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Engevik MA, Thapa S, Lillie IM, Yacyshyn MB, Yacyshyn B, Percy AJ, Chace D, Horvath TD. Repurposing dried blood spot device technology to examine bile acid profiles in human dried fecal spot samples. Am J Physiol Gastrointest Liver Physiol 2024; 326:G95-G106. [PMID: 38014449 DOI: 10.1152/ajpgi.00188.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 11/29/2023]
Abstract
Dried blood spot (DBS) analysis has existed for >50 years, but application of this technique to fecal analysis remains limited. To address whether dried fecal spots (DFS) could be used to measure fecal bile acids, we collected feces from five subjects for each of the following cohorts: 1) healthy individuals, 2) individuals with diarrhea, and 3) Clostridioides difficile-infected patients. Homogenized fecal extracts were loaded onto quantitative DBS (qDBS) devices, dried overnight, and shipped to the bioanalytical lab at ambient temperature. For comparison, source fecal extracts were shipped on dry ice and stored frozen. After 4 mo, frozen fecal extracts and ambient DFS samples were processed and subjected to targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics with stable isotope-labeled standards. We observed no differences in the bile acid levels measured between the traditional extraction and the qDBS-based DFS methods. This pilot data demonstrates that DFS-based analysis is feasible and warrants further development for fecal compounds and microbiome applications.NEW & NOTEWORTHY Stool analysis in remote settings can be challenging, as the samples must be stored at -80°C and transported on dry ice for downstream processing. Our work indicates that dried fecal spots (DFS) on Capitainer quantitative DBS (qDBS) devices can be stored and shipped at ambient temperature and yields the same bile acid profiles as traditional samples. This approach has broad applications for patient home testing and sample collection in rural communities or resource-limited countries.
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Affiliation(s)
- Melinda A Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, South Carolina, United States
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Santosh Thapa
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas, United States
| | - Ian M Lillie
- Department of Materials Science & Engineering, Cornell University, Ithaca, New York, United States
| | - Mary Beth Yacyshyn
- Division of Digestive Diseases, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Bruce Yacyshyn
- Division of Digestive Diseases, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Andrew J Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, Massachusetts, United States
| | | | - Thomas D Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas, United States
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Hober A, Rekanovic M, Forsström B, Hansson S, Kotol D, Percy AJ, Uhlén M, Oscarsson J, Edfors F, Miliotis T. Targeted proteomics using stable isotope labeled protein fragments enables precise and robust determination of total apolipoprotein(a) in human plasma. PLoS One 2023; 18:e0281772. [PMID: 36791076 PMCID: PMC9931122 DOI: 10.1371/journal.pone.0281772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023] Open
Abstract
Lipoprotein(a), also known as Lp(a), is an LDL-like particle composed of apolipoprotein(a) (apo(a)) bound covalently to apolipoprotein B100. Plasma concentrations of Lp(a) are highly heritable and vary widely between individuals. Elevated plasma concentration of Lp(a) is considered as an independent, causal risk factor of cardiovascular disease (CVD). Targeted mass spectrometry (LC-SRM/MS) combined with stable isotope-labeled recombinant proteins provides robust and precise quantification of proteins in the blood, making LC-SRM/MS assays appealing for monitoring plasma proteins for clinical implications. This study presents a novel quantitative approach, based on proteotypic peptides, to determine the absolute concentration of apo(a) from two microliters of plasma and qualified according to guideline requirements for targeted proteomics assays. After optimization, assay parameters such as linearity, lower limits of quantification (LLOQ), intra-assay variability (CV: 4.7%) and inter-assay repeatability (CV: 7.8%) were determined and the LC-SRM/MS results were benchmarked against a commercially available immunoassay. In summary, the measurements of an apo(a) single copy specific peptide and a kringle 4 specific peptide allow for the determination of molar concentration and relative size of apo(a) in individuals.
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Affiliation(s)
- Andreas Hober
- Science for Life Laboratory, Solna, Sweden
- Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, The Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Mirela Rekanovic
- Translational Science and Experimental Medicine, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Björn Forsström
- Science for Life Laboratory, Solna, Sweden
- Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, The Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Sara Hansson
- Translational Science and Experimental Medicine, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - David Kotol
- Science for Life Laboratory, Solna, Sweden
- Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, The Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Andrew J. Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, Massachusetts, United States of America
| | - Mathias Uhlén
- Science for Life Laboratory, Solna, Sweden
- Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, The Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Jan Oscarsson
- Late-stage Development, Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Solna, Sweden
- Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, The Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Tasso Miliotis
- Translational Science and Experimental Medicine, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
- * E-mail:
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Lippa KA, Aristizabal-Henao JJ, Beger RD, Bowden JA, Broeckling C, Beecher C, Clay Davis W, Dunn WB, Flores R, Goodacre R, Gouveia GJ, Harms AC, Hartung T, Jones CM, Lewis MR, Ntai I, Percy AJ, Raftery D, Schock TB, Sun J, Theodoridis G, Tayyari F, Torta F, Ulmer CZ, Wilson I, Ubhi BK. Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC). Metabolomics 2022; 18:24. [PMID: 35397018 PMCID: PMC8994740 DOI: 10.1007/s11306-021-01848-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/07/2021] [Indexed: 12/17/2022]
Abstract
INTRODUCTION The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for untargeted metabolomics research. OBJECTIVES This review aims to highlight current RMs, and methodologies used within untargeted metabolomics and lipidomics communities to ensure standardization of results obtained from data analysis, interpretation and cross-study, and cross-laboratory comparisons. The essence of the aims is also applicable to other 'omics areas that generate high dimensional data. RESULTS The potential for game-changing biochemical discoveries through mass spectrometry-based (MS) untargeted metabolomics and lipidomics are predicated on the evolution of more confident qualitative (and eventually quantitative) results from research laboratories. RMs are thus critical QC tools to be able to assure standardization, comparability, repeatability and reproducibility for untargeted data analysis, interpretation, to compare data within and across studies and across multiple laboratories. Standard operating procedures (SOPs) that promote, describe and exemplify the use of RMs will also improve QC for the metabolomics and lipidomics communities. CONCLUSIONS The application of RMs described in this review may significantly improve data quality to support metabolomics and lipidomics research. The continued development and deployment of new RMs, together with interlaboratory studies and educational outreach and training, will further promote sound QA practices in the community.
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Affiliation(s)
- Katrice A Lippa
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, 20899, USA
| | - Juan J Aristizabal-Henao
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
- BERG LLC, 500 Old Connecticut Path, Building B, 3rd Floor, Framingham, MA, 01710, USA
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, USA
| | - John A Bowden
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Corey Broeckling
- Analytical Resources Core: Bioanalysis and Omics Center, Colorado State University, Fort Collins, CO, 80523, USA
| | | | - W Clay Davis
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | - Warwick B Dunn
- School of Biosciences, Institute of Metabolism and Systems Research and Phenome Centre Birmingham, University of Birmingham, Birmingham, B15, 2TT, UK
| | - Roberto Flores
- Division of Program Coordination, Planning and Strategic Initiatives, Office of Nutrition Research, Office of the Director, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, UK
| | - Gonçalo J Gouveia
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Amy C Harms
- Biomedical Metabolomics Facility Leiden, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Thomas Hartung
- Bloomberg School of Public Health, Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Christina M Jones
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, 20899, USA
| | - Matthew R Lewis
- National Phenome Centre, Imperial College London, London, SW7 2AZ, UK
| | - Ioanna Ntai
- Thermo Fisher Scientific, San Jose, CA, 95134, USA
| | - Andrew J Percy
- Cambridge Isotope Laboratories, Inc., Tewksbury, MA, 01876, USA
| | - Dan Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, 98109, USA
| | - Tracey B Schock
- Chemical Sciences Division, National Institute of Standards and Technology (NIST), Charleston, SC, 29412, USA
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, USA
| | | | - Fariba Tayyari
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Federico Torta
- Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Candice Z Ulmer
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, 30341, USA
| | - Ian Wilson
- Computational & Systems Medicine, Imperial College, Exhibition Rd, London, SW7 2AZ, UK
| | - Baljit K Ubhi
- MOBILion Systems Inc., 4 Hillman Drive Suite 130, Chadds Ford, PA, 19317, USA.
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Hober A, Edfors F, Ryaboshapkina M, Malmqvist J, Rosengren L, Percy AJ, Lind L, Forsström B, Uhlén M, Oscarsson J, Miliotis T. Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-labeled Recombinant Protein Fragments Based SRM Assay. Mol Cell Proteomics 2019; 18:2433-2446. [PMID: 31591263 PMCID: PMC6885709 DOI: 10.1074/mcp.ra119.001765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 11/20/2022] Open
Abstract
Stable isotope-labeled standard (SIS) peptides are used as internal standards in targeted proteomics to provide robust protein quantification, which is required in clinical settings. However, SIS peptides are typically added post trypsin digestion and, as the digestion efficiency can vary significantly between peptides within a protein, the accuracy and precision of the assay may be compromised. These drawbacks can be remedied by a new class of internal standards introduced by the Human Protein Atlas project, which are based on SIS recombinant protein fragments called SIS PrESTs. SIS PrESTs are added initially to the sample and SIS peptides are released on trypsin digestion. The SIS PrEST technology is promising for absolute quantification of protein biomarkers but has not previously been evaluated in a clinical setting. An automated and scalable solid phase extraction workflow for desalting and enrichment of plasma digests was established enabling simultaneous preparation of up to 96 samples. Robust high-precision quantification of 13 apolipoproteins was achieved using a novel multiplex SIS PrEST-based LC-SRM/MS Tier 2 assay in non-depleted human plasma. The assay exhibited inter-day coefficients of variation between 1.5% and 14.5% (median = 3.5%) and was subsequently used to investigate the effects of omega-3 carboxylic acids (OM3-CA) and fenofibrate on these 13 apolipoproteins in human plasma samples from a randomized placebo-controlled trial, EFFECT I (NCT02354976). No significant changes were observed in the OM3-CA arm, whereas treatment with fenofibrate significantly increased apoAII and reduced apoB, apoCI, apoE and apoCIV levels. The reduction in apoCIV following fenofibrate treatment is a novel finding. The study demonstrates that SIS PrESTs can facilitate the generation of robust multiplexed biomarker Tier 2 assays for absolute quantification of proteins in clinical studies.
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Affiliation(s)
- Andreas Hober
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Maria Ryaboshapkina
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Jonas Malmqvist
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Louise Rosengren
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Andrew J Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA 01876
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Björn Forsström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Oscarsson
- Global Medicines Development, Cardiovascular, Renal and Metabolism, AstraZeneca, Gothenburg, Sweden
| | - Tasso Miliotis
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.
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Larina IM, Percy AJ, Yang J, Borchers CH, Nosovsky AM, Grigoriev AI, Nikolaev EN. Publisher Correction: Protein expression changes caused by spaceflight as measured for 18 Russian cosmonauts. Sci Rep 2019; 9:8570. [PMID: 31171809 PMCID: PMC6554333 DOI: 10.1038/s41598-019-43121-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Irina M Larina
- Institute of Biomedical Problems, Russian Academy of Sciences, 76a Khoroshevskoye shosse, 123007, Moscow, Russia
| | - Andrew J Percy
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, British Columbia, V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, British Columbia, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, British Columbia, V8Z 7X8, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Road, Victoria, British Columbia, V8P 5C2, Canada.,Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, Quebec, H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, 3755 Côte Ste-Catherine Road, Montreal, Quebec, H3T 1E2, Canada
| | - Andrei M Nosovsky
- Institute of Biomedical Problems, Russian Academy of Sciences, 76a Khoroshevskoye shosse, 123007, Moscow, Russia
| | - Anatoli I Grigoriev
- Institute of Biomedical Problems, Russian Academy of Sciences, 76a Khoroshevskoye shosse, 123007, Moscow, Russia
| | - Evgeny N Nikolaev
- Skolkovo Institute of Science and Technology, Skoltech, Moscow region, Skolkovo village, Novaya st.100, 143025, Russia. .,Moscow Institute of Physics and Technology, Moscow region, Dolgoprudnyj, Institutskij pr. 9, 141700, Russia. .,Institute of Energy Problems of Chemical Physics Russian Academy of Sciences, 38 k.2 Leninskij pr., 119334, Moscow, Russia.
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Kashirina DN, Percy AJ, Pastushkova LK, Borchers CH, Kireev KS, Ivanisenko VA, Kononikhin AS, Nikolaev EN, Larina IM. The molecular mechanisms driving physiological changes after long duration space flights revealed by quantitative analysis of human blood proteins. BMC Med Genomics 2019; 12:45. [PMID: 30871558 PMCID: PMC6416832 DOI: 10.1186/s12920-019-0490-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background The conditions of space flight have a significant effect on the physiological processes in the human body, yet the molecular mechanisms driving physiological changes remain unknown. Methods Blood samples of 18 Russian cosmonauts who had conducted long-duration missions to the International Space Station were collected 30 days before launch and on the first and seventh days after landing. Results A panel of 125 proteins in the blood plasma was quantitated by a well-established and highly regarded targeted mass spectrometry approach. This method involves the monitoring of multiple reactions in conjunction with stable isotope-labeled standards at the University of Victoria - Genome BC Proteomics Centre. Conclusions Reduction of circulating plasma volume during space flight and activation of fluid retention at the final stage of the flight affect the changes in plasma protein concentrations present in the first days after landing. Using an ANOVA approach, it was revealed that only 1 protein (S100A9) reliably responded to space flight conditions. This protein plays an important role in the functioning of the endothelium and can serve as a marker for activation of inflammatory reactions. Concentrations of the proteins of complement, coagulation cascades, and acute phase reactants increase in the blood of cosmonauts as measured the first day after landing. Most of these proteins’ concentrations continue to increase by the 7th day after space flight. Similar dynamics are observed for proteases and their inhibitors. Thus, there is a shift in proteolytic blood systems, which is necessary for the restoration of muscle tissue and maintenance of oncotic homeostasis. Electronic supplementary material The online version of this article (10.1186/s12920-019-0490-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria N Kashirina
- Institute for Biomedical Problems - Russian Federation State Scientific Research Center of RAS, Moscow, Russia.
| | - Andrew J Percy
- Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Liudmila Kh Pastushkova
- Institute for Biomedical Problems - Russian Federation State Scientific Research Center of RAS, Moscow, Russia
| | - Christoph H Borchers
- Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Kirill S Kireev
- Yu.A.Gagarin Research and Test Cosmonaut Training Center, Star City, Moscow Region, Russia
| | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Alexey S Kononikhin
- Institute for Biomedical Problems - Russian Federation State Scientific Research Center of RAS, Moscow, Russia.,V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | - Eugene N Nikolaev
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia.,Skolkovo Institute of Science and Technology, Skoltech, Moscow region, Russia
| | - Irina M Larina
- Institute for Biomedical Problems - Russian Federation State Scientific Research Center of RAS, Moscow, Russia
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Richard VR, Domanski D, Percy AJ, Borchers CH. An online 2D-reversed-phase – Reversed-phase chromatographic method for sensitive and robust plasma protein quantitation. J Proteomics 2017; 168:28-36. [DOI: 10.1016/j.jprot.2017.07.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/14/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022]
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LeBlanc A, Michaud SA, Percy AJ, Hardie DB, Yang J, Sinclair NJ, Proudfoot JI, Pistawka A, Smith DS, Borchers CH. Multiplexed MRM-Based Protein Quantitation Using Two Different Stable Isotope-Labeled Peptide Isotopologues for Calibration. J Proteome Res 2017; 16:2527-2536. [PMID: 28516774 DOI: 10.1021/acs.jproteome.7b00094] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
When quantifying endogenous plasma proteins for fundamental and biomedical research - as well as for clinical applications - precise, reproducible, and robust assays are required. Targeted detection of peptides in a bottom-up strategy is the most common and precise mass spectrometry-based quantitation approach when combined with the use of stable isotope-labeled peptides. However, when measuring protein in plasma, the unknown endogenous levels prevent the implementation of the best calibration strategies, since no blank matrix is available. Consequently, several alternative calibration strategies are employed by different laboratories. In this study, these methods were compared to a new approach using two different stable isotope-labeled standard (SIS) peptide isotopologues for each endogenous peptide to be quantified, enabling an external calibration curve as well as the quality control samples to be prepared in pooled human plasma without interference from endogenous peptides. This strategy improves the analytical performance of the assay and enables the accuracy of the assay to be monitored, which can also facilitate method development and validation.
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Affiliation(s)
- André LeBlanc
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, McGill University , Montreal, Quebec H3A 0G4, Canada
| | - Sarah A Michaud
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada
| | - Andrew J Percy
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada
| | - Nicholas J Sinclair
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada
| | - Jillaine I Proudfoot
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada
| | - Adam Pistawka
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada
| | - Derek S Smith
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria - Genome BC Proteomics Centre , Victoria, BC V8Z 7X8, Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, McGill University , Montreal, Quebec H3A 0G4, Canada.,Department of Biochemistry and Microbiology, University of Victoria , Victoria, BC V8P 5C2, Canada.,Leibniz Institut für Analytische Wissenschaften - ISAS - e.V. , Dortmund 44139, Germany.,Gerald Bronfman Department of Oncology, Jewish General Hospital , Montreal, Quebec H3T 1E2, Canada
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Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH. Front Cover: Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics 2017. [DOI: 10.1002/pmic.201770050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mohammed Y, Bhowmick P, Smith DS, Domanski D, Jackson AM, Michaud SA, Malchow S, Percy AJ, Chambers AG, Palmer A, Zhang S, Sickmann A, Borchers CH. PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues. Proteomics 2016; 17. [PMID: 27683069 DOI: 10.1002/pmic.201600210] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/31/2016] [Accepted: 09/27/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Yassene Mohammed
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pallab Bhowmick
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Derek S Smith
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Dominik Domanski
- Molecular Pathology, JGH Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, Quebec, Canada
| | - Angela M Jackson
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Sarah A Michaud
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Sebastian Malchow
- Leibniz-Institut für Analytische Wissenschaften - ISAS e.V., Dortmund, Germany
| | - Andrew J Percy
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Andrew G Chambers
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Andrea Palmer
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Suping Zhang
- MRM Proteomics, Inc., Vancouver Island Technology Park, Victoria, British Columbia, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS e.V., Dortmund, Germany
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre, Vancouver Island Technology Park, Victoria, British Columbia, Canada
- Molecular Pathology, JGH Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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11
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Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH. Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600097] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/14/2016] [Accepted: 09/28/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew J. Percy
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Sarah A. Michaud
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Armando Jardim
- Institute of Parasitology; McGill University; Montreal QC Canada
| | - Nicholas J. Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Suping Zhang
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Center for Proteomics and Metabolomics; Leiden University Medical Center; ZA Leiden Netherlands
| | - Andrea L. Palmer
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Darryl B. Hardie
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Andre M. LeBlanc
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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12
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Percy AJ, Hardie DB, Jardim A, Yang J, Elliott MH, Zhang S, Mohammed Y, Borchers CH. Multiplexed panel of precisely quantified salivary proteins for biomarker assessment. Proteomics 2016; 17. [PMID: 27538354 DOI: 10.1002/pmic.201600230] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/21/2016] [Accepted: 08/15/2016] [Indexed: 12/31/2022]
Abstract
An increasingly popular "absolute" quantitative technique involves the SRM or MRM approach with stable isotope-labeled standards (SIS). Using this approach, many proteins in human plasma/serum have been quantified for biomarker assessment and disease stratification. Due to the complexity of plasma and the invasive nature of its collection, alternative biosamples are currently being explored. Here, we present the broadest panel of multiplexed MRM assays with SIS peptides for saliva proteins developed to date. The validated panel consists of 158 candidate human saliva protein biomarkers, inferred from 244 interference-free peptides. The resulting concentrations were reproducibly quantified over a 6 order-of-magnitude concentration range (from 218 μg/mL to 88 pg/mL; average CVs of 12% over analytical triplicates). All concentrations were determined from reverse standard curves, which were generated using a constant concentration of endogenous material with varying concentrations of spiked-in SIS peptides. The large-scale screening of the soluble and membrane-associated proteins contained within the 158-plex assay could present new opportunities for biomarker assessment and clinical diagnostics.
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Affiliation(s)
- Andrew J Percy
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Armando Jardim
- Institute of Parasitology, McGill University, Montreal, QC, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Monica H Elliott
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Suping Zhang
- MRM Proteomics, Vancouver Island Technology Park, Victoria, BC, Canada
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada.,Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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13
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Yang J, Finke JC, Yang J, Percy AJ, von Fritschen U, Borchers CH, Glocker MO. Early risk prognosis of free-flap transplant failure by quantitation of the macrophage colony-stimulating factor in patient plasma using 2-dimensional liquid-chromatography multiple reaction monitoring-mass spectrometry. Medicine (Baltimore) 2016; 95:e4808. [PMID: 27684807 PMCID: PMC5265900 DOI: 10.1097/md.0000000000004808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Although great success of microvascular free-flap transplantation surgery has been achieved in recent years, between 1.5% and 15% of flaps are still lost due to vascular occlusion. The clinical challenge remains to salvage a transplant in the case of vascular complications. Since flap loss is devastating for the patient, it is of utmost importance to detect signs of complications or of conspicuities as soon as possible. Rescue success rates highly depend on early revision. In this study, we collected blood samples during transplantation surgery from either the contributory artery or the effluent vein of the flap and applied a targeted mass spectrometry-based approach to quantify 24 acute phase proteins, cytokines, and growth factors in 63 plasma samples from 21 hospitalized patients, generating a dataset with 9450 protein concentration values. Biostatistical analyses of the targeted plasma protein concentrations in all 63 plasma samples showed that venous concentrations of macrophage colony-stimulating factor (M-CSF) provided the highest accuracy for discriminating patients with either clinical conspicuities or complications from control individuals. Using 21.33 ng/mL of M-CSF as the diagnostic threshold when analyzing venous blood plasma samples, the assay obtained a sensitivity of 0.93 and a specificity of 0.85 with an area under the curve value of 0.902 in the receiver operating characteristic analysis. Overall, our results indicate that M-CSF is a potential molecular marker for early risk prognosis of free-flap transplant failure.
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Affiliation(s)
- Jingzhi Yang
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock
| | - Juliane C. Finke
- Division of Plastic Surgery and Hand Surgery, HELIOS Clinic Emil von Behring, Berlin, Germany
| | - Juncong Yang
- University of Victoria – Genome British Columbia Proteomics Center, Vancouver Island Technology Park
| | - Andrew J. Percy
- University of Victoria – Genome British Columbia Proteomics Center, Vancouver Island Technology Park
| | - Uwe von Fritschen
- Division of Plastic Surgery and Hand Surgery, HELIOS Clinic Emil von Behring, Berlin, Germany
| | - Christoph H. Borchers
- University of Victoria – Genome British Columbia Proteomics Center, Vancouver Island Technology Park
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Michael O. Glocker
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock
- Correspondence: Michael O. Glocker, Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Schillingallee 69, 18059 Rostock, Germany (e-mail: )
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14
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Percy AJ, Byrns S, Pennington SR, Holmes DT, Anderson NL, Agreste TM, Duffy MA. Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential. Expert Rev Proteomics 2016; 13:673-84. [DOI: 10.1080/14789450.2016.1205950] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew J. Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Simon Byrns
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Stephen R. Pennington
- Department of Pathology, School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Daniel T. Holmes
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - N. Leigh Anderson
- Department of Clinical Biomarkers, SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Tasha M. Agreste
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Maureen A. Duffy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
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15
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Percy AJ, Yang J, Chambers AG, Borchers CH. Increased Depth and Breadth of Plasma Protein Quantitation via Two-Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards. Methods Mol Biol 2016; 1410:1-21. [PMID: 26867735 DOI: 10.1007/978-1-4939-3524-6_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Absolute quantitative strategies are emerging as a powerful and preferable means of deriving concentrations in biological samples for systems biology applications. Method development is driven by the need to establish new-and validate current-protein biomarkers of high-to-low abundance for clinical utility. In this chapter, we describe a methodology involving two-dimensional (2D) reversed-phase liquid chromatography (RPLC), operated under alkaline and acidic pH conditions, combined with multiple reaction monitoring (MRM)-mass spectrometry (MS) (also called selected reaction monitoring (SRM)-MS) and a complex mixture of stable isotope-labeled standard (SIS) peptides, to quantify a broad and diverse panel of 253 proteins in human blood plasma. The quantitation range spans 8 orders of magnitude-from 15 mg/mL (for vitamin D-binding protein) to 450 pg/mL (for protein S100-B)-and includes 31 low-abundance proteins (defined as being <10 ng/mL) of potential disease relevance. The method is designed to assess candidates at the discovery and/or verification phases of the biomarker pipeline and can be adapted to examine smaller or alternate panels of proteins for higher sample throughput. Also detailed here is the application of our recently developed software tool-Qualis-SIS-for protein quantitation (via regression analysis of standard curves) and quality assessment of the resulting data. Overall, this chapter provides the blueprint for the replication of this quantitative proteomic method by proteomic scientists of all skill levels.
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Affiliation(s)
- Andrew J Percy
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada.
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada
| | - Andrew G Chambers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC, V8Z 7X8, Canada.
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada.
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16
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Percy AJ, Yang J, Chambers AG, Mohammed Y, Miliotis T, Borchers CH. Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach. Modern Proteomics – Sample Preparation, Analysis and Practical Applications 2016; 919:515-530. [DOI: 10.1007/978-3-319-41448-5_24] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Chambers AG, Percy AJ, Yang J, Borchers CH. Multiple Reaction Monitoring Enables Precise Quantification of 97 Proteins in Dried Blood Spots. Mol Cell Proteomics 2015; 14:3094-104. [PMID: 26342038 DOI: 10.1074/mcp.o115.049957] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 01/19/2023] Open
Abstract
The dried blood spot (DBS) methodology provides a minimally invasive approach to sample collection and enables room-temperature storage for most analytes. DBS samples have successfully been analyzed by liquid chromatography multiple reaction monitoring mass spectrometry (LC/MRM-MS) to quantify a large range of small molecule biomarkers and drugs; however, this strategy has only recently been explored for MS-based proteomics applications. Here we report the development of a highly multiplexed MRM assay to quantify endogenous proteins in human DBS samples. This assay uses matching stable isotope-labeled standard peptides for precise, relative quantification, and standard curves to characterize the analytical performance. A total of 169 peptides, corresponding to 97 proteins, were quantified in the final assay with an average linear dynamic range of 207-fold and an average R(2) value of 0.987. The total range of this assay spanned almost 5 orders of magnitude from serum albumin (P02768) at 18.0 mg/ml down to cholinesterase (P06276) at 190 ng/ml. The average intra-assay and inter-assay precision for 6 biological samples ranged from 6.1-7.5% CV and 9.5-11.0% CV, respectively. The majority of peptide targets were stable after 154 days at storage temperatures from -20 °C to 37 °C. Furthermore, protein concentration ratios between matching DBS and whole blood samples were largely constant (<20% CV) across six biological samples. This assay represents the highest multiplexing yet achieved for targeted protein quantification in DBS samples and is suitable for biomedical research applications.
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Affiliation(s)
- Andrew G Chambers
- From the ‡University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101 - 4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Andrew J Percy
- From the ‡University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101 - 4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Juncong Yang
- From the ‡University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101 - 4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- From the ‡University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101 - 4464 Markham St., Victoria, BC V8Z 7X8, Canada; §Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
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18
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Percy AJ, Tamura-Wells J, Albar JP, Aloria K, Amirkhani A, Araujo GD, Arizmendi JM, Blanco FJ, Canals F, Cho JY, Colomé-Calls N, Corrales FJ, Domont G, Espadas G, Fernandez-Puente P, Gil C, Haynes PA, Hernáez ML, Kim JY, Kopylov A, Marcilla M, McKay MJ, Mirzaei M, Molloy MP, Ohlund LB, Paik YK, Paradela A, Raftery M, Sabidó E, Sleno L, Wilffert D, Wolters JC, Yoo JS, Zgoda V, Parker CE, Borchers CH. Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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19
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Percy AJ, Yang J, Hardie DB, Chambers AG, Tamura-Wells J, Borchers CH. Precise quantitation of 136 urinary proteins by LC/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and/or verification studies. Methods 2015; 81:24-33. [DOI: 10.1016/j.ymeth.2015.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/13/2015] [Accepted: 04/01/2015] [Indexed: 01/01/2023] Open
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20
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Mohammed Y, Percy AJ, Chambers AG, Borchers CH. Qualis-SIS: automated standard curve generation and quality assessment for multiplexed targeted quantitative proteomic experiments with labeled standards. J Proteome Res 2015; 14:1137-46. [PMID: 25546269 DOI: 10.1021/pr5010955] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiplexed targeted quantitative proteomics typically utilizes multiple reaction monitoring and allows the optimized quantification of a large number of proteins. One challenge, however, is the large amount of data that needs to be reviewed, analyzed, and interpreted. Different vendors provide software for their instruments, which determine the recorded responses of the heavy and endogenous peptides and perform the response-curve integration. Bringing multiplexed data together and generating standard curves is often an off-line step accomplished, for example, with spreadsheet software. This can be laborious, as it requires determining the concentration levels that meet the required accuracy and precision criteria in an iterative process. We present here a computer program, Qualis-SIS, that generates standard curves from multiplexed MRM experiments and determines analyte concentrations in biological samples. Multiple level-removal algorithms and acceptance criteria for concentration levels are implemented. When used to apply the standard curve to new samples, the software flags each measurement according to its quality. From the user's perspective, the data processing is instantaneous due to the reactivity paradigm used, and the user can download the results of the stepwise calculations for further processing, if necessary. This allows for more consistent data analysis and can dramatically accelerate the downstream data analysis.
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Affiliation(s)
- Yassene Mohammed
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria , Vancouver Island Technology Park, #3101-4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
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21
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Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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22
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Percy AJ, Simon R, Chambers AG, Borchers CH. Enhanced sensitivity and multiplexing with 2D LC/MRM-MS and labeled standards for deeper and more comprehensive protein quantitation. J Proteomics 2014; 106:113-24. [PMID: 24769237 DOI: 10.1016/j.jprot.2014.04.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 04/10/2014] [Accepted: 04/14/2014] [Indexed: 01/04/2023]
Abstract
UNLABELLED Mass spectrometry (MS)-based protein quantitation is increasingly being employed to verify candidate protein biomarkers. Multiple or selected reaction monitoring-mass spectrometry (MRM-MS or SRM-MS) with isotopically labeled internal standards has proven to be a successful approach in that regard, but has yet to reach its full potential in terms of multiplexing and sensitivity. Here, we report the development of a new MRM method for the quantitation of 253 disease-associated proteins (represented by 625 interference-free peptides) in 13 LC fractions. This 2D RPLC/MRM-MS approach extends the depth and breadth of the assay by 2 orders of magnitude over pre-fractionation-free assays, with 31 proteins below 10 ng/mL and 41 proteins above 10 ng/mL now quantifiable. Standard flow rates are used in both chromatographic dimensions, and up-front depletion or antibody-based enrichment is not required. The LC separations utilize high and low pH conditions, with the former employing an ammonium hydroxide-based eluent, instead of the conventional ammonium formate, resulting in improved LC column lifetime and performance. The high sensitivity (determined concentration range: 15 mg/mL to 452 pg/mL) and robustness afforded by this method makes the full MRM panel, or subsets thereof, useful for the verification of disease-associated plasma protein biomarkers in patient samples. BIOLOGICAL SIGNIFICANCE The described research extends the breadth and depth of protein quantitation in undepleted and non-enriched human plasma by employing standard-flow 2D RPLC/MRM-MS in conjunction with a complex mixture of isotopically labeled peptide standards. The proteins quantified are mainly putative biomarkers of non-communicable (i.e., non-infectious) disease (e.g., cardiovascular or cancer), which require pre-clinical verification and validation before clinical implementation. Based on the enhanced sensitivity and multiplexing, this quantitative plasma proteomic method should prove useful in future candidate biomarker verification studies.
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Affiliation(s)
- Andrew J Percy
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Romain Simon
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Andrew G Chambers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.
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23
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Chambers AG, Percy AJ, Simon R, Borchers CH. MRM for the verification of cancer biomarker proteins: recent applications to human plasma and serum. Expert Rev Proteomics 2014; 11:137-48. [PMID: 24476379 DOI: 10.1586/14789450.2014.877346] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Accurate cancer biomarkers are needed for early detection, disease classification, prediction of therapeutic response and monitoring treatment. While there appears to be no shortage of candidate biomarker proteins, a major bottleneck in the biomarker pipeline continues to be their verification by enzyme linked immunosorbent assays. Multiple reaction monitoring (MRM), also known as selected reaction monitoring, is a targeted mass spectrometry approach to protein quantitation and is emerging to bridge the gap between biomarker discovery and clinical validation. Highly multiplexed MRM assays are readily configured and enable simultaneous verification of large numbers of candidates facilitating the development of biomarker panels which can increase specificity. This review focuses on recent applications of MRM to the analysis of plasma and serum from cancer patients for biomarker verification. The current status of this approach is discussed along with future directions for targeted mass spectrometry in clinical biomarker validation.
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Affiliation(s)
- Andrew G Chambers
- University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101 - 4464 Markham St, Victoria, BC V8Z 7X8, Canada
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24
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Percy AJ, Byrns S, Chambers AG, Borchers CH. Targeted quantitation of CVD-linked plasma proteins for biomarker verification and validation. Expert Rev Proteomics 2014; 10:567-78. [DOI: 10.1586/14789450.2013.856763] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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Percy AJ, Chambers AG, Yang J, Jackson AM, Domanski D, Burkhart J, Sickmann A, Borchers CH. Method and platform standardization in MRM-based quantitative plasma proteomics. J Proteomics 2013; 95:66-76. [DOI: 10.1016/j.jprot.2013.07.026] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/11/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
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26
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Percy AJ, Chambers AG, Parker CE, Borchers CH. Absolute quantitation of proteins in human blood by multiplexed multiple reaction monitoring mass spectrometry. Methods Mol Biol 2013; 1000:167-89. [PMID: 23585092 DOI: 10.1007/978-1-62703-405-0_13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Multiple reaction monitoring (MRM)-mass spectrometry (MS) with stable isotope-labeled standards (SIS) has proven adept in rapidly, precisely, and accurately quantifying proteins in complex biological samples. The impetus behind the early use of multiplexed MRM in proteomics was to expedite the verification and validation stages of the protein biomarker pipeline for clinical utility, which involves the analysis of hundreds or even thousands of samples. Moreover, once a multiplexed assay has been developed, however, it can be turned around and used for biomarker discovery, as has been demonstrated for cancer biomarkers by our laboratory and by others. Overall, these MRM-based methods compare favorably with antibody-based techniques, such as ELISAs or protein arrays, in that MRM-based methods are less expensive and can be developed more rapidly. There are two MRM-based platforms that are currently being developed: a standard-flow and a nano-flow LC/ESI-MRM-MS (liquid chromatography-electrospray ionization) platform. In this book chapter, we describe a recent study in which we evaluated these two platforms, both interfaced to the same mass spectrometer. This study demonstrated the enhanced performance metrics (in terms of sensitivity, dynamic range, and robustness) of the standard-flow ultra-high performance liquid chromatography (UHPLC) system compared to the nano-flow HPLC-Chip for the absolute quantitation of 48 plasma proteins. Using the standard-flow platform, we also developed two high-throughput assays for the analysis of a panel of 67 cardiovascular disease (CVD) biomarkers in non-depleted and non-enriched human plasma and a panel of 25 putative biomarkers in dried human blood spots (DBS). Since the nanoLC/MRM-MS platform has advantages under sample-limited conditions and for the analysis of certain specific peptides, the protocols for both systems are described here.
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Affiliation(s)
- Andrew J Percy
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada
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Chambers AG, Percy AJ, Hardie DB, Borchers CH. Comparison of proteins in whole blood and dried blood spot samples by LC/MS/MS. J Am Soc Mass Spectrom 2013; 24:1338-1345. [PMID: 23821375 DOI: 10.1007/s13361-013-0678-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 06/02/2023]
Abstract
Dried blood spot (DBS) sampling methods are desirable for population-wide biomarker screening programs because of their ease of collection, transportation, and storage. Immunoassays are traditionally used to quantify endogenous proteins in these samples but require a separate assay for each protein. Recently, targeted mass spectrometry (MS) has been proposed for generating highly-multiplexed assays for biomarker proteins in DBS samples. In this work, we report the first comparison of proteins in whole blood and DBS samples using an untargeted MS approach. The average number of proteins identified in undepleted whole blood and DBS samples by liquid chromatography (LC)/MS/MS was 223 and 253, respectively. Protein identification repeatability was between 77%-92% within replicates and the majority of these repeated proteins (70%) were observed in both sample formats. Proteins exclusively identified in the liquid or dried fluid spot format were unbiased based on their molecular weight, isoelectric point, aliphatic index, and grand average hydrophobicity. In addition, we extended this comparison to include proteins in matching plasma and serum samples with their dried fluid spot equivalents, dried plasma spot (DPS), and dried serum spot (DSS). This work begins to define the accessibility of endogenous proteins in dried fluid spot samples for analysis by MS and is useful in evaluating the scope of this new approach.
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Affiliation(s)
- Andrew G Chambers
- Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, Victoria, BC, Canada
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Percy AJ, Chambers AG, Yang J, Borchers CH. Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma. Proteomics 2013; 13:2202-15. [DOI: 10.1002/pmic.201200316] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/06/2013] [Accepted: 03/26/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Andrew J. Percy
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Andrew G. Chambers
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Juncong Yang
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria - Genome British Columbia Proteomics Centre; Vancouver Island Technology Park; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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Chambers AG, Percy AJ, Yang J, Camenzind AG, Borchers CH. Multiplexed quantitation of endogenous proteins in dried blood spots by multiple reaction monitoring-mass spectrometry. Mol Cell Proteomics 2013; 12:781-91. [PMID: 23221968 PMCID: PMC3591668 DOI: 10.1074/mcp.m112.022442] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 11/26/2012] [Indexed: 11/06/2022] Open
Abstract
Dried blood spot (DBS) sampling, coupled with multiple reaction monitoring mass spectrometry (MRM-MS), is a well-established approach for quantifying a wide range of small molecule biomarkers and drugs. This sampling procedure is simpler and less-invasive than those required for traditional plasma or serum samples enabling collection by minimally trained personnel. Many analytes are stable in the DBS format without refrigeration, which reduces the cost and logistical challenges of sample collection in remote locations. These advantages make DBS sample collection desirable for advancing personalized medicine through population-wide biomarker screening. Here we expand this technology by demonstrating the first multiplexed method for the quantitation of endogenous proteins in DBS samples. A panel of 60 abundant proteins in human blood was targeted by monitoring proteotypic tryptic peptides and their stable isotope-labeled analogs by MRM. Linear calibration curves were obtained for 40 of the 65 peptide targets demonstrating multiple proteins can be quantitatively extracted from DBS collection cards. The method was also highly reproducible with a coefficient of variation of <15% for all 40 peptides. Overall, this assay quantified 37 proteins spanning a range of more than four orders of magnitude in concentration within a single 25 min LC/MRM-MS analysis. The protein abundances of the 33 proteins quantified in matching DBS and whole blood samples showed an excellent correlation, with a slope of 0.96 and an R(2) value of 0.97. Furthermore, the measured concentrations for 80% of the proteins were stable for at least 10 days when stored at -20 °C, 4 °C and 37 °C. This work represents an important first step in evaluating the integration of DBS sampling with highly-multiplexed MRM for quantitation of endogenous proteins.
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Affiliation(s)
- Andrew G. Chambers
- From the ‡University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101, 4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Andrew J. Percy
- From the ‡University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101, 4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Juncong Yang
- From the ‡University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101, 4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Alexander G. Camenzind
- From the ‡University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101, 4464 Markham St., Victoria, BC V8Z 7X8, Canada
| | - Christoph H. Borchers
- From the ‡University of Victoria-Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101, 4464 Markham St., Victoria, BC V8Z 7X8, Canada
- §Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada
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Percy AJ, Chambers AG, Smith DS, Borchers CH. Standardized protocols for quality control of MRM-based plasma proteomic workflows. J Proteome Res 2012; 12:222-33. [PMID: 23245390 DOI: 10.1021/pr300893w] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mass spectrometry (MS)-based proteomics is rapidly emerging as a viable technology for the identification and quantitation of biological samples, such as human plasma--the most complex yet commonly employed biofluid in clinical analyses. The transition from a qualitative to quantitative science is required if proteomics is going to successfully make the transition to a clinically useful technique. MS, however, has been criticized for a lack of reproducibility and interlaboratory transferability. Currently, the MS and plasma proteomics communities lack standardized protocols and reagents to ensure that high-quality quantitative data can be accurately and precisely reproduced by laboratories across the world using different MS technologies. Toward addressing this issue, we have developed standard protocols for multiple reaction monitoring (MRM)-based assays with customized isotopically labeled internal standards for quality control of the sample preparation workflow and the MS platform in quantitative plasma proteomic analyses. The development of reference standards and their application to a single MS platform is discussed herein, along with the results from intralaboratory tests. The tests highlighted the importance of the reference standards in assessing the efficiency and reproducibility of the entire bottom-up proteomic workflow and revealed errors related to the sample preparation and performance quality and deficits of the MS and LC systems. Such evaluations are necessary if MRM-based quantitative plasma proteomics is to be used in verifying and validating putative disease biomarkers across different research laboratories and eventually in clinical laboratories.
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Affiliation(s)
- Andrew J Percy
- University of Victoria - Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101 - 4464 Markham Street, Victoria, BC V8Z 7X8, Canada
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Domanski D, Percy AJ, Yang J, Chambers AG, Hill JS, Freue GVC, Borchers CH. MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma. Proteomics 2012; 12:1222-43. [PMID: 22577024 DOI: 10.1002/pmic.201100568] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A highly-multiplexed MRM-based assay for determination of cardiovascular disease (CVD) status and disease classification has been developed for clinical research. A high-flow system using ultra-high performance LC and an Agilent 6490 triple quadrupole mass spectrometer, equipped with an ion funnel, provided ease of use and increased the robustness of the assay. The assay uses 135 stable isotope-labeled peptide standards for the quantitation of 67 putative biomarkers of CVD in tryptic digests of whole plasma in a 30-min assay. Eighty-five analyses of the same sample showed no loss of sensitivity (<20% CV for 134/135 peptides) and no loss of retention time accuracy (<0.5% CV for all peptides). The maximum linear dynamic range of the MRM assays ranged from 10(3) -10(5) for 106 of the assays. Excellent linear responses (r >0.98) were obtained for 117 of the 135 peptide targets with attomole level limits of quantitation (<20% CV and accuracy 80-120%) for 81 of the 135 peptides. The assay presented in this study is easy to use, robust, sensitive, and has high-throughput capabilities through short analysis time and complete automated sample preparation. It is therefore well suited for CVD biomarker validation and discovery in plasma.
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Affiliation(s)
- Dominik Domanski
- University of Victoria - Genome British Columbia Proteomics Centre, Victoria, BC, Canada
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Percy AJ, Rey M, Burns KM, Schriemer DC. Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-a review. Anal Chim Acta 2012; 721:7-21. [PMID: 22405295 DOI: 10.1016/j.aca.2012.01.037] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 11/17/2022]
Abstract
Assessing the functional outcome of protein interactions in structural terms is a goal of structural biology, however most techniques have a limited capacity for making structure-function determinations with both high resolution and high throughput. Mass spectrometry can be applied as a reader of protein chemistries in order to fill this void, and enable methodologies whereby protein structure-function determinations may be made on a proteome-wide level. Protein hydrogen/deuterium exchange (H/DX) offers a chemical labeling strategy suitable for tracking changes in "dynamic topography" and thus represents a powerful means of monitoring protein structure-function relationships. This review presents the exchange method in the context of interaction analysis. Applications involving interface detection, quantitation of binding, and conformational responses to ligation are discussed, and commentary on recent analytical developments is provided.
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Affiliation(s)
- Andrew J Percy
- Department of Chemistry, University of Calgary, Alberta, Canada
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Parker CE, Domanski D, Percy AJ, Chambers AG, Camenzind AG, Smith DS, Borchers CH. Mass spectrometry in high-throughput clinical biomarker assays: multiple reaction monitoring. Top Curr Chem (Cham) 2012; 336:117-37. [PMID: 22886709 DOI: 10.1007/128_2012_353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Clinical biomarker discovery, verification, and validation are facilitated by the latest technological advances in mass spectrometry. It is now possible to analyze simultaneously group of tens or hundreds of biomarkers in a blood sample using multiple reaction monitoring (MRM), a tandem mass spectrometric method. However, these newly-developed methods face new challenges, including standardization, calibration, and the determination of analytical and biological variation. Here we illustrate the background, pre-analytical sample preparation, and biomarker assay development using an MRM-mass spectrometric method. In addition, special attention is given to future standardization methods to enable widespread use of the technology.
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Affiliation(s)
- Carol E Parker
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
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Percy AJ, Schriemer DC. Rheostatic control of tryptic digestion in a microscale fluidic system. Anal Chim Acta 2010; 657:53-9. [DOI: 10.1016/j.aca.2009.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/17/2009] [Accepted: 10/09/2009] [Indexed: 11/25/2022]
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Affiliation(s)
- Andrew J. Percy
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Gordon W. Slysz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - David C. Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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Slysz GW, Baker CAH, Bozsa BM, Dang A, Percy AJ, Bennett M, Schriemer DC. Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses. BMC Bioinformatics 2009; 10:162. [PMID: 19473537 PMCID: PMC2696453 DOI: 10.1186/1471-2105-10-162] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 05/27/2009] [Indexed: 11/10/2022] Open
Abstract
Background Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing data requires an automated solution, particularly when accommodating new tandem mass spectrometry modes for H/DX measurement. We sought to develop software that offers flexibility in defining workflows so as to support exploratory treatments of H/DX-MS data, with a particular focus on the analysis of very large protein systems and the mining of tandem mass spectrometry data. Results We present a software package ("Hydra") that supports both traditional and exploratory treatments of H/DX-MS data. Hydra's software architecture tolerates flexible data analysis procedures by allowing the addition of new algorithms without significant change to the underlying code base. Convenient user interfaces ease the organization of raw data files and input of peptide data. After executing a user-defined workflow, extracted deuterium incorporation values can be visualized in tabular and graphical formats. Hydra also automates the extraction and visualization of deuterium distribution values. Manual validation and assessment of results is aided by an interface that aligns extracted ion chromatograms and mass spectra, while providing a means of rapidly reprocessing the data following manual adjustment. A unique feature of Hydra is the automated processing of tandem mass spectrometry data, demonstrated on a large test data set in which 40,000 deuterium incorporation values were extracted from replicate analysis of approximately 1000 fragment ions in one hour using a typical PC. Conclusion The customizable workflows and user-friendly interfaces of Hydra removes a significant bottleneck in processing and visualizing H/DX-MS data and helps the researcher spend more time executing new experiments and interpreting results. This increased efficiency will encourage the analysis of larger protein systems. The ability to accommodate the tandem MS dimension supports alternative data collection and analysis strategies, as well as higher resolution localization of deuteration where permitted by the fragmentation mechanism.
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Affiliation(s)
- Gordon W Slysz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.
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Slysz GW, Percy AJ, Schriemer DC. Restraining Expansion of the Peak Envelope in H/D Exchange-MS and Its Application in Detecting Perturbations of Protein Structure/Dynamics. Anal Chem 2008; 80:7004-11. [DOI: 10.1021/ac800897q] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gordon W. Slysz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Andrew J. Percy
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - David C. Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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Korbas M, Percy AJ, Gailer J, George GN. A possible molecular link between the toxicological effects of arsenic, selenium and methylmercury: methylmercury(II) seleno bis(S-glutathionyl) arsenic(III). J Biol Inorg Chem 2008; 13:461-70. [DOI: 10.1007/s00775-007-0336-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2007] [Accepted: 12/09/2007] [Indexed: 11/30/2022]
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Percy AJ, Korbas M, George GN, Gailer J. Reversed-phase high-performance liquid chromatographic separation of inorganic mercury and methylmercury driven by their different coordination chemistry towards thiols. J Chromatogr A 2007; 1156:331-9. [PMID: 17222858 DOI: 10.1016/j.chroma.2006.12.061] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 12/02/2006] [Accepted: 12/18/2006] [Indexed: 11/17/2022]
Abstract
Since mercuric mercury (Hg(2+)) and methylmercury (CH(3)Hg(+)) display different toxicological properties in mammals, methods for their quantification in dietary items must be available. Employing Hg-specific detection, we have developed a rapid, isocratic, and affordable RP-HPLC separation of these mercurials using thiol-containing mobile phases. Optimal separation was achieved with a 50mM phosphate-buffer containing 10mM L-cysteine at pH 7.5. The separation is driven by the on-column formation of complexes between each mercurial and L-cysteine, which are then separated according to their different hydrophobicities. The developed method is compatible with inductively coupled plasma atomic emission spectrometry and was applied to analyze spiked human urine.
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Affiliation(s)
- Andrew J Percy
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
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Affiliation(s)
- S H Weitzel
- Department of Trauma and Orthopedic Surgery, Queen Mary's Hospital, Sidcup, United Kingdom
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Bingold AC, Percy AJ. Prosthetic replacement of a chondrosarcoma of the upper end of the femur: a 43-year follow-up. J Bone Joint Surg Br 1996; 78:663-4. [PMID: 8682840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- A C Bingold
- Queen Mary's Hospital NHS Trust, Sidkup, Kent
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Percy AJ, Trainor DA, Rittenhouse J, Phelps J, Koda JE. Development of sensitive immunoassays to detect amylin and amylin-like peptides in unextracted plasma. Clin Chem 1996. [DOI: 10.1093/clinchem/42.4.576] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Amylin is a 37-amino-acid polypeptide synthesized in and secreted from pancreatic beta cells along with insulin. Its biological actions include the slowing and reduction of postmeal increases in plasma glucose concentrations. Studies of the basic amylin biology in humans have been hampered by the lack of a rapid, sensitive assay capable of measuring physiological concentrations of amylin in small volumes of plasma. We report here two sandwich-type immunoassays that use pairs of monoclonal antibodies, the fluorescent substrate 4-methylumbelliferyl phosphate, and the enzyme alkaline phosphatase. The minimum detectable concentration of amylin in 50 microL of plasma was 0.5 to 2 pmol/L, and the dynamic range was 2 to 100 pmol/L. The assays had average intraassay CVs of <10%, average interassay CVs of <15%, and good linearity on dilution and recovery of added amylin. The two assays use the same detection antibody, which binds to the carboxyl terminus of the molecule, but different capture antibodies. One of the assays measures only human amylin; the other also detects amylin-like peptides. Examples of measurements in human plasma are provided in subjects with impaired glucose tolerance and in nondiabetic controls.
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Affiliation(s)
- A J Percy
- Amylin Pharmaceuticals, Inc., San Diego, CA 92121, USA
| | - D A Trainor
- Amylin Pharmaceuticals, Inc., San Diego, CA 92121, USA
| | - J Rittenhouse
- Amylin Pharmaceuticals, Inc., San Diego, CA 92121, USA
| | - J Phelps
- Amylin Pharmaceuticals, Inc., San Diego, CA 92121, USA
| | - J E Koda
- Amylin Pharmaceuticals, Inc., San Diego, CA 92121, USA
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Percy AJ, Trainor DA, Rittenhouse J, Phelps J, Koda JE. Development of sensitive immunoassays to detect amylin and amylin-like peptides in unextracted plasma. Clin Chem 1996; 42:576-85. [PMID: 8605675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Amylin is a 37-amino-acid polypeptide synthesized in and secreted from pancreatic beta cells along with insulin. Its biological actions include the slowing and reduction of postmeal increases in plasma glucose concentrations. Studies of the basic amylin biology in humans have been hampered by the lack of a rapid, sensitive assay capable of measuring physiological concentrations of amylin in small volumes of plasma. We report here two sandwich-type immunoassays that use pairs of monoclonal antibodies, the fluorescent substrate 4-methylumbelliferyl phosphate, and the enzyme alkaline phosphatase. The minimum detectable concentration of amylin in 50 microL of plasma was 0.5 to 2 pmol/L, and the dynamic range was 2 to 100 pmol/L. The assays had average intraassay CVs of <10%, average interassay CVs of <15%, and good linearity on dilution and recovery of added amylin. The two assays use the same detection antibody, which binds to the carboxyl terminus of the molecule, but different capture antibodies. One of the assays measures only human amylin; the other also detects amylin-like peptides. Examples of measurements in human plasma are provided in subjects with impaired glucose tolerance and in nondiabetic controls.
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Affiliation(s)
- A J Percy
- Amylin Pharmaceuticals, Inc., San Diego, CA 92121, USA
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Abstract
A report of a case of osteochondral fracture of the lateral femoral condyle in a patient doing a karate kick. The problems related to fixation of osteochondral fragments with protruding screws are highlighted and the suitability of Herbert screw fixation noted.
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Abstract
We describe the detection of DNA strand breaks in the rat colonic mucosa (in vivo and in vitro) by fluorometric analysis of DNA unwinding. DNA strand breaks were detected, in a dose-dependent manner, 2 h following an intracaecal dose of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG, 5-100 mg/kg). Levels of double-stranded DNA in the colonic mucosa of control animals, after 60 min unwinding time, were 62.8 +/- 3.4% (n = 6) and were significantly reduced at 5 mg/kg to 52.1 +/- 1.9% (n = 3). DNA strand breaks were also detected in isolated rat colonic mucosal cells following 15 min treatment with MNNG (0.1-1 mM) in vitro. The percentage of double-stranded DNA, after 60 min unwinding time, was significantly reduced (13.6 +/- 5.4%, n = 3) from control levels following treatment with 0.1 mM. A post-treatment incubation (30 min) of cells treated at a MNNG concentration of 0.25 mM resulted in 78.2 +/- 24.0% (n = 3) of these lesions being repaired.
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Affiliation(s)
- A J Percy
- School of Biochemistry, University of Birmingham, U.K
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Abstract
Administration of benzidine (BZ) by intraperitoneal injection (i.p.) to rats (0-100 mg/kg) produced, after 24 h, a dose-dependent formation of nuclear anomalies (micronuclei, pyknotic and karyorrhectic nuclei) in intestinal epithelial cells analysed both in isolated cell suspensions and in the intestinal crypts in tissue sections. When bile collected (0-4 h) from rats treated with BZ (150 mg/kg, i.p.) was infused into the duodenum of recipient rats, nuclear anomalies were observed in mucosal epithelial cells, after 24 h, with a similar distribution to that in rats given BZ by i.p. injection. The formation of nuclear anomalies in the intestine is in accord with the intestinal carcinogenic effect of BZ and is, at least partially, dependent on exposure of epithelial cells to biliary metabolites of BZ.
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Affiliation(s)
- A J Percy
- School of Biochemistry, University of Birmingham, U.K
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Percy AJ, Harn DA. Monoclonal anti-idiotypic and anti-anti-idiotypic antibodies from mice immunized with a protective monoclonal antibody against Schistosoma mansoni. The Journal of Immunology 1988. [DOI: 10.4049/jimmunol.140.8.2760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
To study the role of idiotypic anti-idiotypic interactions in schistosomiasis, mice were immunized with a mAb, E.1, which bound to soluble egg and larval stage Ag and also passively transferred resistance to cercarial challenge in mice. Subsequently, hybridomas were produced from E.1 immunized mice and tested for the ability to inhibit E.1 binding to soluble egg Ag. The results showed that anti-idiotypic mAb (Ab2) were produced. The range of inhibitory activity was from 33 to 100%. By using a direct Ab2 binding assay, the Ab2 were shown to be idiotypic specific, not isotype specific. It was also found that six of the hybridomas bound to soluble egg Ag and were therefore anti-anti-idiotypic antibodies (Ab3). Ab3 were shown to be inhibited from binding to soluble egg Ag by Ab2. To the authors' knowledge, this is the first time that an in vivo network relevant to an infectious organism has been reproduced in vitro such that both Ab2 and Ab3 were produced from the same animals independent of exposure to parasite Ag.
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Affiliation(s)
- A J Percy
- Department of Tropical Public Health, Harvard School of Public Health, Boston, MA 02115
| | - D A Harn
- Department of Tropical Public Health, Harvard School of Public Health, Boston, MA 02115
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Percy AJ, Harn DA. Monoclonal anti-idiotypic and anti-anti-idiotypic antibodies from mice immunized with a protective monoclonal antibody against Schistosoma mansoni. J Immunol 1988; 140:2760-2. [PMID: 3128609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
To study the role of idiotypic anti-idiotypic interactions in schistosomiasis, mice were immunized with a mAb, E.1, which bound to soluble egg and larval stage Ag and also passively transferred resistance to cercarial challenge in mice. Subsequently, hybridomas were produced from E.1 immunized mice and tested for the ability to inhibit E.1 binding to soluble egg Ag. The results showed that anti-idiotypic mAb (Ab2) were produced. The range of inhibitory activity was from 33 to 100%. By using a direct Ab2 binding assay, the Ab2 were shown to be idiotypic specific, not isotype specific. It was also found that six of the hybridomas bound to soluble egg Ag and were therefore anti-anti-idiotypic antibodies (Ab3). Ab3 were shown to be inhibited from binding to soluble egg Ag by Ab2. To the authors' knowledge, this is the first time that an in vivo network relevant to an infectious organism has been reproduced in vitro such that both Ab2 and Ab3 were produced from the same animals independent of exposure to parasite Ag.
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Affiliation(s)
- A J Percy
- Department of Tropical Public Health, Harvard School of Public Health, Boston, MA 02115
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Abstract
A 22 kDa antigen (Sm22) was purified from schistosomula membrane extracts by immunoaffinity chromatography with monoclonal antibody M.2. Western blotting suggested that the epitope bound by M.2 required a specific conformational folding of the molecule, which was sensitive to reducing agents. Two-dimensional electrophoresis of purified Sm22 demonstrated that the single 22 kDa protein recognized by M.2 on one-dimensional gel analysis was composed of at least two isomorphs. Additional Western blotting showed that Sm2 was one of the major antigens recognized by mouse anti-irradiated cercariae serum, and that this same serum recognized at least one epitope which was not sensitive to reducing agents. The mice vaccinated with irradiated cercariae were shown to be 75% protected from cercarial challenge. Sera from a rabbit immunized with Sm22 contained antibodies which bound to the surface of schistosomula and detected a single protein at 22 kDa by immunoprecipitation or Western blot. The rabbit anti-Sm22 sera also immunoprecipitated a 22 kDa in vitro translation product, indicating that at least one epitope on Sm22 is not dependent on glycosylation.
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Affiliation(s)
- L D Oligino
- Dept. of Tropical Public Health, Harvard School of Public Health, Boston, MA 02115
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Abstract
The temperature dependence of the hydrogen-tritium and deuterium-hydrogen exchange reactions in poly(DL-alanine) has been reexamined. The results indicate a significant contribution to the observed exchange rates from the water-catalyzed reaction at pD values near pDmin. The activation enthalpy for water-catalyzed deuterium-hydrogen exchange in poly(DL-alanine) is found to be 21 kcal mol-1. As a result, the contribution to the observed exchange rate from the water-catalyzed reaction increases with increasing temperature which in turn leads to broad, shallow pD minima and the appearance of apparent reaction orders with respect to [D+] and [OD-] that are substantially less than first order over an extended range of pD values. The importance of water catalysis in protein hydrogen exchange is demonstrated by a reanalysis of data for the exchange of single protons in bovine pancreatic trypsin inhibitor [Hilton, B.D., & Woodward, C. K. (1979) Biochemistry 18, 5834; Richarz, R., Sehr, P., Wagner, G., & Wüthrich, K. (1979) J. Mol. Biol. 130, 19]. The pD dependence of these protons can be explained in terms of an increased contribution from water catalysis.
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