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Malarvannan M, Ravichandiran V, Paul D. Advances in analytical technologies for emerging drug modalities and their separation challenges in LC-MS systems. J Chromatogr A 2024; 1732:465226. [PMID: 39111181 DOI: 10.1016/j.chroma.2024.465226] [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: 05/31/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024]
Abstract
The last few years have seen a rise in the identification and development of bio-therapeutics through the use of cutting-edge delivery methods or bio-formulations, which has created bio-analytical difficulties. Every year, new bio-pharmaceutical product innovations come out, but the analytical development of these products is challenging. Quantifying the products and components of conjugated molecular structures is essential for preclinical and clinical research in order to guide therapeutic development, given their intrinsic complexity. Furthermore, a significant amount of information is needed for the measurement of these unique modalities by LC-MS techniques. Numerous LC-MS based methods have been developed, including AEX-HPLC-MS, RP-IP-LCMS, HILIC-MS, LCHRMS, Microflow-LC-MS, ASMS, Hybrid LBA/LC-MS, and more. However, these methods continue to face problems, prompting the development of alternative approaches. Therefore, developing bio-molecules that are this complicated and, low in concentration requires a skilled LC-MS based approach and knowledgeable personnel. This review covers general novel modalities classifications, sample preparation techniques, current status and bio-analytical strategies for analyzing various novel modalities, including gene bio-therapeutics, oligonucleotides, antibody-drug conjugates, monoclonal antibodies and PROTACs. It also covers how these strategies have been used in the past and how they are being used now to address challenges in the development of LC-MS based methods, as well as improvement strategies, current advancements and recent developed methods. We additionally covered on the benefits and drawbacks of different LC-MS based techniques for the examination of bio-pharmaceutical products and the future perspectives.
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Affiliation(s)
- M Malarvannan
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India
| | - V Ravichandiran
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India
| | - David Paul
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India.
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2
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Hallin EI, Serkland TT, Bjånes TK, Skrede S. High-throughput, low-cost quantification of 11 therapeutic antibodies using caprylic acid precipitation and LC-MS/MS. Anal Chim Acta 2024; 1313:342789. [PMID: 38862206 DOI: 10.1016/j.aca.2024.342789] [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: 04/19/2024] [Accepted: 05/25/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Therapeutic drug monitoring of treatment with therapeutic antibodies is hampered by the application of a wide range of different methods in the quantification of serum levels. LC-MS based methods could significantly improve comparability of results from different laboratories, but such methods are often considered complicated and costly. We developed a method for LC-MS/MS based quantification of 11 therapeutic antibodies concomitantly measured in a single run, with emphasis on simplicity in sample preparation and low cost. RESULTS After a single-step sample purification using caprylic acid precipitation to remove interfering proteins, the sample underwent proteolysis followed by LC-MS/MS analysis. Infliximab is used as internal standard for sample preparation while isotope-labeled signature peptides identified for each analyte are internal standards for the LC-MS/MS normalization. The method was validated according to recognized guidelines, and pipetting steps can be performed by automated liquid handling systems. The total precision of the method ranged between 2.7 and 7.3 % (5.1 % average) across the quantification range of 4-256 μg/ml for all 11 drugs, with an average accuracy of 96.3 %. Matrix effects were xamined in 55 individual patient samples instead of the recommended 6, and 147 individual patient samples were screened for interfering compounds. SIGNIFICANCE AND NOVELTY Our method for simultaneous quantification of 11 t-mAb in human serum allows an unprecedented integration of robustness, speed and reduced complexity, which could pave the way for uniform use in research projects and clinical settings alike. In addition, the first LC-MS protocol for signature peptide-based quantification of durvalumab is described. This high throughput method can be readily adapted to a drug panel of choice.
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Affiliation(s)
- Erik I Hallin
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Jonas Lies vei 87, N-5021, Bergen, Norway
| | - Trond Trætteberg Serkland
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Jonas Lies vei 87, N-5021, Bergen, Norway; Department of Clinical Science, Faculty of Medicine, University of Bergen, Jonas Lies vei 87, N-5021, Bergen, Norway
| | - Tormod K Bjånes
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Jonas Lies vei 87, N-5021, Bergen, Norway
| | - Silje Skrede
- Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Jonas Lies vei 87, N-5021, Bergen, Norway; Department of Clinical Science, Faculty of Medicine, University of Bergen, Jonas Lies vei 87, N-5021, Bergen, Norway.
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3
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Pamela BE, Patole C, Thamizhmaran S, Moorthy RK, Manoj J, Thanigachalam A, Hocker JRS, Drevets DA, Oommen A, Rajshekhar V, Carabin H, Vasudevan P. Mass Spectrometry Identifies Taenia solium Proteins in Sera of Patients With and Without Parenchymal Neurocysticercosis. Parasite Immunol 2024; 46:e13058. [PMID: 39072810 DOI: 10.1111/pim.13058] [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: 12/14/2023] [Revised: 05/31/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
Neurocysticercosis (NCC), a major cause of global acquired epilepsy, results from Taenia solium larval brain infection. T. solium adult worms release large numbers of infective eggs into the environment contributing to high levels of exposure in endemic areas. This study identifies T. solium proteins in the sera of individuals with and without NCC using mass spectrometry to examine exposure in endemic regions. Forty-seven patients (18-51 years), 24 parenchymal NCC (pNCC), 8 epilepsy of unknown aetiology, 7 glioma, 8 brain tuberculoma, and 7 healthy volunteers were studied. Trypsin digested sera were subject to liquid chromatography-tandem mass spectrometry and spectra of 375-1700 m/z matched against T. solium WormBase ParaSite database with MaxQuant software to identify T. solium proteins. Three hundred and nineteen T. solium proteins were identified in 87.5% of pNCC and 56.6% of non-NCC subjects. Three hundred and four proteins were exclusive to pNCC sera, seven to non-NCC sera and eight in both. Ten percent, exhibiting immune-modulatory properties, originated from the oncosphere and cyst vesicular fluid. In conclusion, in endemic regions, T. solium proteins are detected in sera of individuals with and without pNCC. The immunomodulatory nature of these proteins may influence susceptibility and course of infection.
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Affiliation(s)
| | - Chhaya Patole
- Proteomic Facility, National Centre for Biological Sciences, Bangalore, Karnataka, India
| | - Subashini Thamizhmaran
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ranjith K Moorthy
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Josephin Manoj
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anupriya Thanigachalam
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - James R S Hocker
- Laboratory of Carol F. Webb, Section of Rheumatology, Immunology and Allergy (Previously at Biochemistry and Molecular Biology), University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Douglas A Drevets
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, USA
| | - Anna Oommen
- Gudalur Adivasi Hospital, Gudalur, Tamil Nadu, India
| | - Vedantam Rajshekhar
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamil Nadu, India
| | - Hélène Carabin
- Department of Pathology and Microbiology, University of Montreal, Montreal, Canada
- Department of Social and Preventive Medicine, University of Montreal, Montreal, Canada
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Centre, Oklahoma City, USA
- Centre de Recherche en Santé Publique (CReSP), Montreal, Canada
- Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique (GREZOSP), Saint-Hyacinthe, Canada
| | - Prabhakaran Vasudevan
- Department of Neurological Sciences, Christian Medical College, Vellore, Tamil Nadu, India
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4
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Kline JT, Belford MW, Boeser CL, Huguet R, Fellers RT, Greer JB, Greer SM, Horn DM, Durbin KR, Dunyach JJ, Ahsan N, Fornelli L. Orbitrap Mass Spectrometry and High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Enable the in-Depth Analysis of Human Serum Proteoforms. J Proteome Res 2023; 22:3418-3426. [PMID: 37774690 PMCID: PMC10629265 DOI: 10.1021/acs.jproteome.3c00488] [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: 08/04/2023] [Indexed: 10/01/2023]
Abstract
Blood serum and plasma are arguably the most commonly analyzed clinical samples, with dozens of proteins serving as validated biomarkers for various human diseases. Top-down proteomics may provide additional insights into disease etiopathogenesis since this approach focuses on protein forms, or proteoforms, originally circulating in blood, potentially providing access to information about relevant post-translational modifications, truncations, single amino acid substitutions, and many other sources of protein variation. However, the vast majority of proteomic studies on serum and plasma are carried out using peptide-centric, bottom-up approaches that cannot recapitulate the original proteoform content of samples. Clinical laboratories have been slow to adopt top-down analysis, also due to higher sample handling requirements. In this study, we describe a straightforward protocol for intact proteoform sample preparation based on the depletion of albumin and immunoglobulins, followed by simplified protein fractionation via polyacrylamide gel electrophoresis. After molecular weight-based fractionation, we supplemented the traditional liquid chromatography-tandem mass spectrometry (LC-MS2) data acquisition with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to further simplify serum proteoform mixtures. This LC-FAIMS-MS2 method led to the identification of over 1000 serum proteoforms < 30 kDa, outperforming traditional LC-MS2 data acquisition and more than doubling the number of proteoforms identified in previous studies.
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Affiliation(s)
- Jake T. Kline
- Department
of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | | | | | - Romain Huguet
- Thermo
Scientific, San Jose, California 95134, United States
| | - Ryan T. Fellers
- Proteinaceous,
Inc., Evanston, Illinois 60204, United
States
| | - Joseph B. Greer
- Proteinaceous,
Inc., Evanston, Illinois 60204, United
States
| | | | - David M. Horn
- Thermo
Scientific, San Jose, California 95134, United States
| | | | | | - Nagib Ahsan
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
- Mass
Spectrometry, Proteomics and Metabolomics Core Facility, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Luca Fornelli
- Department
of Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
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5
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Sleumer B, Zwerwer J, van Faassen M, Vos MJ, Bischoff R, Kema IP, van de Merbel NC. An antibody-free LC-MS/MS method for the quantification of sex hormone binding globulin in human serum and plasma. Clin Chem Lab Med 2023; 61:1266-1274. [PMID: 36773321 DOI: 10.1515/cclm-2022-1225] [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: 11/29/2022] [Accepted: 01/26/2023] [Indexed: 02/13/2023]
Abstract
OBJECTIVES Sex hormone binding globulin (SHBG) is a hormone binding protein which plays an important role in regulating the transport and availability of biologically active androgens and estradiol to target cells and used to calculate free testosterone concentrations. METHODS A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed, featuring an albumin removal step followed by a tryptic digestion. After a reduction step with dithiothreitol and alkylation with iodoacetamide three signature peptides were used for the quantification of SHBG. RESULTS The method enables the quantification of serum and plasma SHBG over the clinically relevant range of 200-20,000 ng/mL and was validated according to the most recent guidelines. The LC-MS/MS method correlates well with the Abbott Alinity immunoassay (R2>0.95), but the LC-MS/MS results are on average 16-17% lower than the immunoassay results, which is consistent for all three signature peptides. CONCLUSIONS The LC-MS/MS method which includes an albumin depletion step allows quantification of SHBG in serum and plasma without an immunocapture step at clinically relevant SHBG levels, thus contributing to better lab-to-lab consistency of results.
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Affiliation(s)
- Bas Sleumer
- ICON Bioanalytical Laboratories, Assen, The Netherlands
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jordan Zwerwer
- ICON Bioanalytical Laboratories, Assen, The Netherlands
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Michel J Vos
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
| | - Ido P Kema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nico C van de Merbel
- ICON Bioanalytical Laboratories, Assen, The Netherlands
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
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Lee JY, Mehta PK, Subedi S, Lee KH. Development of ratiometric fluorescent probes based on peptides for sensing Pb 2+ in aquatic environments and human serum. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 294:122502. [PMID: 36841137 DOI: 10.1016/j.saa.2023.122502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/31/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The detection of Pb2+ ions in aquatic environments and biofluid samples is crucial for assessment of human health. Herein, we synthesized two fluorescent probes (1 and 2) consisting of the peptide receptor for Pb2+ and a benzothiazolyl-cyanovinylene fluorophore that exhibited excimer-like emission when it aggregated. The peptide-based probes sensitively detected Pb2+ in purely aqueous solution (1% DMF) through ratiometric fluorescent response with a decrease in monomer emission at 520 nm and an increase in excimer emission at 570 nm. Specially, probe 2 showed remarkable detection features such as high selectivity for Pb2+over 15 metal ions, high binding affinity (Kd = 5.83 × 10-7 M) for Pb2+, significant emission intensity changes, low detection limit (3.8 nM) of Pb2+, high water solubility, and visible light excitation (450 nm). Probe 2 was successfully used to quantify nanomolar concentration (0 ∼ 800 nM) of Pb2+ in real water samples (ground water and tap water). Specially, 2 was successfully applied for the quantification of Pb2+ in human serum by combination of microwave-assisted human serum digestion and filtration of digested serum by anion exchange cartridge. We clearly investigated the binding mode of 2 with Pb2+ using 1H NMR, IR spectroscopy, pH titration, confocal microscopy, and size analysis. The peptide-based fluorescent probe might have great application potential for sensing Pb2+ in aquatic environments and biofluid samples.
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Affiliation(s)
- Jae Yoon Lee
- Research Center for Controlling Intercellular Communication and Education and Research Center for Smart Energy Materials and Process, Department of Chemistry and Chemical Engineering, Inha University, Incheon 402-751, South Korea
| | - Pramod Kumar Mehta
- Research Center for Controlling Intercellular Communication and Education and Research Center for Smart Energy Materials and Process, Department of Chemistry and Chemical Engineering, Inha University, Incheon 402-751, South Korea
| | - Sumita Subedi
- Research Center for Controlling Intercellular Communication and Education and Research Center for Smart Energy Materials and Process, Department of Chemistry and Chemical Engineering, Inha University, Incheon 402-751, South Korea
| | - Keun-Hyeung Lee
- Research Center for Controlling Intercellular Communication and Education and Research Center for Smart Energy Materials and Process, Department of Chemistry and Chemical Engineering, Inha University, Incheon 402-751, South Korea.
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7
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Bader JM, Albrecht V, Mann M. MS-based proteomics of body fluids: The end of the beginning. Mol Cell Proteomics 2023:100577. [PMID: 37209816 PMCID: PMC10388585 DOI: 10.1016/j.mcpro.2023.100577] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet existing ones are often unspecific and new ones have been very slow to enter the clinic. Mass spectrometry (MS)-based proteomics excels by its untargeted nature, specificity of identification and quantification making it an ideal technology for biomarker discovery and routine measurement. It has unique attributes compared to affinity binder technologies, such as OLINK Proximity Extension Assay and SOMAscan. In a previous review we described technological and conceptual limitations that had held back success (Geyer et al., 2017). We proposed a 'rectangular strategy' to better separate true biomarkers by minimizing cohort-specific effects. Today, this has converged with advances in MS-based proteomics technology, such as increased sample throughput, depth of identification and quantification. As a result, biomarker discovery studies have become more successful, producing biomarker candidates that withstand independent verification and, in some cases, already outperform state-of-the-art clinical assays. We summarize developments over the last years, including the benefits of large and independent cohorts, which are necessary for clinical acceptance. They are also required for machine learning or deep learning. Shorter gradients, new scan modes and multiplexing are about to drastically increase throughput, cross-study integration, and quantification, including proxies for absolute levels. We have found that multi-protein panels are inherently more robust than current single analyte tests and better capture the complexity of human phenotypes. Routine MS measurement in the clinic is fast becoming a viable option. The full set of proteins in a body fluid (global proteome) is the most important reference and the best process control. Additionally, it increasingly has all the information that could be obtained from targeted analysis although the latter may be the most straightforward way to enter into regular use. Many challenges remain, not least of a regulatory and ethical nature, but the outlook for MS-based clinical applications has never been brighter.
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Affiliation(s)
- Jakob M Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Vincent Albrecht
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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Sun Y, Xu J, Xie X, Song H. An effective pre-treatment method for eliminating interference by serum albumin for analysis of anti-rHSA antibodies. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1116-1122. [PMID: 36756782 DOI: 10.1039/d2ay01528e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Analysis of anti-drug antibodies (ADAs) is important for risk assessment in clinical trials. ADA detection can be very difficult in the presence of high circulating levels of drugs or target proteins. We present an effective pretreatment method for eliminating interference by endogenous albumin for analyses of recombinant human serum albumin (rHSA) ADAs. Polyethylene glycol (PEG) precipitation was used to extract albumin-ADA immune complexes from serum samples. Following acid dissociation, albumin-reactive antibodies could be detected through an electrochemiluminescence (ECL) method. Normal human serum was used to establish detectable cut points. Goat anti-human albumin was used as the positive control to evaluate the assay performance. With regard to detection of anti-HSA antibodies, pretreatment with PEG could reduce the interference from albumin in serum. We discovered that the optimized PEG precipitation and acid dissociation (PandA) method had good performance in terms of sensitivity, drug tolerance, and selectivity.
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Affiliation(s)
- Yunjuan Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
| | - Jingzhi Xu
- United-Power Pharma Tech Co., Ltd, Beijing, China
| | - Xinyao Xie
- United-Power Pharma Tech Co., Ltd, Beijing, China
| | - Haifeng Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.
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9
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Roopashri AN, Divyashree M, Savitha J. High-sensitivity profiling of glycoproteins from ovarian cancer sera using lectin-affinity and LC-ESI-Q-TOF-MS/MS. CURRENT RESEARCH IN BIOTECHNOLOGY 2023. [DOI: 10.1016/j.crbiot.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
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10
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Kruger L, Yue G, Paquette A, Sathyanarayana S, Enquobahrie DA, Bammler TK, MacDonald J, Zhao Q, Prasad B. An optimized proteomics-based approach to estimate blood contamination and cellular heterogeneity of frozen placental tissue. Placenta 2023; 131:111-118. [PMID: 36584637 PMCID: PMC9912121 DOI: 10.1016/j.placenta.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/07/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Archived human placental tissue specimens are vital for studying placenta pathophysiology and toxicology. Proteomics analysis of placental tissue provides mechanistic and translational information, but the highly perfused and heterogenous nature of the placenta creates confounding technical variability. In this study, we developed an optimized proteomics-based approach to address the technical variability of proteomics data by normalizing blood contamination and cellular heterogeneity of archived placenta samples. METHODS Placenta samples (n = 99) were homogenized, digested using trypsin, and analyzed by liquid chromatography mass-spectrometry. Label-free quantification (LFQ) intensities of the proteins were analyzed for their correlation with blood (albumin) and placenta (aromatase) markers. Proteins that positively correlated with albumin and negatively correlated with aromatase or vice versa were considered blood and placental proteins, respectively. Next, the cellular heterogeneity of individual placenta samples was evaluated by quantifying specific cellular markers of cytotrophoblasts, syncytiotrophoblasts, extravillous trophoblasts, fibroblasts, Hofbauer cells, and decidual cells. RESULTS We found that placental proteins were contaminated by 41 to 85% blood proteins. Analysis of cellular markers confirmed syncytiotrophoblasts as the major cell type in placenta (i.e., 41 ± 9% of all cell types). Two samples showed distinct cell compositions with higher levels of the extravillous trophoblasts and decidual cells. DISCUSSION In summary, the optimized proteomics-based approach to estimate blood contamination and cellular heterogeneity of placental tissues has the potential to address technical variability in placenta proteomics analysis, which can be extended to other highly perfused and heterogenous tissues.
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Affiliation(s)
- Laken Kruger
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Guihua Yue
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Alison Paquette
- Seattle Children's Research Institute, Seattle, WA, USA; University of Washington, Seattle, WA, USA
| | - Sheela Sathyanarayana
- Seattle Children's Research Institute, Seattle, WA, USA; University of Washington, Seattle, WA, USA
| | | | | | | | - Qi Zhao
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA.
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11
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Development of simple and rapid method for Emicizumab quantification by LC-MS/MS in human plasma. J Pharm Biomed Anal 2022; 223:115163. [DOI: 10.1016/j.jpba.2022.115163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/07/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022]
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12
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Nanostructured Silicon Enabled HR-MS for the Label-Free Detection of Biomarkers in Colorectal Cancer Plasma Small Extracellular Vesicles. JOURNAL OF NANOTHERANOSTICS 2022. [DOI: 10.3390/jnt3040013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Despite improvements in treatment options for advanced colorectal cancer (CRC), survival outcomes are still best for patients with non-metastasised disease. Diagnostic tools to identify blood-based biomarkers and assist in CRC subtype classification could afford a means to track CRC progression and treatment response. Cancer cell-derived small extracellular vesicles (EVs) circulating in blood carry an elevated cargo of lipids and proteins that could be used as a signature of tumour suppressor/promoting events or stages leading up to and including metastasis. Here, we used pre-characterised biobanked plasma samples from surgical units, typically with a low volume (~100 µL), to generate and discover signatures of CRC-derived EVs. We employed nanostructured porous silicon (pSi) surface assisted-laser desorption/ionisation (SALDI) coupled with high-resolution mass spectrometry (HR-MS), to allow sensitive detection of low abundant analytes in plasma EVs. When applied to CRC samples, SALDI-HR-MS enabled the detection of the peptide mass fingerprint of cancer suppressor proteins, including serine/threonine phosphatases and activating-transcription factor 3. SALDI-HR-MS also allowed the detection of a spectrum of glycerophospholipids and sphingolipid signatures in metastatic CRC. We observed that lithium chloride enhanced detection sensitivity to elucidate the structure of low abundant lipids in plasma EVs. pSi SALDI can be used as an effective system for label-free and high throughput analysis of low-volume patient samples, allowing rapid and sensitive analysis for CRC classification.
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13
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Development and validation of an LC-MS/MS method for the quantification of fascin proteins in human serum. Bioanalysis 2022; 14:1095-1109. [PMID: 36154676 DOI: 10.4155/bio-2022-0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Fascin is an actin-bundling protein that has been linked to tumor cell migration, invasion, metastasis, disease progression and mortality, thus serving as a novel cancer biomarker. Bioanalytical methods to measure fascin in biological matrices are sparsely reported, while accurate quantitation of fascin levels may lend support for fascin as a promising therapeutic target. Method: An LC-MS/MS-based method involving protein precipitation, enzymatic digestion and solid phase extraction was developed and validated for the quantitation of fascin in human serum. Linearity over a calibration range of 5-500 ng/ml with a LLOQ of 5 ng/ml, great accuracy and precision, excellent parallelism as well as high extraction recovery were achieved. Conclusion: This method provides a valuable tool for anticancer drug development and cancer treatment.
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14
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Byerley LO, Chang HM, Lorenzen B, Guidry J, Hardman WE. Impact of dietary walnuts, a nutraceutical option, on circulating markers of metabolic dysregulation in a rodent cachectic tumor model. Biomed Pharmacother 2022; 155:113728. [PMID: 36152410 PMCID: PMC9618292 DOI: 10.1016/j.biopha.2022.113728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Nutraceutical foods, like walnuts which are rich in immunonutrients, can have medicinal benefits. Dietary walnuts have been shown to slow or prevent tumor growth in mice genetically programmed to grow breast or prostate tumors. This study investigated whether walnuts could exert the same preventable effect in a transplantable carcinoma rat model. Methods: Eighteen rats were randomly fed a diet containing walnuts (10% of food by weight), and 36 were fed a diet without walnuts (control) for 21 days. On day 22, 18 control diet rats were switched to the walnut diet. All other animals remained on their same diet. Within each diet group, 6 rats were implanted with the Ward colon carcinoma (TB), and 12 were sham-operated. Five days later, 6 sham-operated animals were weight-matched to a TB and then pair-fed for the remainder of the study. The remaining 6 sham-operated, or non-tumor-bearing rats, were ad-lib fed. Results: The tissue of the walnut-eating rats showed higher omega-3 fatty acid (immunonutrient) content which did not slow or prevent tumor growth or the loss of lean and fat mass typical of this TB model. In addition, blood glucose, insulin, IGF-1, and adiponectin levels were significantly lower in the TB, demonstrating metabolic dysregulation. Again, these changes were unaltered by consuming walnuts. Plasma proteomics identified six proteins elevated in the TB, but none could be connected with the observed metabolic dysregulation. Conclusion: Although walnuts’ rich immunonutrient content prevented tumor growth in genetically programmed mice models, there was no effect in this model.
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Affiliation(s)
- Lauri O Byerley
- Department of Physiology, School of Medicine, Louisiana State University Health Sciences Center, 1901 Perdido, New Orleans, LA 70112-1393, USA.
| | - Hsiao-Man Chang
- Department of Physiology, School of Medicine, Louisiana State University Health Sciences Center, 1901 Perdido, New Orleans, LA 70112-1393, USA.
| | - Brittany Lorenzen
- Department of Physiology, School of Medicine, Louisiana State University Health Sciences Center, 1901 Perdido, New Orleans, LA 70112-1393, USA.
| | - Jessie Guidry
- Proteomics Core Facility and The Biochemistry and Molecular Biology Department, Louisiana State University Health Sciences Center, 1901 Perdido, New Orleans, LA 70112-1393, USA.
| | - W Elaine Hardman
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, 1600 Medical Center Drive, Huntington, WV 25701, USA.
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15
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Bezstarosti K, Lamers MM, Doff WAS, Wever PC, Thai KTD, van Kampen JJA, Haagmans BL, Demmers JAA. Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens. PLoS One 2021; 16:e0259165. [PMID: 34762662 PMCID: PMC8584957 DOI: 10.1371/journal.pone.0259165] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/13/2021] [Indexed: 01/22/2023] Open
Abstract
The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was estimated to be in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.
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Affiliation(s)
- Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wouter A. S. Doff
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Peter C. Wever
- Jeroen Bosch Hospital, ‘s-Hertogenbosch, the Netherlands
| | - Khoa T. D. Thai
- Star-shl Medical Diagnostic Center, Rotterdam, the Netherlands
| | | | - Bart L. Haagmans
- Viroscience Department, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeroen A. A. Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
- * E-mail:
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16
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Amrani ME, Gerencser L, Huitema ADR, Hack CE, van Luin M, van der Elst KCM. A generic sample preparation method for the multiplex analysis of seven therapeutic monoclonal antibodies in human plasma or serum with liquid chromatography-tandem mass spectrometry. J Chromatogr A 2021; 1655:462489. [PMID: 34509691 DOI: 10.1016/j.chroma.2021.462489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 11/26/2022]
Abstract
Due to the increasing number of therapeutic monoclonal antibodies (mAbs) used in the clinic, there is an increasing need for robust analytical methods to quantify total mAb concentrations in human plasma for clinical studies and therapeutic drug monitoring. We developed an easy, rapid, and robust sample preparation method for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The method was validated for infliximab (IFX), rituximab (RTX), cetuximab (CTX), dupilumab (DPL), dinutuximab (DNX), vedolizumab (VDZ), and emicizumab (EMZ). Saturated ammonium sulfate (AS) was used to precipitate immunoglobulins in human plasma. After centrifugation, supernatant containing albumin was decanted, and the precipitated immunoglobulin fraction was re-dissolved in buffer containing 6M guanidine. This fraction was then completely denatured, reduced, alkylated, and trypsin digested. Finally, signature peptides from the seven mAbs were simultaneously quantified on LC-MS/MS together with their internal standards stable isotopically labeled peptide counterparts. The linear dynamic ranges (1 - 512 mg/L) of IFX, CTX, RTX, and EMZ showed excellent (R2 > 0.999) linearity and those of DPL, DNX, and VDZ showed good (R2 > 0.995) linearity. The method was validated in accordance with the EMA guidelines. EDTA plasma, sodium citrate plasma, heparin plasma, and serum yielded similar results. Prepared samples were stable at room temperature (20°C) and at 5°C for 3 days, and showed no decline in concentration for all tested mAbs. This described method, which has the advantage of an easy, rapid, and robust pre-analytical sample preparation, can be used as a template to quantify other mAbs in human plasma or serum.
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Affiliation(s)
- Mohsin El Amrani
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands.
| | - Laszlo Gerencser
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Alwin D R Huitema
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands; Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, Amsterdam, the Netherlands; Department of Pharmacology, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - C Erik Hack
- Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Matthijs van Luin
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Kim C M van der Elst
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
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17
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Dunphy K, O’Mahoney K, Dowling P, O’Gorman P, Bazou D. Clinical Proteomics of Biofluids in Haematological Malignancies. Int J Mol Sci 2021; 22:ijms22158021. [PMID: 34360786 PMCID: PMC8348619 DOI: 10.3390/ijms22158021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/25/2022] Open
Abstract
Since the emergence of high-throughput proteomic techniques and advances in clinical technologies, there has been a steady rise in the number of cancer-associated diagnostic, prognostic, and predictive biomarkers being identified and translated into clinical use. The characterisation of biofluids has become a core objective for many proteomic researchers in order to detect disease-associated protein biomarkers in a minimally invasive manner. The proteomes of biofluids, including serum, saliva, cerebrospinal fluid, and urine, are highly dynamic with protein abundance fluctuating depending on the physiological and/or pathophysiological context. Improvements in mass-spectrometric technologies have facilitated the in-depth characterisation of biofluid proteomes which are now considered hosts of a wide array of clinically relevant biomarkers. Promising efforts are being made in the field of biomarker diagnostics for haematologic malignancies. Several serum and urine-based biomarkers such as free light chains, β-microglobulin, and lactate dehydrogenase are quantified as part of the clinical assessment of haematological malignancies. However, novel, minimally invasive proteomic markers are required to aid diagnosis and prognosis and to monitor therapeutic response and minimal residual disease. This review focuses on biofluids as a promising source of proteomic biomarkers in haematologic malignancies and a key component of future diagnostic, prognostic, and disease-monitoring applications.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Kelly O’Mahoney
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
- Correspondence:
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18
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Millet A, Khoudour N, Lebert D, Machon C, Terrier B, Blanchet B, Guitton J. Development, Validation, and Comparison of Two Mass Spectrometry Methods (LC-MS/HRMS and LC-MS/MS) for the Quantification of Rituximab in Human Plasma. Molecules 2021; 26:molecules26051383. [PMID: 33806585 PMCID: PMC7961417 DOI: 10.3390/molecules26051383] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/16/2021] [Accepted: 02/25/2021] [Indexed: 11/16/2022] Open
Abstract
Rituximab is a chimeric immunoglobulin G1-kappa (IgG1κ) antibody targeting the CD20 antigen on B-lymphocytes. Its applications are various, such as for the treatment of chronic lymphoid leukemia or non-Hodgkin’s lymphoma in oncology, and it can also be used in the treatment of certain autoimmune diseases. Several studies support the interest in therapeutic drug monitoring to optimize dosing regimens of rituximab. Thus, two different laboratories have developed accurate and reproductive methods to quantify rituximab in human plasma: one using liquid chromatography quadripolar tandem mass spectrometer (LC-MS/MS) and the other, liquid chromatography orbitrap tandem mass spectrometer (LC-MS/HRMS). For both assays, quantification was based on albumin depletion or IgG-immunocapture, surrogate peptide analysis, and full-length stable isotope-labeled rituximab. With LC-MS/MS, the concentration range was from 5 to 500 µg/mL, the within- and between-run precisions were <8.5%, and the limit of quantitation was 5 µg/mL. With LC-MS/HRMS, the concentration range was from 10 to 200 µg/mL, the within- and between-run accuracy were <11.5%, and the limit of quantitation was 2 µg/mL. Rituximab plasma concentrations from 63 patients treated for vasculitis were compared. Bland–Altman analysis and Passing–Bablok regression showed the interchangeability between these two methods. Overall, these methods were robust and reliable and could be applied to routine clinical samples.
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Affiliation(s)
- Aurélien Millet
- Biochemistry and Pharmacology-Toxicology Laboratory, Lyon-Sud Hospital, Hospices Civils de Lyon, F-69495 Pierre Bénite, France; (A.M.); (C.M.)
- Inserm U1052, CNRS UMR5286 Cancer Research Center of Lyon, F-69000 Lyon, France
| | - Nihel Khoudour
- Department of Pharmacokinetics and Pharmacochemistry, Cochin Hospital, AP-HP, CARPEM 75014 Paris, France; (N.K.); (B.B.)
| | - Dorothée Lebert
- Promise Proteomics, 7 Parvis Louis Néel, F-38040 Grenoble, France;
| | - Christelle Machon
- Biochemistry and Pharmacology-Toxicology Laboratory, Lyon-Sud Hospital, Hospices Civils de Lyon, F-69495 Pierre Bénite, France; (A.M.); (C.M.)
- Inserm U1052, CNRS UMR5286 Cancer Research Center of Lyon, F-69000 Lyon, France
- Analytical Chemistry Laboratory, Faculty of Pharmacy ISPBL, University Lyon 1, F-69373 Lyon, France
| | - Benjamin Terrier
- Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), University of Paris, F-75014 Paris, France;
- INSERM U970, PARCC, Université de Paris, F-75006 Paris, France
| | - Benoit Blanchet
- Department of Pharmacokinetics and Pharmacochemistry, Cochin Hospital, AP-HP, CARPEM 75014 Paris, France; (N.K.); (B.B.)
- UMR8038 CNRS, U1268 INSERM, Faculty of Pharmacy, University of Paris, PRES Sorbonne Paris Cité, CARPEM 75006 Paris, France
| | - Jérôme Guitton
- Biochemistry and Pharmacology-Toxicology Laboratory, Lyon-Sud Hospital, Hospices Civils de Lyon, F-69495 Pierre Bénite, France; (A.M.); (C.M.)
- Inserm U1052, CNRS UMR5286 Cancer Research Center of Lyon, F-69000 Lyon, France
- Toxicology Laboratory, Faculty of Pharmacy ISPBL, University of Lyon 1, F-69373 Lyon, France
- Correspondence:
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19
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Balestrieri K, Kew K, McDaniel M, Ramez M, Pittman HK, Murray G, Vohra NA, Verbanac KM. Proteomic identification of tumor- and metastasis-associated galectin-1 in claudin-low breast cancer. Biochim Biophys Acta Gen Subj 2021; 1865:129784. [PMID: 33166603 DOI: 10.1016/j.bbagen.2020.129784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Metastasis and mortality remain high among breast cancer patients with the claudin-low subtype because these tumors are aggressive, chemoresistant, and lack targeted therapies. Our objective was to utilize discovery-based proteomics to identify proteins associated with claudin-low primary and metastatic tumors to gain insight into pathways and mechanisms of tumor progression. METHODS We used nano-LC-MS/MS proteomics to analyze orthotopic and metastatic tumors from the syngeneic murine T11 tumor model, which displays gene expression profiles mirroring human claudin-low tumors. Galectin-1 identity, expression and spatial distribution were investigated by biochemical and immunochemical methods and MALDI/IMS. RNA seq data from mouse and human tumors in our study and publicly available microarray data were analyzed for differential galectin-1 expression across breast cancer subtypes. RESULTS Galectin-1, an N-acetyllactosamine-binding protein, exhibited the highest sequence coverage and high abundance rank order among nano-LC-MS/MS-identified proteins shared by T11 claudin-low tumors but not normal tissue. Label-free quantitation, Western immunoblot and ELISA confirmed galectin-1 identity and significant differential expression. MALDI/IMS spatial mapping and immunohistochemistry detected galectin-1 in T11 metastatic lung foci. Immunohistochemistry of human claudin-low tumors demonstrated intermediate-to-high intensity galectin-1 staining of tumor and stroma. Gene expression analysis of mouse and human tumors found the highest galectin-1 levels in the claudin-low breast cancer subtype. CONCLUSIONS Proteomics and genomics reveal high expression of galectin-1 protein and RNA in primary and metastatic claudin-low breast cancer. GENERAL SIGNIFICANCE This work endorses proteomic approaches in cancer research and supports further investigations of the function and significance of galectin-1 overexpression in claudin-low tumor progression.
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Affiliation(s)
- Kassondra Balestrieri
- Brody School of Medicine, East Carolina University, Department of Surgery, 600 Moye Boulevard, Greenville, NC 27834, United States of America
| | - Kimberly Kew
- Brody School of Medicine, East Carolina University, Department of Biochemistry and Molecular Biology, 600 Moye Boulevard, Greenville, NC 27834, United States of America
| | - Moses McDaniel
- Brody School of Medicine, East Carolina University, Department of Surgery, 600 Moye Boulevard, Greenville, NC 27834, United States of America
| | - Mohamed Ramez
- Brody School of Medicine, East Carolina University, Department of Surgery, 600 Moye Boulevard, Greenville, NC 27834, United States of America
| | - H Keith Pittman
- Brody School of Medicine, East Carolina University, Department of Surgery, 600 Moye Boulevard, Greenville, NC 27834, United States of America
| | - Gina Murray
- Brody School of Medicine, East Carolina University, Department of Pathology, 600 Moye Boulevard, Greenville, NC 27834, United States of America
| | - Nasreen A Vohra
- Brody School of Medicine, East Carolina University, Department of Surgery, 600 Moye Boulevard, Greenville, NC 27834, United States of America
| | - Kathryn M Verbanac
- Brody School of Medicine, East Carolina University, Department of Surgery, 600 Moye Boulevard, Greenville, NC 27834, United States of America.
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20
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Saadi J, Oueslati S, Bellanger L, Gallais F, Dortet L, Roque-Afonso AM, Junot C, Naas T, Fenaille F, Becher F. Quantitative Assessment of SARS-CoV-2 Virus in Nasopharyngeal Swabs Stored in Transport Medium by a Straightforward LC-MS/MS Assay Targeting Nucleocapsid, Membrane, and Spike Proteins. J Proteome Res 2021; 20:1434-1443. [PMID: 33497234 DOI: 10.1021/acs.jproteome.0c00887] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alternative methods to RT-PCR for SARS-CoV-2 detection are investigated to provide complementary data on viral proteins, increase the number of tests performed, or identify false positive/negative results. Here, we have developed a simple mass spectrometry assay for SARS-CoV-2 in nasopharyngeal swab samples using common laboratory reagents. The method employs high sensitivity and selectivity targeted mass spectrometry detection, monitoring nine constitutive peptides representative of the three main viral proteins and a straightforward pellet digestion protocol for convenient routine applications. Absolute quantification of N, M, and S proteins was achieved by addition of isotope-labeled versions of best peptides. Limit of detection, recovery, precision, and linearity were thoroughly evaluated in four representative viral transport media (VTM) containing distinct total protein content. The protocol was sensitive in all swab media with limit of detection determined at 2 × 103 pfu/mL, corresponding to as low as 30 pfu injected into the LC-MS/MS system. When tested on VTM-stored nasopharyngeal swab samples from positive and control patients, sensitivity was similar to or better than rapid immunoassay dipsticks, revealing a corresponding RT-PCR detection threshold at Ct ∼ 24. The study represents the first thorough evaluation of sensitivity and robustness of targeted mass spectrometry in nasal swabs, constituting a promising SARS-CoV-2 antigen assay for the first-line diagnosis of COVID-19 and compatible with the constraints of clinical settings. The raw files generated in this study can be found on PASSEL (Peptide Atlas) under data set identifier PASS01646.
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Affiliation(s)
- Justyna Saadi
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - Saoussen Oueslati
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - Laurent Bellanger
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Gallais
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Laurent Dortet
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - Anne-Marie Roque-Afonso
- Service de Virologie, Hôpital Paul-Brousse, APHP Paris Saclay, and UMR 1193 Physiopathogénèse et Traitement des Maladies du Foie, 94800 Villejuif, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - Thierry Naas
- Bacteriology-Hygiene Unit, Hôpital Bicêtre, APHP Paris Saclay, Team ReSIST, INSERM U1184, Université Paris-Saclay, LabEx LERMIT, 94270 Le Kremlin-Bicêtre, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
| | - François Becher
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 91191 Gif sur Yvette, France
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21
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Gao X, Chen C, Geng D, Bateman KP, Shi S, Woolf EJ, Xu Y. Volumetric absorptive microsampling (VAMS®) in therapeutic protein quantification by LC-MS/MS: Investigation of anticoagulant impact on assay performance and recommendations for best practices in method development. J Pharm Biomed Anal 2021; 196:113895. [PMID: 33486450 DOI: 10.1016/j.jpba.2021.113895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/02/2020] [Accepted: 01/05/2021] [Indexed: 01/01/2023]
Abstract
Microsampling techniques have been employed as an alternative to traditional serum/plasma sampling because of their inherently proven and desirable advantages across the pharmaceutical industry. These include reduced animal usage in pre-clinical studies, as well as, permitting the collection of samples that would otherwise be inaccessible in clinical studies. The application of volumetric absorptive microsampling (VAMS®) technology, a second-generation dried microsampling method, coupled with LC-MS, has been extensively explored for small molecule drugs at various drug development stages. However, the potential of using VAMS technology and LC-MS analysis for biological therapeutic development has yet to be well-established. In this work, we describe the method development, validation, and a proof-of-concept non-human primate study of a LC-MS/MS method for VAMS utilized to obtain pharmacokinetic (PK) data for a therapeutic monoclonal antibody. A good correlation between VAMS data and data from conventional serum samples was established in rhesus monkeys and indicated the possibility of using of this novel sampling technology in clinical studies. However, during the initial clinical study, a significant difference in internal standard (IS) response between the patient fingerstick samples and the standard/QC samples was observed, which posed a question on the accuracy of the clinical results. A comprehensive investigation confirmed that the EDTA anticoagulant used in the standard/QC samples was the root cause of the observed anomalous IS responses. Special considerations and corresponding best practices during method development and validation are proposed to ensure early detection of potential issues and appropriate implementation of VAMS technology in clinical studies in the future.
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Affiliation(s)
- Xinliu Gao
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 2000 Galloping Hill Road Kenilworth, NJ, 07033, USA.
| | - Cindy Chen
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc, 770 Sumneytown Pike, WP75B-300, West Point, PA, 19486, USA
| | - Dong Geng
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc, 770 Sumneytown Pike, WP75B-300, West Point, PA, 19486, USA
| | - Kevin P Bateman
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc, 770 Sumneytown Pike, WP75B-300, West Point, PA, 19486, USA
| | - Shuangping Shi
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc, 770 Sumneytown Pike, WP75B-300, West Point, PA, 19486, USA
| | - Eric J Woolf
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc, 770 Sumneytown Pike, WP75B-300, West Point, PA, 19486, USA
| | - Yang Xu
- Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc, 770 Sumneytown Pike, WP75B-300, West Point, PA, 19486, USA.
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22
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Proteomics of Muscle Microdialysates Identifies Potential Circulating Biomarkers in Facioscapulohumeral Muscular Dystrophy. Int J Mol Sci 2020; 22:ijms22010290. [PMID: 33396627 PMCID: PMC7795508 DOI: 10.3390/ijms22010290] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/18/2020] [Accepted: 12/25/2020] [Indexed: 12/14/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by a complex epigenetic mechanism finally leading to the misexpression of DUX4 in skeletal muscle. Detecting DUX4 and quantifying disease progression in FSHD is extremely challenging, thus increasing the need for surrogate biomarkers. We applied a shotgun proteomic approach with two different setups to analyze the protein repertoire of interstitial fluids obtained from 20 muscles in different disease stages classified by magnetic resonance imaging (MRI) and serum samples from 10 FSHD patients. A total of 1156 proteins were identified in the microdialysates by data independent acquisition, 130 of which only found in muscles in active disease stage. Proteomic profiles were able to distinguish FSHD patients from controls. Two innate immunity mediators (S100-A8 and A9) and Dermcidin were upregulated in muscles with active disease and selectively present in the sera of FSHD patients. Structural muscle and plasminogen pathway proteins were downregulated. Together with the upstream inhibition of myogenic factors, this suggests defective muscle regeneration and increased fibrosis in early/active FSHD. Our MRI targeted exploratory approach confirmed that inflammatory response has a prominent role, together with impaired muscle regeneration, before clear muscle wasting occurs. We also identified three proteins as tissue and possibly circulating biomarkers in FSHD.
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23
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Takemori A, Ishizaki J, Nakashima K, Shibata T, Kato H, Kodera Y, Suzuki T, Hasegawa H, Takemori N. BAC-DROP: Rapid Digestion of Proteome Fractionated via Dissolvable Polyacrylamide Gel Electrophoresis and Its Application to Bottom-Up Proteomics Workflow. J Proteome Res 2020; 20:1535-1543. [PMID: 33356312 DOI: 10.1021/acs.jproteome.0c00749] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The GeLC-MS workflow, which combines low-cost, easy-to-use sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (SDS-PAGE) with liquid chromatography-mass spectrometry (LC-MS), is very popular in current bottom-up proteomics. However, GeLC-MS requires that PAGE-separated proteins undergo overnight enzymatic digestion in a gel, resulting in more than 20 h of sample preparation for LC-MS. In this study, we overcame the limitations of GeLC-MS by developing a rapid digestion workflow for PAGE separation of proteins using N,N'-bis(acryloyl)cystamine (BAC) cross-linked gels that can be solubilized by reductive treatment. Making use of an established workflow called BAC-DROP (BAC-gel dissolution to digest PAGE-resolved objective proteins), crude proteome samples were fractionated based on molecular weight by BAC cross-linked PAGE. After fractionation, the gel fragments were reductively dissolved in under 5 min, and in-solution trypsin digestion of the protein released from the gel was completed in less than 1 h at 70 °C, equivalent to a 90-95% reduction in time compared to conventional in-gel trypsin digestion. The introduction of the BAC-DROP workflow to the MS assays for inflammatory biomarker CRP and viral marker HBsAg allowed for serum sample preparation to be completed in as little as 5 h, demonstrating successful marker quantification from a 0.5 μL sample of human serum.
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Affiliation(s)
- Ayako Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 790-8577, Ehime, Japan
| | - Jun Ishizaki
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 790-8577, Ehime, Japan
| | - Kenji Nakashima
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Shizuoka, Japan
| | | | - Hidemasa Kato
- Division of Functional Histology, Department of Functional Biomedicine, Graduate School of Medicine, Ehime University, Toon 790-8577, Ehime, Japan
| | - Yoshio Kodera
- Center for Disease Proteomics, Kitasato University School of Science, Sagamihara 252-0373, Kanagawa, Japan
| | - Tetsuro Suzuki
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Shizuoka, Japan
| | - Hitoshi Hasegawa
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 790-8577, Ehime, Japan
| | - Nobuaki Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 790-8577, Ehime, Japan
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Bottom-up sample preparation for the LC-MS/MS quantification of anti-cancer monoclonal antibodies in bio matrices. Bioanalysis 2020; 12:1405-1425. [PMID: 32975434 DOI: 10.4155/bio-2020-0204] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are rapidly taking over the treatment of many malignancies, and an astonishing number of mAbs is in development. This causes a high demand for quantification of mAbs in biomatrices both for measuring therapeutic mAb concentrations and to support pharmacokinetics and pharmacodynamics studies. Conventionally, ligand-binding assays are used for these purposes, but LC-MS is gaining popularity. Although intact (top-down) and subunit (middle-down) mAb quantification is reported, signature peptide (bottom-up) quantification is currently most advantageous. This review provides an overview of the reported bottom-up mAb quantification methods in biomatrices as well as general recommendations regarding signature peptide and internal standard selection, reagent use and optimization of digestion in bottom-up quantification methods.
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25
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Goyal G, Ammanath G, Palaniappan A, Liedberg B. Stoichiometric Tuning of PNA Probes to Au 0.8Ag 0.2 Alloy Nanoparticles for Visual Detection of Nucleic Acids in Plasma. ACS Sens 2020; 5:2476-2485. [PMID: 32700531 DOI: 10.1021/acssensors.0c00667] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Standard detection methods for nucleic acids, an important class of diagnostic biomarkers, are often laborious and cumbersome. In need for development of facile methodologies, localized surface plasmon resonance (LSPR) assays have been widely explored for both spectroscopic and visual detection of nucleic acids. Our sensing approach is based on monitoring changes in the LSPR band due to interaction between peptide nucleic acid (PNA) and plasmonic nanoparticles (NPs) in the presence/absence of target nucleic acid. We have investigated the importance of tuning the stoichiometry of PNA to NPs to enable "naked-eye" detection of nucleic acids at clinically relevant concentration ranges. Assaying in plasma is achieved by incorporation of silver in gold NPs (AuNPs) via an alloying process. The synthesized gold/silver alloy NPs reduce nonspecific adsorption of proteinaceous interferents in plasma. Furthermore, the gold/silver alloy NPs absorb in the most sensitive cyan to green transition zone (∼500 nm) yielding highly competitive visual limits of detection (LODs). The visual LOD (calculated objectively using the ΔE algorithm) for a model microRNA (mir21) using a productive combination of stoichiometric tuning of the PNA to NP ratio and compositional tuning of the NPs in buffer and plasma extract equals 200 pM (∼250 times lower than existing reports) and 3 nM, respectively. We envision that the proposed LSPR assay based on Au0.8Ag0.2NPs offers an avenue for rapid and sensitive on-site detection of nucleic acids in complex matrixes in combination with efficient target extraction kits.
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Affiliation(s)
- Garima Goyal
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore 639798
- Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
| | - Gopal Ammanath
- Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
| | - Alagappan Palaniappan
- Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
| | - Bo Liedberg
- Interdisciplinary Graduate School, Nanyang Technological University, Singapore 639798
- Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798
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26
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Development and validation of immunoassay for whole cell detection of Brucella abortus and Brucella melitensis. Sci Rep 2020; 10:8543. [PMID: 32444793 PMCID: PMC7244763 DOI: 10.1038/s41598-020-65347-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 03/16/2020] [Indexed: 01/30/2023] Open
Abstract
Brucella is alpha-2 Proteobacteria mainly responsible for multi-factorial bacterial zoonotic disease brucellosis with low concentration (10–100 CFU) required to establish the infection. In this study, we developed sandwich ELISA with detection range of 102 to 108 cells mL−1 and limit of detection at 103 cells mL−1 by employing polyclonal rabbit IgG (capture antibody, 10 µg mL−1) and mice IgG (detection antibody, 50 µg mL−1) antibody for its detection. Surface Plasmon Resonance evaluated the interaction of detection antibody with whole cell spiked serum samples at LOD of 102 cells mL−1 along with non co-operative interaction of protein albumin. Further, kinetic evaluation study using detection antibody against cell envelope antigen was performed whereby, Equilibrium Dissociation Constant (KD) and Maximum Binding Capacity (Bmax) were found to be 16.48 pM and 81.67 m° for Brucella abortus S99 and 0.42 pM and 54.50 m° for Brucella melitensis 16 M, respectively. During interference study, sandwich ELISA assay cross-reacted with either of the polyclonal antibody of above Brucella species. Upon validation, no cross-reactivity observed with bacteria-closely related to Brucella. In conclusion, developed semi-quantitative sandwich immunoassay is sensitively rapid in whole cell detection of Brucella and will be useful in development of detection assays from environmental and clinical matrices.
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27
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Basit A, Prasad B, Estergreen JK, Sabath DE, Alade N, Veenstra DL, Rettie AE, Thummel KE. A Novel LC-MS/MS Assay for Quantification of Des-carboxy Prothrombin and Characterization of Warfarin-Induced Changes. Clin Transl Sci 2020; 13:718-726. [PMID: 32004415 PMCID: PMC7359935 DOI: 10.1111/cts.12757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022] Open
Abstract
Warfarin is a narrow therapeutic index anticoagulant drug and its use is associated with infrequent but significant adverse bleeding events. The international normalized ratio (INR) is the most commonly used biomarker to monitor and titrate warfarin therapy. However, INR is derived from a functional assay, which determines clotting efficiency at the time of measurement and is susceptible to technical variability. Protein induced by vitamin K antagonist-II (PIVKA-II) has been suggested as a biomarker of long-term vitamin K status, providing mechanistic insights about variation in the functional assay. However, the currently available antibody-based PIVKA-II assay does not inform on the position and number of des-carboxylation sites in prothrombin. The assay presented in this paper provides simultaneous quantification of carboxy and des-carboxy prothrombin that are essential for monitoring early changes in INR and, thus, serves as the superior tool for managing warfarin therapy. Additionally, this assay permits the quantification of total prothrombin level, which is affected by warfarin treatment. Prothrombin recovery from plasma was 95% and the liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was linear (r2 = 0.98) with a dynamic range of 1-100 µg/mL. The assay interday precision was within 20%. A des-carboxy peptide of prothrombin (GNLER) was negatively correlated with active prothrombin (Pearson r = 0.99, P < 0.0001), whereas its association was positively linked with INR values (Pearson r = 0.75, P < 0.015). This novel LC-MS/MS assay for active and inactive prothrombin quantification can be applied to titrate anticoagulant therapy and to monitor the impact of diseases, such as hepatocellular carcinoma on clotting physiology.
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Affiliation(s)
- Abdul Basit
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Joanne K Estergreen
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel E Sabath
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, Washington, USA
| | - Nathan Alade
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - David L Veenstra
- Department of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
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Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery. Bioanalysis 2019; 11:1799-1812. [PMID: 31617391 DOI: 10.4155/bio-2019-0145] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.
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Chetwynd AJ, Wheeler KE, Lynch I. Best practice in reporting corona studies: Minimum information about Nanomaterial Biocorona Experiments (MINBE). NANO TODAY 2019; 28:100758. [PMID: 32774443 PMCID: PMC7405976 DOI: 10.1016/j.nantod.2019.06.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Characterisation of the adsorption of biomolecules, or a biocorona, on nanomaterials has proliferated in the past 10 years, as protein corona studies provide molecular level insight into mechanisms of cellular recognition, uptake, and toxicity of nanomaterials. At the crossroads of two rapidly evolving orthogonal fields, nanoscience and proteomics, the interdisciplinarity of protein corona studies creates challenges for experimental design and reporting. Here we propose a flexible checklist for experimental design and reporting guidelines to outline Minimum Information about Nanomaterial Biocorona Experiments (MINBE). The checklist for experimental design, compiled after review of reporting within the protein corona literature, provides researchers with prompts to ensure best practice experimental approaches for each stage of the workflow, collated from the nanoscience, proteomics, and bioinformatics fields. Reporting guidelines are also assembled from established sources, integrated to span the entire workflow and extended and modified to aid interdisciplinary researchers in the most challenging stages of the workflow. Where appropriate, de novo guidelines to address areas specific to protein corona studies, including exposure conditions and isolation of adsorbed proteins, were written. The MINBE guidelines provide protein corona researchers with a conduit between materials science techniques and proteomics. Implementation of these guidelines is anticipated to catalyse enhanced quality, impact, and extent of data mining and computational modelling of protein corona composition and its role in nanosafety and nanomedicine. Furthermore, high quality experimental design and reporting in the bio-nanosciences will enhance the next phase of targeted nanomedicines and sustainable nanotechnologies.
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Affiliation(s)
- Andrew J. Chetwynd
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
| | - Korin E. Wheeler
- Department of Chemistry and Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, CA 95053, United States
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK
- Corresponding author.
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30
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Bioanalytical method development and validation for determination of fibroblast growth factor peptide and its application to pharmacokinetic studies. Eur J Pharm Biopharm 2019; 135:83-93. [PMID: 30582960 DOI: 10.1016/j.ejpb.2018.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/22/2018] [Accepted: 12/20/2018] [Indexed: 01/10/2023]
Abstract
Fibroblast growth factor peptide (FGF-P) is a polypeptide analog of FGF-2 that could be a potential mitigation and treatment agent for radiation syndromes. Prior to conducting preclinical pharmacokinetics, we developed and validated the LC-MS/MS bioanalytical method for determination of FGF-P in rat plasma for the first time. FGF-P was extracted from rat plasma using the protein precipitation technique followed liquid-liquid extraction using dichloromethane as a solvent. The mobile phases consisted of two components: (a) 0.1% formic acid in water; and (b) acetonitrile: 0.1% formic acid in water (95:5) under gradient elution. The validated method was also successfully applied to a pharmacokinetic study of FGF-P (10 mg/kg, intravenous) in Wistar rats. The method proved to be specific, accurate, precise, and linear over the concentration range of 2-500 ng/mL with coefficient of determination greater than 0.99 in all validation batches. The within-run and between-run accuracy was 87.97-115.00% with a precision of less than 14%. The mean recoveries ranged from 88.14% to 101.73%. The stability of the compound in plasma samples was proven under various storage conditions. After intravenous administration of FGF-P (10 mg/kg) the C0 was 70.4 µg/mL and the AUC was 86.2 µg*min/mL.
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31
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Proteomics: Tools of the Trade. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:1-22. [DOI: 10.1007/978-3-030-12298-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Pietrowska M, Wlosowicz A, Gawin M, Widlak P. MS-Based Proteomic Analysis of Serum and Plasma: Problem of High Abundant Components and Lights and Shadows of Albumin Removal. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:57-76. [PMID: 31236839 DOI: 10.1007/978-3-030-12298-0_3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Blood serum or plasma proteome is a gold mine of disease biomarkers. However, complexity and a huge dynamic range of their components, combined with multiple mechanisms of degradation and posttranslational modifications, further complicated by the presence of lipids, salts, and other metabolites, represent a real challenge for analytical sensitivity, resolution, and reproducibility. This problem exists particularly in the case of potential disease-specific markers, most typically represented by low-abundant proteins (LAPs), whose detection is usually impaired by the dominance of albumins, immunoglobulins, and other high-abundant serum/plasma proteins (HAPs). Hence, analysis of biomarker candidates in serum/plasma samples frequently requires separation of their components, usually including depletion of albumin in a fraction of interest. Such "preprocessing" of serum/plasma specimens is critical in proteomic analysis based on mass spectrometry. This approach is very potent; nevertheless a wide range of protein concentrations in serum/plasma represents a particular challenge, since high-abundant proteins (mostly albumin) dominate in a sample subjected to mass spectrometry and suppress peptide ions originating from low-abundant proteins, thus limiting probability and reliability of their detection. An emerging approach in serum-/plasma-based biomarker-oriented studies is the proteome component of exosomes - nanovesicles secreted by cells and involved in multiple aspects of intercellular communication. However, the presence of albumin, frequent contaminant of exosomes isolated from human serum/plasma, represents a real challenge also in this type of study. A similar problem is encountered in proteomic studies based on exosomes obtained in in vitro experiments where culture media are normally supplemented with fetal bovine serum containing growth factors and hormones. In this case exosomes are frequently contaminated with bovine serum albumin and other bovine serum proteins which should be removed before proteomic analysis of exosome cargo.
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Affiliation(s)
- Monika Pietrowska
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Agata Wlosowicz
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Marta Gawin
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Piotr Widlak
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland.
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Serrano MAC, Gao J, Kelly KA, Thayumanavan S, Vachet RW. Supramolecular Polymeric Assemblies for the Selective Depletion of Abundant Acidic Proteins in Serum. ACS APPLIED MATERIALS & INTERFACES 2018; 10:40443-40451. [PMID: 30394728 PMCID: PMC6791357 DOI: 10.1021/acsami.8b15976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The analysis of low-level protein biomarkers in serum is precluded by the presence of other highly abundant serum proteins. Hence, the preliminary removal of serum albumin along with other abundant proteins in serum (i.e., immunoglobulins, transferrin, haptoglobin, α-2-macroglobulin, and apolipoproteins) is often a requirement prior to any biomarker analysis. In this work, we take advantage of the low isoelectric points (pI's) of these highly abundant proteins to selectively deplete them from serum by extraction using functionalized amphiphilic polymeric nanoassemblies. The selectivity of extraction is dependent on the pI of the protein and the extraction pH, which holds true even for extremely complex protein mixtures like serum. High extraction capacity is achieved by optimizing the extraction conditions and is found to be comparable to currently available methods for depletion. Depletion of these abundant acidic proteins allows for the enhanced detection of higher pI proteins and enables a 3 orders of magnitude increase in detection sensitivity for a putative cancer biomarker, demonstrating the utility of these polymeric assemblies for enhancing the analysis of the serum proteome.
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POLTEP K, TESENA P, YINGCHUTRAKUL Y, TAYLOR J, WONGTAWAN T. Optimisation of a serum albumin removal protocol for use in a proteomic study to identify the protein biomarkers for silent gastric ulceration in horses. J Equine Sci 2018; 29:53-60. [PMID: 30250392 PMCID: PMC6145863 DOI: 10.1294/jes.29.53] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/24/2018] [Indexed: 11/29/2022] Open
Abstract
Silent gastric ulceration occurs without evidence of clinical signs and is common in horses. There is currently no a simple and effective method to diagnose this disease. Proteomics can be used to identify serum biomarkers, but the most abundant serum protein, albumin, could conceal candidate biomarkers. Therefore, it is recommended to remove albumin before a proteomic study; however, there is no specific albumin depletion kit or standard protocol available for horse samples. The objectives of this study were to optimise a protocol to remove equine serum albumin and to use albumin-depleted serum to identify the protein biomarkers for silent gastric ulceration. Gastroscopy was used to identify gastric ulceration, and serum was obtained from horses with either a healthy gastric mucosa or gastric ulceration. Serum albumin was removed using the trichloroacetic acid (TCA) protein precipitation method, and this protocol was optimised by varying the concentration of TCA, type of organic solvents, ratio of serum to protein precipitation solution, and incubation times. Electrophoresis and image analysis were used to compare the amounts of albumin, immunoglobulins G (IgG), and protein degradation before and after TCA precipitation. The best protocol was chosen to remove albumin for a proteomic study (electrophoresis and mass spectrometry). The results revealed that protocol 2 (ratio of serum to solution 1:5, 10% TCA in acetone, and 90 min incubation) was the most efficient protocol to remove albumin (98%) and IgG heavy (80%) and light (98%) chains without degrading other proteins. After electrophoresis and mass spectrometry analysis, KRT1, KRT6A and KRT18 were identified as potential markers for silent gastric ulceration.
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Affiliation(s)
- Kanaporn POLTEP
- The Monitoring and Surveillance Centre for
Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol
University, Nakhon Pathom 73170, Thailand
- Laboratory of Cellular Biomedicine and
Veterinary Medicine, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom
73170, Thailand
| | - Parichart TESENA
- Department of Clinical Science and Public
Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170,
Thailand
| | - Yodying YINGCHUTRAKUL
- Proteomics Research Laboratory, Genome
Technology Research Unit, National Centre for Genetics Engineering and Biotechnology,
Pathum Thani 12120, Thailand
| | - Jane TAYLOR
- Biomedical Teaching Organisation, Biomedical
Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, EH8 9AG,
U.K.
| | - Tuempong WONGTAWAN
- Department of Preclinic and Applied Animal
Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170,
Thailand
- Laboratory of Cellular Biomedicine and
Veterinary Medicine, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom
73170, Thailand
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35
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Silva MLS. Lectin-based biosensors as analytical tools for clinical oncology. Cancer Lett 2018; 436:63-74. [PMID: 30125611 DOI: 10.1016/j.canlet.2018.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/17/2022]
Abstract
The review focus on the use of lectin-based biosensors in the oncology field, and ponders the potentialities of using these devices as analytical tools to monitor the levels of cancer glycobiomarkers in biological fluids, helping in the diagnosis, prognosis and treatment assessment. Several examples of lectin-based biosensors directed for cancer biomarkers are described and discussed, and their potential application in the clinic is considered, taking into account their analytical features, advantages and performance in sample analysis. Technical and practical aspects in the construction process, which are specific for lectin biosensors, are debated, as well as the requirements in sample collection and processing, and biosensor validation. Today's challenges for real implementation of these devices in the clinic are presented, along with the future trends in the field.
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Affiliation(s)
- M Luísa S Silva
- Centre of Chemical Research, Autonomous University of Hidalgo State, Carr. Pachuca-Tulancingo Km 4.5, 42076, Pachuca, Hidalgo, Mexico; LAQV/REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy of the University of Porto, Rua Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal.
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36
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Dong L, Li C, Locuson C, Chen S, Qian MG. A Two-Step Immunocapture LC/MS/MS Assay for Plasma Stability and Payload Migration Assessment of Cysteine–Maleimide-Based Antibody Drug Conjugates. Anal Chem 2018; 90:5989-5994. [DOI: 10.1021/acs.analchem.8b00694] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Linlin Dong
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International, Inc., 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Chao Li
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International, Inc., 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Charles Locuson
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International, Inc., 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Susan Chen
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International, Inc., 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Mark G. Qian
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International, Inc., 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
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37
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Qu M, An B, Shen S, Zhang M, Shen X, Duan X, Balthasar JP, Qu J. Qualitative and quantitative characterization of protein biotherapeutics with liquid chromatography mass spectrometry. MASS SPECTROMETRY REVIEWS 2017; 36:734-754. [PMID: 27097288 DOI: 10.1002/mas.21500] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
In the last decade, the advancement of liquid chromatography mass spectrometry (LC/MS) techniques has enabled their broad application in protein characterization, both quantitatively and qualitatively. Owing to certain important merits of LC/MS techniques (e.g., high selectivity, flexibility, and rapid method development), LC/MS assays are often deemed as preferable alternatives to conventional methods (e.g., ligand-binding assays) for the analysis of protein biotherapeutics. At the discovery and development stages, LC/MS is generally employed for two purposes absolute quantification of protein biotherapeutics in biological samples and qualitative characterization of proteins. For absolute quantification of a target protein in bio-matrices, recent work has led to improvements in the efficiency of LC/MS method development, sample treatment, enrichment and digestion, and high-performance low-flow-LC separation. These advances have enhanced analytical sensitivity, specificity, and robustness. As to qualitative analysis, a range of techniques have been developed to characterize intramolecular disulfide bonds, glycosylation, charge variants, primary sequence heterogeneity, and the drug-to-antibody ratio of antibody drug conjugate (ADC), which has enabled a refined ability to assess product quality. In this review, we will focus on the discussion of technical challenges and strategies of LC/MS-based quantification and characterization of biotherapeutics, with the emphasis on the analysis of antibody-based biotherapeutics such as monoclonal antibodies (mAbs) and ADCs. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:734-754, 2017.
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Affiliation(s)
- Miao Qu
- Beijing University of Chinese Medicine, Beijing, 100029, China
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, 14203
| | - Bo An
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, 14203
| | - Shichen Shen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, 14203
| | - Ming Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, 14203
| | - Xiaomeng Shen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, 14203
| | - Xiaotao Duan
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Joseph P Balthasar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214
| | - Jun Qu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, 14203
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Wang M, Siddiqui G, Gustafsson OJR, Käkinen A, Javed I, Voelcker NH, Creek DJ, Ke PC, Davis TP. Plasma Proteome Association and Catalytic Activity of Stealth Polymer-Grafted Iron Oxide Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1701528. [PMID: 28783260 DOI: 10.1002/smll.201701528] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Polyethylene glycol (PEG) is widely used as an antifouling and stealth polymer in surface engineering and nanomedicine. However, recent research has revealed adverse effects of bioaccumulation and immunogenicity following the administration of PEG, prompting this proteomic examination of the plasma protein coronae association with superparamagnetic iron oxide nanoparticles (IONPs) grafted with brushed PEG (bPEG) and an alternative, brushed phosphorylcholine (bPC). Using label-free quantitation by liquid chromatography tandem-mass spectrometry, this study determines protein abundances for the in vitro hard coronae of bare, bPC-, and bPEG-grafted IONPs in human plasma. This study also shows unique protein compositions in the plasma coronae of each IONP, including enrichment of coagulation factors and immunogenic complement proteins with bPEG, and enhanced binding of apolipoproteins with bPC. Functional analysis reveals that plasma protein coronae elevate the horseradish peroxidase-like activities of the bPC- and bPEG-IONPs by approximately twofold, an effect likely mediated by the diverse composition and physicochemical properties of the polymers as well as their associated plasma proteins. Taken together, these observations support the rational design of stealth polymers based on a quantitative understanding of the interplay between IONPs and the plasma proteome, and should prove beneficial for the development of materials for nanomedicine, biosensing, and catalysis.
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Affiliation(s)
- Miaoyi Wang
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ghizal Siddiqui
- Drug Delivers, Diposition adn Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ove J R Gustafsson
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA, 5095, Australia
| | - Aleksandr Käkinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ibrahim Javed
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Nicolas H Voelcker
- Drug Delivers, Diposition adn Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA, 5095, Australia
| | - Darren J Creek
- Drug Delivers, Diposition adn Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Thomas P Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, UK
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39
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Malik P, Bhushan R. Development of liquid chromatographic methods for enantioseparation and sensitive detection of β-adrenolytics/β2-agonists in human plasma using a single enantiomer reagent. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1061-1062:117-122. [PMID: 28732286 DOI: 10.1016/j.jchromb.2017.06.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/22/2017] [Accepted: 06/24/2017] [Indexed: 11/16/2022]
Abstract
Enantioseparation of four commonly used β-adrenolytics (bisoprolol, salbutamol, and carvedilol, marketed as racemic mixtures) has been achieved by both TLC and RPHPLC via an indirect approach. A new chiral reagent, (S)-naproxen benzotriazole ester, was synthesized and it was characterized by UV, IR, 1HNMR, elemental analysis and polarimetry. It was used to synthesize diastereomeric derivatives of the three β-adrenolytics under microwave irradiation. TLC separation of diastereomeric derivatives was achieved which were then isolated by preparative approach; these were characterized and were used as standard reference for determining absolute configuration of diastereomeric derivatives and for establishing validated HPLC method for enantioseparation and sensitive detection of the three β-adrenolytics in human plasma. Mobile phase in gradient mode containing methanol and aqueous triethylaminephosphate (TEAP) was successful for HPLC separation; conditions with respect to pH, flow rate, and buffer concentration were optimized. The method is capable to accurately quantitate β-adrenolytics in human plasma with minimal sample clean-up and rapid separation by TLC and RPHPLC. The limit of detection values were 0.97 and 0.87ng/mL for diastereomeric derivatives of (S)- and (R)-bisoprolol, respectively, which are very low in comparison to literature reports.
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Affiliation(s)
- Poonam Malik
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
| | - Ravi Bhushan
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247667, India.
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40
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Zhao Y, Liu G, Yuan X, Gan J, Peterson JE, Shen JX. Strategy for the Quantitation of a Protein Conjugate via Hybrid Immunocapture-Liquid Chromatography with Sequential HRMS and SRM-Based LC-MS/MS Analyses. Anal Chem 2017; 89:5144-5151. [DOI: 10.1021/acs.analchem.7b00926] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yue Zhao
- Analytical and Bioanalytical
Operations, Research and Development, Bristol-Myers Squibb Co., Princeton, New Jersey 08543, United States
| | - Guowen Liu
- Analytical and Bioanalytical
Operations, Research and Development, Bristol-Myers Squibb Co., Princeton, New Jersey 08543, United States
| | - Xiling Yuan
- Analytical and Bioanalytical
Operations, Research and Development, Bristol-Myers Squibb Co., Princeton, New Jersey 08543, United States
| | - Jinping Gan
- Analytical and Bioanalytical
Operations, Research and Development, Bristol-Myers Squibb Co., Princeton, New Jersey 08543, United States
| | - Jon E. Peterson
- Analytical and Bioanalytical
Operations, Research and Development, Bristol-Myers Squibb Co., Princeton, New Jersey 08543, United States
| | - Jim X. Shen
- Analytical and Bioanalytical
Operations, Research and Development, Bristol-Myers Squibb Co., Princeton, New Jersey 08543, United States
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41
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Reagent-free LC–MS/MS-based pharmacokinetic quantification of polyhistidine-tagged therapeutic proteins. Bioanalysis 2017; 9:251-264. [DOI: 10.4155/bio-2016-0126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: Immobilized metal ion affinity chromatography is widely employed for purifying polyhistidine-tagged recombinant proteins from cell lysates. The technique can be applied for quantification of therapeutic proteins in biological matrices by LC–MS/MS. Results: A protein reagent-free workflow was developed for quantifying polyhistidine-tagged proteins by LC–MS/MS. The workflow includes target protein enrichment by immobilized metal ion affinity chromatography, on-bead trypsin digestion and quantification of signature peptides by LC–MS/MS. It was applied to quantify a 6×His-tagged protein in a mouse pharmacokinetic study with assay sensitivity of 10.0 ng/ml and linearity up to 10,000 ng/ml. Conclusion: The protein reagent-free workflow developed herein can overcome reagent limitation and serve as a viable approach for quantifying polyhistidine-tagged therapeutic proteins to support discovery pharmacokinetic and pharmacodynamic studies.
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42
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Bollineni RC, Guldvik IJ, Grönberg H, Wiklund F, Mills IG, Thiede B. A differential protein solubility approach for the depletion of highly abundant proteins in plasma using ammonium sulfate. Analyst 2016; 140:8109-17. [PMID: 26541119 DOI: 10.1039/c5an01560j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Depletion of highly abundant proteins is an approved step in blood plasma analysis by mass spectrometry (MS). In this study, we explored a precipitation and differential protein solubility approach as a fractionation strategy for abundant protein removal from plasma. Total proteins from plasma were precipitated with 90% saturated ammonium sulfate, followed by differential solubilization in 55% and 35% saturated ammonium sulfate solutions. Using a four hour liquid chromatography (LC) gradient and an LTQ-Orbitrap XL mass spectrometer, a total of 167 and 224 proteins were identified from the 55% and 35% ammonium sulfate fractions, whereas 235 proteins were found in the remaining protein fractions with at least two unique peptides. SDS-PAGE and exclusive total spectrum counts from LC-MS/MS analyses clearly showed that majority of the abundant plasma proteins were solubilized in 55% and 35% ammonium sulfate solutions, indicating that the remaining protein fraction is of potential interest for identification of less abundant plasma proteins. Serum albumin, serotransferrin, alpha-1-antitrypsin and transthyretin were the abundant proteins that were highly enriched in 55% ammonium sulfate fractions. Immunoglobulins, complement system proteins, and apolipoproteins were among other abundant plasma proteins that were enriched in 35% ammonium sulfate fractions. In the remaining protein fractions a total of 40 unique proteins were identified of which, 32 proteins were identified with at least 10 exclusive spectrum counts. According to PeptideAtlas, 9 of these 32 proteins were estimated to be present at low μg ml(-1) (0.12-1.9 μg ml(-1)) concentrations in the plasma, and 17 at low ng ml(-1) (0.1-55 ng ml(-1)) range.
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Affiliation(s)
- Ravi Chand Bollineni
- Department of Biosciences, University of Oslo, Oslo, Norway. and Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway
| | - Ingrid J Guldvik
- Centre for Molecular Medicine Norway (NCMM), University of Oslo and Oslo University Hospitals, Norway
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Ian G Mills
- Centre for Molecular Medicine Norway (NCMM), University of Oslo and Oslo University Hospitals, Norway and Department of Cancer Prevention, Oslo University Hospitals, Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, Oslo, Norway. and Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway
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El Amrani M, van den Broek MPH, Göbel C, van Maarseveen EM. Quantification of active infliximab in human serum with liquid chromatography-tandem mass spectrometry using a tumor necrosis factor alpha -based pre-analytical sample purification and a stable isotopic labeled infliximab bio-similar as internal standard: A target-based, sensitive and cost-effective method. J Chromatogr A 2016; 1454:42-8. [PMID: 27264745 DOI: 10.1016/j.chroma.2016.05.070] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/20/2016] [Accepted: 05/21/2016] [Indexed: 10/21/2022]
Abstract
The therapeutic monoclonal antibody Infliximab (IFX) is a widely used drug for the treatment of several inflammatory autoimmune diseases. However, approximately 10% of patients develop anti-infliximab antibodies (ATIs) rendering the treatment ineffective. Early detection of underexposure to unbound IFX would result in a timely switch of therapy which could aid in the treatment of this disease. Streptavidin coated 96 well plates were used to capture biotinylated-tumor necrosis factor -alpha (b-TNF-α), which in turn was used to selectively extract the active form of IFX in human serum. After elution, IFX was digested using trypsin and one signature peptide was selected for subsequent analysis on liquid chromatography-tandem mass spectrometry (LC-MS/MS). The internal standard used was a stable isotopic labeled IFX bio-similar. The assay was successfully validated according to European Medicines Agency (EMA) guidelines and was found to be linear in a range of 0.5-20μg/mL (r(2)=0.994). Lower limit of quantification for the assay (<20% CV) was 0.5μg/mL, requiring only 2μL of sample. Cross-validation against enzyme-linked immunosorbent assay (ELISA) resulted in a high correlation between methods (r(2)=0.95 with a ρc=0.83) and the accuracy was in line with previously published results. In conclusion, a sensitive, robust and cost-effective method was developed for the bio-analysis of IFX with LC-MS/MS by means of a target-based pre-analytical sample purification. Moreover, low volume and costs of consumables per sample promote its feasibility in (pre)clinical studies and in therapeutic drug monitoring. This method should be considered as first choice due to its accuracy and multiple degree of selectivity.
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Affiliation(s)
- Mohsin El Amrani
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Marcel P H van den Broek
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Camiel Göbel
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erik M van Maarseveen
- Department of Clinical Pharmacy, Division of Laboratory Medicine and Pharmacy, University Medical Center Utrecht, Utrecht, The Netherlands
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44
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Techniques for quantitative LC–MS/MS analysis of protein therapeutics: advances in enzyme digestion and immunocapture. Bioanalysis 2016; 8:847-56. [DOI: 10.4155/bio.16.24] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
LC–MS/MS has been investigated to quantify protein therapeutics in biological matrices. The protein therapeutics is digested by an enzyme to generate surrogate peptide(s) before LC–MS/MS analysis. One challenge is isolating protein therapeutics in the presence of large number of endogenous proteins in biological matrices. Immunocapture, in which a capture agent is used to preferentially bind the protein therapeutics over other proteins, is gaining traction. The protein therapeutics is eluted for digestion and LC–MS/MS analysis. One area of tremendous potential for immunocapture-LC–MS/MS is to obtain quantitative data where ligand-binding assay alone is not sufficient, for example, quantitation of antidrug antibody complexes. Herein, we present an overview of recent advance in enzyme digestion and immunocapture applicable to protein quantitation.
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45
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Abstract
Boston Society's 11th Annual Applied Pharmaceutical Analysis conference, Hyatt Regency Hotel, Cambridge, MA, USA, 14-16 September 2015 The Boston Society's 11th Annual Applied Pharmaceutical Analysis (APA) conference took place at the Hyatt Regency hotel in Cambridge, MA, on 14-16 September 2015. The 3-day conference affords pharmaceutical professionals, academic researchers and industry regulators the opportunity to collectively participate in meaningful and relevant discussions impacting the areas of pharmaceutical drug development. The APA conference was organized in three workshops encompassing the disciplines of regulated bioanalysis, discovery bioanalysis (encompassing new and emerging technologies) and biotransformation. The conference included a short course titled 'Bioanalytical considerations for the clinical development of antibody-drug conjugates (ADCs)', an engaging poster session, several panel and round table discussions and over 50 diverse talks from leading industry and academic scientists.
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46
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Gong C, Zheng N, Zeng J, Aubry AF, Arnold ME. Post-pellet-digestion precipitation and solid phase extraction: A practical and efficient workflow to extract surrogate peptides for ultra-high performance liquid chromatography--tandem mass spectrometry bioanalysis of a therapeutic antibody in the low ng/mL range. J Chromatogr A 2015; 1424:27-36. [PMID: 26525666 DOI: 10.1016/j.chroma.2015.10.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/10/2015] [Accepted: 10/16/2015] [Indexed: 01/14/2023]
Abstract
The current LC-MS/MS approach for bioanalysis of protein therapeutics requires generating peptides from protein molecules via trypsin digestion, followed by sensitive detection of these surrogate peptides by multiple reaction monitoring (MRM). However, the presence of huge amount of matrix-related interference peptides generated from trypsin digestion often causes substantial matrix effect or isobaric interferences during LC-MS/MS analysis. Solid phase extraction (SPE) exhibits great potential in sample extraction to overcome these challenges due to its characteristic features of high selectivity, reproducibility, cost-effectiveness and potential to be automated. Here, we report an effective SPE methodology for the bioanalysis of protein therapeutics involving post-pellet-digestion precipitation and SPE cleanup prior to UHPLC-MS/MS analysis. Specifically, proteins in serum samples were first precipitated with methanol to enrich the protein analyte in the pellet prior to trypsin digestion of the pellet (pellet-digestion). The trypsin digest was further processed by a post-pellet-digestion precipitation (second precipitation) to remove matrix-related clog-causing components prior to SPE on OASIS™ MAX (Mixed-Mode Anion-Exchange) SPE plate. This methodology successfully overcame SPE clogging issue and enabled extraction of 100μL of monkey serum on SPE with significant sensitivity improvement to achieve a lower limit of quantitation (LLOQ) of 50ng/mL for a human monoclonal antibody of the IgG4 subclass. This UHPLC-MS/MS assay was validated in a concentration range of 50-5000ng/mL with intra- and inter-assay precisions of within 9.6% CV, and assay accuracy of within ±2.9% Dev of their nominal concentrations. To our best knowledge, this is the pellet digestion with SPE method for LC-MS/MS bioanalysis of a monoclonal antibody for the first time to achieve a LLOQ in the low ng/mL concentration range.
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Affiliation(s)
- Chao Gong
- Analytical & Bioanalytical Development, Bristol-Myers Squibb Company, Princeton, NJ 08540, USA
| | - Naiyu Zheng
- Analytical & Bioanalytical Development, Bristol-Myers Squibb Company, Princeton, NJ 08540, USA.
| | - Jianing Zeng
- Analytical & Bioanalytical Development, Bristol-Myers Squibb Company, Princeton, NJ 08540, USA.
| | - Anne-Françoise Aubry
- Analytical & Bioanalytical Development, Bristol-Myers Squibb Company, Princeton, NJ 08540, USA
| | - Mark E Arnold
- Analytical & Bioanalytical Development, Bristol-Myers Squibb Company, Princeton, NJ 08540, USA
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47
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Bronsema KJ, Bischoff R, Pijnappel WWMP, van der Ploeg AT, van de Merbel NC. Absolute Quantification of the Total and Antidrug Antibody-Bound Concentrations of Recombinant Human α-Glucosidase in Human Plasma Using Protein G Extraction and LC-MS/MS. Anal Chem 2015; 87:4394-401. [DOI: 10.1021/acs.analchem.5b00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Kees J. Bronsema
- Bioanalytical
Laboratory, PRA Health Sciences, Early Development Services, Westerbrink 3, 9405
BJ Assen, The Netherlands
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9700 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9700 AV Groningen, The Netherlands
| | - W. W. M. Pim Pijnappel
- Center
for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Dr. Molewaterplein 60, 3015 GJ Rotterdam, The Netherlands
- Molecular
Stem Cell Biology, Department of Clinical Genetics, Erasmus MC University Medical Center, Wytemaweg 80, 3015
CN Rotterdam, The Netherlands
- Department
of Pediatrics, Rotterdam Erasmus MC University Medical Center, Dr. Molewaterplein
60, 3015 GJ, Rotterdam, The Netherlands
| | - Ans T. van der Ploeg
- Center
for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Dr. Molewaterplein 60, 3015 GJ Rotterdam, The Netherlands
- Department
of Pediatrics, Rotterdam Erasmus MC University Medical Center, Dr. Molewaterplein
60, 3015 GJ, Rotterdam, The Netherlands
| | - Nico C. van de Merbel
- Bioanalytical
Laboratory, PRA Health Sciences, Early Development Services, Westerbrink 3, 9405
BJ Assen, The Netherlands
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9700 AV Groningen, The Netherlands
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48
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Development and validation of a liquid chromatography tandem mass spectrometry assay for the quantitation of a protein therapeutic in cynomolgus monkey serum. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 988:81-7. [DOI: 10.1016/j.jchromb.2015.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 02/06/2015] [Accepted: 02/08/2015] [Indexed: 11/22/2022]
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49
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Abstract
Antibody-free approaches for quantitative LC–MS/MS-based protein bioanalysis are reviewed and critically evaluated, and compared with the more widely used immunoaffinity-based approaches. Antibody-free workflows will be divided into four groups and discussed in the following order: direct analysis of signature peptides after proteolytic digestion; enrichment of target proteins and signature peptides by fractionated protein precipitation; enrichment of target proteins and signature peptides by reversed-phase and ion-exchange solid-phase extraction; and enrichment of target proteins and signature peptides by (antibody-free) affinity-solid-phase extraction.
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50
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Shen JX, Liu G, Zhao Y. Strategies for improving sensitivity and selectivity for the quantitation of biotherapeutics in biological matrix using LC-MS/MS. Expert Rev Proteomics 2015; 12:125-31. [DOI: 10.1586/14789450.2015.1024225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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