometry (MRM/SRM) is a targeted proteomic method that can be used for relative and absolute quantification. Multiple reports exist supporting the potential of the approach in proteomic biomarker validation. Areas covered: To get an overview of the applications of MRM in protein quantification in plasma, a search in MedLine/PubMed was performed using the keywords: 'MRM/SRM plasma proteomic/proteomics/proteome'. The retrieved studies were further filtered to focus on disease biomarkers and the main results are summarized. Expert opinion: MRM is increasingly employed for the quantification of both well-established but also newly discovered putative biomarkers and occasionally their post-translationally modified forms in plasma. Fractionation is regularly required for the detection of low abundance proteins. Standardized procedures to facilitate assay establishment and marker quantification have been proposed and, in few cases, implemented. Nevertheless, in most cases, absolute quantification is not performed. To advance, multiple technical issues including the regular use of standard labeled peptides and appropriate quality controls to monitor assay performance should be considered. Additionally, clinical aspects involving careful study design to address biomarker clinical use should also be considered.
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Affiliation(s)
- Georgia Kontostathi
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Manousos Makridakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Jerome Zoidakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Antonia Vlahou
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
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Koike H, Kanda M, Hayashi H, Matsushima Y, Ohba Y, Nakagawa Y, Nagano C, Sekimura K, Hirai A, Shindo T, Otsuka K, Kamiie J, Sasamoto T, Hashimoto T. Quantification of staphylococcal enterotoxin type A in cow milk by using a stable isotope-labelled peptide via liquid chromatography-tandem mass spectrometry. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:1098-1108. [PMID: 31094669 DOI: 10.1080/19440049.2019.1615641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, the staphylococcal enterotoxin type A (SEA) contaminant was quantified in cow milk by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with the use of a stable isotope-labelled peptide of SEA as an internal standard. SEA was cleaned up in a two-step process that included pH control and trichloroacetic acid (TCA) precipitation. The pH control phase eliminated other proteins. TCA precipitation cleaned up SEA without special equipment. An appropriate enzyme-to-protein ratio maximised tryptic digestion. A desalting process guaranteed the stable retention of SEA-digested peptides. The coverage of amino-acid sequences (>10%) clearly identified the toxin's presence. SEA was accurately quantified using LC-MS/MS based on a multiple-reaction monitoring mode. The developed method was validated based on spiked recovery tests at 50 and 100 µg kg-1 conducted with two samples collected on a daily basis for five days based on Japanese validation guidelines. The new method exhibited good accuracy which ranged from 80% to 82%. The relative standard deviations of repeatability were 13-14% and the relative standard deviations of within-laboratory reproducibility were 13-18%. These standard deviations satisfied the criteria of the Japanese validation guidelines. The quantification limit was estimated to be 10 µg kg-1.
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Affiliation(s)
- Hiroshi Koike
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Maki Kanda
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Hiroshi Hayashi
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yoko Matsushima
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yumi Ohba
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Yukiko Nakagawa
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Chieko Nagano
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Kotaro Sekimura
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Akihiko Hirai
- b Department of Microbiology , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Tetsuya Shindo
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Kenji Otsuka
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Junichi Kamiie
- c Laboratory of Veterinary Pathology, School of Veterinary Medicine , Azabu University , Sagamihara , Japan
| | - Takeo Sasamoto
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
| | - Tsuneo Hashimoto
- a Department of Food Safety , Tokyo Metropolitan Institute of Public Health , Tokyo , Japan
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Zhou M, Duong DM, Johnson ECB, Dai J, Lah JJ, Levey AI, Seyfried NT. Mass Spectrometry-Based Quantification of Tau in Human Cerebrospinal Fluid Using a Complementary Tryptic Peptide Standard. J Proteome Res 2019; 18:2422-2432. [PMID: 30983353 DOI: 10.1021/acs.jproteome.8b00920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here, we report a method for the generation of complementary tryptic (CompTryp) isotope-labeled peptide standards for the relative and absolute quantification of proteins by mass spectrometry (MS). These standards can be digested in parallel with either trypsin (Tryp-C) or trypsin-N (Tryp-N), to generate peptides that significantly overlap in primary sequence having C- and N-terminal arginine and lysine residues, respectively. As a proof of concept, an isotope-labeled CompTryp standard was synthesized for Tau, a well-established biomarker in Alzheimer's disease (AD), which included both N- and C-terminal heavy isotope-labeled (15N and 13C) arginine residues and flanking amino acid sequences to monitor proteolytic digestion. Despite having the exact same mass, the N- and C-terminal heavy Tau peptides are distinguishable by retention time and MS/MS fragmentation profiles. The isotope-labeled Tau CompTryp standard was added to human cerebrospinal fluid (CSF) followed by parallel digestion with Tryp-N and Tryp-C. The native and isotope-labeled peptide pairs were quantified by parallel reaction monitoring (PRM) in a single assay. Notably, both tryptic peptides were effective at quantifying Tau in human CSF, and both showed a significant difference in CSF Tau levels between AD and controls. Treating these CompTryp Tau peptide measurements as independent replicates also improved the coefficient of variation and correlation with Tau immunoassays. More broadly, we propose that CompTryp standards can be generated for any protein of interest, providing an efficient method to improve the robustness and reproducibility for MS analysis of clinical and research samples.
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Affiliation(s)
| | | | | | - Jingting Dai
- Department of Neurology, Second Xiangya Hospital , Central South University , Changsha , Hunan 410078 , China
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