301
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Zinn N, Winter D, Lehmann WD. Recombinant Isotope Labeled and Selenium Quantified Proteins for Absolute Protein Quantification. Anal Chem 2010; 82:2334-40. [DOI: 10.1021/ac9025412] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nico Zinn
- Molecular Structure Analysis, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Dominic Winter
- Molecular Structure Analysis, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Wolf D. Lehmann
- Molecular Structure Analysis, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg, Germany
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302
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Abstract
The ability to conduct validated analyses of biomarkers is critically important in order to establish the sensitivity and selectivity of the biomarker in identifying a particular disease. The use of stable-isotope dilution (SID) methodology in combination with LC–MS/MS provides the highest possible analytical specificity for quantitative determinations. This methodology is now widely used in the discovery and validation of putative exposure and disease biomarkers. This review will describe the application of SID LC–MS methodology for the analysis of small-molecule and protein biomarkers. It will also discuss potential future directions for the use of this methodology for rigorous biomarker analysis.
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Affiliation(s)
- Eugene Ciccimaro
- Thermo Fisher Scientific, 265 Davidson Avenue, Somerset, NJ 08873–4120, USA
| | - Ian A Blair
- Centers of Excellence in Environmental Toxicology and Cancer Pharmacology, Department of Pharmacology, University of Pennsylvania School of Medicine, 421 Curie Blvd, Philadelphia, PA 19104–6160, USA
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303
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An immunoaffinity liquid chromatography-tandem mass spectrometry assay for the quantitation of matrix metalloproteinase 9 in mouse serum. Anal Biochem 2010; 399:202-10. [PMID: 20060801 DOI: 10.1016/j.ab.2010.01.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 12/10/2009] [Accepted: 01/06/2010] [Indexed: 11/21/2022]
Abstract
An immunoaffinity liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the quantitation of the zinc endopeptidase matrix metalloproteinase 9 (MMP-9) from mouse serum. Sample preparation for the assay included magnetic bead-based enrichment using an MMP-9 antibody and was performed in a 96-well plate format using a liquid-handling robotic platform. The surrogate peptide GSPLQGPFLTAR derived from MMP-9 by trypsin digestion was monitored using an on-line capillary flow trap-release chromatography setup incorporating a series of trap columns (C18, strong cation exchange, and another C18) prior to nanoflow chromatography and nanospray ionization with selected reaction monitoring (SRM) detection. The assay was fit-for-purpose validated and found to be accurate (<15% interbatch relative error) and precise (<15% interbatch coefficient of variation) across a range from 0.03 to 7.3nM mouse MMP-9. Finally, the method was employed to measure MMP-9 concentrations in 30 naïve mouse serum samples, and results were compared with those obtained by an immunoassay.
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304
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Dayon L, Turck N, Kienle S, Schulz-Knappe P, Hochstrasser DF, Scherl A, Sanchez JC. Isobaric Tagging-Based Selection and Quantitation of Cerebrospinal Fluid Tryptic Peptides with Reporter Calibration Curves. Anal Chem 2010; 82:848-58. [DOI: 10.1021/ac901854k] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Loïc Dayon
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Natacha Turck
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Stefan Kienle
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Peter Schulz-Knappe
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Denis F. Hochstrasser
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Alexander Scherl
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
| | - Jean-Charles Sanchez
- Biomedical Proteomics Group, Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva, Switzerland, Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany, and Clinical Proteomics Group, Genetics and Laboratory Medicine Department, Geneva University Hospital, Geneva, Switzerland
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305
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Shuford CM, Comins DL, Whitten JL, Burnett JC, Muddiman DC. Improving limits of detection for B-type natriuretic peptide using PC-IDMS: an application of the ALiPHAT strategy. Analyst 2010; 135:36-41. [PMID: 20024179 PMCID: PMC3129710 DOI: 10.1039/b919484c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Hydrophobic tagging of biomolecules has been reported by our group and others to increase their ionization efficiency during electrospray ionization and facilitate their detection by mass spectrometry. As such, hydrophobic tagging should provide a viable method for augmenting MS-based quantification of low abundance proteins by decreasing their detection limits. Herein we have evaluated two commercial alkylation reagents and several newly synthesized hydrophobic alkylation reagents for their utility in quantifying B-type Natriuretic Peptide, a low abundance cardiac biomarker, by protein cleavage isotope dilution mass spectrometry. For the cysteine containing tryptic peptide evaluated, a approximately 3.5-fold decrease in the detection limit was observed for the best performing hydrophobic reagent, 2-iodo-N-octylacetamide, relative to the commonly used alkylation reagent, iodoacetamide. Additionally, we have evaluated the use of nonpolar surface areas as a metric for assessing the effectiveness of the alkylation reagents in improving ESI response.
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Affiliation(s)
- Christopher M. Shuford
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Daniel L. Comins
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - Jerry L. Whitten
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
| | - John C. Burnett
- Division for Cardiovascular Disease, Mayo Clinic College of Medicine, Rochester, Minnesota 55905
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27695
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306
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Holzmann J, Pichler P, Madalinski M, Kurzbauer R, Mechtler K. Stoichiometry Determination of the MP1−p14 Complex Using a Novel and Cost-Efficient Method To Produce an Equimolar Mixture of Standard Peptides. Anal Chem 2009; 81:10254-61. [DOI: 10.1021/ac902286m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johann Holzmann
- Research Institute of Molecular Pathology (IMP), CD-Laboratory for Proteome Analysis, and Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
| | - Peter Pichler
- Research Institute of Molecular Pathology (IMP), CD-Laboratory for Proteome Analysis, and Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
| | - Mathias Madalinski
- Research Institute of Molecular Pathology (IMP), CD-Laboratory for Proteome Analysis, and Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
| | - Robert Kurzbauer
- Research Institute of Molecular Pathology (IMP), CD-Laboratory for Proteome Analysis, and Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), CD-Laboratory for Proteome Analysis, and Institute of Molecular Biotechnology (IMBA), 1030 Vienna, Austria
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307
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Lesur A, Varesio E, Hopfgartner G. Accelerated tryptic digestion for the analysis of biopharmaceutical monoclonal antibodies in plasma by liquid chromatography with tandem mass spectrometric detection. J Chromatogr A 2009; 1217:57-64. [PMID: 19939394 DOI: 10.1016/j.chroma.2009.11.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 10/29/2009] [Accepted: 11/02/2009] [Indexed: 11/27/2022]
Abstract
Accelerated tryptic digestion of a therapeutic protein including microwave irradiation and thermal transfer by convection at 60 degrees C and 37 degrees C was investigated. An analytical setup was devised to follow the protein digestion rate using 1D gel electrophoresis and liquid chromatography coupled a triple quadrupole linear ion trap mass spectrometer. The formation kinetic of its tryptic peptides was monitored in the selected monitoring mode (LC-SRM/MS). Different digestion end points (e.g. 2, 5, 10, 15, 30 and 60min) as well as an overnight digestion were tested using a therapeutic human monoclonal antibody (mAb) with the goal of its LC-SRM/MS quantification in human plasma. The peptides from the human mAb were generated at different rates and were classified into three categories: (1) the fast forming peptides, (2) the slow forming peptides and (3) the peptides degrading over time. For many monitored peptides, a heating temperature of 37 degrees C with a 750rpm mixing applied for at least 30min provided equivalent results to microwave-assisted digestion and generally allowed the achievement of an equivalent peptide concentration as an overnight digestion carried out at 37 degrees C. The disappearance of the protein of the heavy and light chains can be monitored by 1D gel electrophoresis but was found not to be representative of the final tryptic peptide concentrations. For quantitative purposes a stable isotope labeled version ((13)C(4), (15)N(1)) of the therapeutic protein was used. The labeled protein as internal standard was found to be very efficient to compensate for incomplete digestion or losses during sample preparation.
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Affiliation(s)
- Antoine Lesur
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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308
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Critical comparison of MS and immunoassays for the bioanalysis of therapeutic antibodies. Bioanalysis 2009; 1:1375-88. [DOI: 10.4155/bio.09.121] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Therapeutic antibody assessment in biofluids requires fit-for-purpose bioanalytical methods. The reference is the immunoassay, the accuracy of which may be compromised by interference by endogenous components. Here, we report the inherent analytical problems posed by immunoassays and propose an alternative based on LC–MS that should be readily applicable to the analysis of therapeutic antibodies in biological fluids. We review problems linked to assay sensitivity, the choice of the assay format involving either immunodetection or MS, and strategies in the assessment of bound versus free forms.
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309
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Bordeerat NK, Georgieva NI, Klapper DG, Collins LB, Cross TJ, Borchers CH, Swenberg JA, Boysen G. Accurate quantitation of standard peptides used for quantitative proteomics. Proteomics 2009; 9:3939-44. [PMID: 19637239 DOI: 10.1002/pmic.200900043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
MS-based proteomics has become an indispensable tool in system biology generating a need for accurate and precise quantitation of peptide standards. The presented method utilizes ultra performance LC-MS/MS (UPLC-MS/MS) to accurately quantify peptide standards at concentrations of 0.1-10 microM. The ability for accurate quantitation of micro-molar concentrations has the advantages that quantitation can be performed routinely with high precision and the high sensitivity of the method minimizes the amounts required.
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Affiliation(s)
- Narisa K Bordeerat
- Department of Environmental Sciences and Engineering, The University of North Carolina at Chapel Hill, USA
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310
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Fortin T, Salvador A, Charrier JP, Lenz C, Bettsworth F, Lacoux X, Choquet-Kastylevsky G, Lemoine J. Multiple Reaction Monitoring Cubed for Protein Quantification at the Low Nanogram/Milliliter Level in Nondepleted Human Serum. Anal Chem 2009; 81:9343-52. [DOI: 10.1021/ac901447h] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- T. Fortin
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - A. Salvador
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - J. P. Charrier
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - C. Lenz
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - F. Bettsworth
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - X. Lacoux
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - G. Choquet-Kastylevsky
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - J. Lemoine
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
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311
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Kutscher DJ, Bettmer J. Absolute and Relative Protein Quantification with the Use of Isotopically Labeled p-Hydroxymercuribenzoic Acid and Complementary MALDI-MS and ICPMS Detection. Anal Chem 2009; 81:9172-7. [DOI: 10.1021/ac901571s] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel J. Kutscher
- Department of Physical and Analytical Chemistry, University of Oviedo, C/ Julián Clavería 8, E-33006 Oviedo, Spain
| | - Jörg Bettmer
- Department of Physical and Analytical Chemistry, University of Oviedo, C/ Julián Clavería 8, E-33006 Oviedo, Spain
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312
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313
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Kilpatrick EL, Bunk DM. Reference Measurement Procedure Development for C-Reactive Protein in Human Serum. Anal Chem 2009; 81:8610-6. [DOI: 10.1021/ac901597h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Eric L. Kilpatrick
- National Institute of Standards and Technology, Chemical Sciences Technology Laboratory, Analytical Chemistry Division, 331 Fort Johnson Road, Charleston, South Carolina 29412, and National Institute of Standards and Technology, Chemical Sciences Technology Laboratory, Analytical Chemistry Division, 100 Bureau Drive, Gaithersburg, Maryland 20899
| | - David M. Bunk
- National Institute of Standards and Technology, Chemical Sciences Technology Laboratory, Analytical Chemistry Division, 331 Fort Johnson Road, Charleston, South Carolina 29412, and National Institute of Standards and Technology, Chemical Sciences Technology Laboratory, Analytical Chemistry Division, 100 Bureau Drive, Gaithersburg, Maryland 20899
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314
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Izrael-Tomasevic A, Phu L, Phung QT, Lill JR, Arnott D. Targeting interferon alpha subtypes in serum: a comparison of analytical approaches to the detection and quantitation of proteins in complex biological matrices. J Proteome Res 2009; 8:3132-40. [PMID: 19351188 DOI: 10.1021/pr900076q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The targeted detection and quantitation of proteins in complex biological fluids such as blood is as analytically challenging as it is crucial for biomedical research. Antibody-based techniques such as the ELISA are the current standards for such measurements, having in favorable cases high specificity and pg/mL detection limits. Long development timelines and susceptibility to cross reactivity have led researchers to investigate mass spectrometric alternatives. The literature contains diverse schemes for sample preparation and multiple platforms for mass spectrometric detection. Critical evaluations of competing technologies are, however, badly needed. Taking closely related subtypes of the pro-inflammatory cytokine interferon alpha as a test case, we compared a sample preparation workflow based on affinity enrichment to one based on generic multidimensional chromatography, and evaluated mass spectrometric techniques using tandem mass spectrometry on low resolution ion traps, high resolution "accurate mass tags," and triple quadrupole selective reaction monitoring. Each workflow and detection method proved capable of detecting and discriminating between these proteins at or below the ng/mL level in human serum. Quantitation by isotope dilution was evaluated using full length protein as the internal standard. Both triple quadrupole selected reaction monitoring and orbitrap selected ion monitoring produced linear calibration curves from 1 ng/mL to 1 microg/mL, with lower limits of quantitation below 5 and 50 ng/mL, respectively.
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Affiliation(s)
- Anita Izrael-Tomasevic
- Protein Chemistry Department, Genentech Inc., South San Francisco, California 94080, USA
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315
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Kim K, Kim Y. Preparing multiple-reaction monitoring for quantitative clinical proteomics. Expert Rev Proteomics 2009; 6:225-9. [PMID: 19489693 DOI: 10.1586/epr.09.11] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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316
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Bettmer J, Montes Bayón M, Ruiz Encinar J, Fernández Sánchez ML, Fernández de la Campa MDR, Sanz Medel A. The emerging role of ICP-MS in proteomic analysis. J Proteomics 2009; 72:989-1005. [DOI: 10.1016/j.jprot.2009.05.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/08/2009] [Accepted: 05/17/2009] [Indexed: 12/13/2022]
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317
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Brun V, Masselon C, Garin J, Dupuis A. Isotope dilution strategies for absolute quantitative proteomics. J Proteomics 2009; 72:740-9. [DOI: 10.1016/j.jprot.2009.03.007] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 03/05/2009] [Accepted: 03/24/2009] [Indexed: 10/20/2022]
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318
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Ciccimaro E, Hanks SK, Yu KH, Blair IA. Absolute quantification of phosphorylation on the kinase activation loop of cellular focal adhesion kinase by stable isotope dilution liquid chromatography/mass spectrometry. Anal Chem 2009; 81:3304-13. [PMID: 19354260 DOI: 10.1021/ac900204f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A vital point of convergence for many signaling pathways at cellular focal adhesions is the interaction of two nonreceptor tyrosine kinases, focal adhesion kinase (FAK) and Src. The binding of Src to FAK leads to the phosphorylation of Y(576) and Y(577), located within the activation loop domain of FAK. However, it has not been possible previously to determine the absolute quantitative relationship between phosphorylated and nonphosphorylated forms of this activation loop domain in cells undergoing normal metabolism. We have developed a stable isotope dilution liquid chromatography-multiple reaction monitoring/mass spectrometry (LC-MRM/MS) technique that allows such determinations to be made. Isotopically labeled and phosphorylated FAK protein standards were synthesized and used to control for loss during immunoprecipitation of FAK. A control tryptic peptide, representing an unmodified region of FAK, was employed to monitor the mass balance of post-translational modifications (PTMs) on the activation loop domain. Absolute quantification was conducted using stable isotope labeled peptide standards with four endogenous amino acid overhangs at the trypsin digestion sites of both the amino and carboxy terminus. The LC-MRM/MS method was rigorously validated using in vitro kinase assays and employed to conduct absolute quantification of FAK phosphorylation in normal mouse embryonic fibroblasts (MEFs). This methodology will have particular utility for biomarker studies of kinase-inhibiting anticancer drugs and for quantitative proteomic investigations that examine kinase- and phosphatase-mediated cellular signal transduction pathways.
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Affiliation(s)
- Eugene Ciccimaro
- Center for Cancer Pharmacology, Department of Pharmacology, University of Pennsylvania, 854 BRB II/III, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104-6160, USA
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319
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Singh S, Springer M, Steen J, Kirschner MW, Steen H. FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides. J Proteome Res 2009; 8:2201-10. [PMID: 19344176 DOI: 10.1021/pr800654s] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Measurements of protein abundance and quantitative assessment of multiple post-translational modifications (PTMs) within a single protein are increasingly used to understand the control of protein activity, particularly in metazoan cells. General methods of wide applicability and precision/accuracy for quantitative estimation of protein post-translational regulation are lacking. Protein mass spectrometry has evolved from a high-throughput qualitative technique to a potentially general quantitative tool, but there are still serious limitations in dynamic range and coverage. To address some of these limitations, we introduce a novel MS-based quantitative strategy, FLEXIQuant, (Full-Length Expressed Stable Isotope-labeled Proteins for Quantification), which can track changes in relative peptide abundances as a function of PTM, and determine absolute quantity of a protein from its lysate. We examined two subunits of the anaphase-promoting complex, CDC27 and APC5, as a test of our ability to monitor quantitatively, the PTM status of several peptides over time. We find evidence of differential regulation at different sites, a phenomenon we believe will be very widespread. FLEXIQuant proved itself to be capable of serving as a general quantitative tool.
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Affiliation(s)
- Sasha Singh
- Department of Pathology, Harvard Medical School and Children's Hospital Boston, Boston, Massachusetts 02115, USA
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320
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Kirsch S, Fourdrilis S, Dobson R, Scippo ML, Maghuin-Rogister G, De Pauw E. Quantitative methods for food allergens: a review. Anal Bioanal Chem 2009; 395:57-67. [DOI: 10.1007/s00216-009-2869-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 05/19/2009] [Accepted: 05/26/2009] [Indexed: 10/20/2022]
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321
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Kraut A, Marcellin M, Adrait A, Kuhn L, Louwagie M, Kieffer-Jaquinod S, Lebert D, Masselon CD, Dupuis A, Bruley C, Jaquinod M, Garin J, Gallagher-Gambarelli M. Peptide Storage: Are You Getting the Best Return on Your Investment? Defining Optimal Storage Conditions for Proteomics Samples. J Proteome Res 2009; 8:3778-85. [DOI: 10.1021/pr900095u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexandra Kraut
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Marlène Marcellin
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Annie Adrait
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Lauriane Kuhn
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Mathilde Louwagie
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Sylvie Kieffer-Jaquinod
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Dorothée Lebert
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Christophe D. Masselon
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Alain Dupuis
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Christophe Bruley
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Michel Jaquinod
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Jérôme Garin
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
| | - Maighread Gallagher-Gambarelli
- CEA, DSV, iRTSV, Laboratoire d’Etude de la Dynamique des Protéomes, Grenoble, F-38054, France, INSERM, U880, Grenoble, F-38054, France, and Université Joseph Fourier, Grenoble, F-38054, France
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322
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Langenfeld E, Zanger UM, Jung K, Meyer HE, Marcus K. Mass spectrometry-based absolute quantification of microsomal cytochrome P450 2D6 in human liver. Proteomics 2009; 9:2313-23. [DOI: 10.1002/pmic.200800680] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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323
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Gao Y, Holland RD, Yu LR. Quantitative proteomics for drug toxicity. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:158-66. [DOI: 10.1093/bfgp/elp006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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324
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Ezan E, Dubois M, Becher F. Bioanalysis of recombinant proteins and antibodies by mass spectrometry. Analyst 2009; 134:825-34. [PMID: 19381370 DOI: 10.1039/b819706g] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In recent years, biotechnologically-derived drugs have been a major focus of research and development in the pharmaceutical industry. Their pharmacokinetics and pharmacokinetic/pharmacodynamic relationships impact every stage of the development process and require their assessment in the circulation in preclinical species and in humans. To this end, immunoassays are a reference, but standardisation remains an issue owing to the restricted pattern of antibody specificity and interference with endogenous components. As an alternative, we report here analytical strategies involving liquid chromatography coupled to mass spectrometry (LC-MS) for the accurate quantification of therapeutic proteins and antibodies in biological fluids.
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Affiliation(s)
- Eric Ezan
- CEA, IBITECS, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France.
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325
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Gielbert A, Davis LA, Sayers AR, Hope J, Gill AC, Sauer MJ. High-resolution differentiation of transmissible spongiform encephalopathy strains by quantitative N-terminal amino acid profiling (N-TAAP) of PK-digested abnormal prion protein. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:384-396. [PMID: 19053160 DOI: 10.1002/jms.1516] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
New forms of transmissible spongiform encephalopathy (TSE) continue to be identified, and consequently sensitive differential diagnosis is increasingly important both for the management of disease in humans and livestock and in providing confidence in the safety of the food chain. TSE diseases are associated with accumulation of protease-resistant prion protein (PrP(Sc)) and detection of this marker protein is central to diagnosis. Proteolysis by proteinase K (PK) generates protease-resistant products (PrP(res)) with partially variable N-termini. The conformation(s) of PrP(Sc) and thus the points of PK cleavage are thought to be dependent on the strain of prion disease. Western blot (WB) analysis of PrP(res) gives characteristic migration patterns that can be used to diagnose TSEs, but the relatively low resolution of this technique limits its ability to differentiate certain disease strains. Mass spectrometry (MS) has the capability to resolve these various PK cleavage sites to the level of individual amino acid residues. In the present study multiple selected reaction monitoring (mSRM) was used to detect and quantify PrP(res) N-terminal tryptic peptides by MS and thus to define the N-terminal amino acid profiles (N-TAAPs) of PrP(res) characteristic for various TSEs in sheep. The fragmentation behaviour of the N-terminal tryptic peptides was studied to allow selection of the transitions specific for each peptide. Different PrP(res) preparation methods were evaluated and the most effective approach applied to differentiate the N-TAAPs corresponding to various sheep TSE isolates. Marked differences were identified between the N-TAAPs of bovine spongiform encephalopathy (BSE) and classical scrapie, and between classical scrapie and the experimental strains SSBP/1 and CH1641, thereby validating this approach as a means of TSE-strain specific diagnosis.
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Affiliation(s)
- Adriana Gielbert
- Department of Molecular Pathogenesis and Genetics, Veterinary Laboratories Agency-Weybridge, Woodham Lane, New Haw, Addlestone KT15 3NB, UK
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326
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Li N, Palandra J, Nemirovskiy OV, Lai Y. LC−MS/MS Mediated Absolute Quantification and Comparison of Bile Salt Export Pump and Breast Cancer Resistance Protein in Livers and Hepatocytes across Species. Anal Chem 2009; 81:2251-9. [DOI: 10.1021/ac8024009] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Na Li
- Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Pfizer Global Research and Development, St. Louis Laboratories, Pfizer Inc., St. Louis, Missouri 63017
| | - Joe Palandra
- Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Pfizer Global Research and Development, St. Louis Laboratories, Pfizer Inc., St. Louis, Missouri 63017
| | - Olga V. Nemirovskiy
- Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Pfizer Global Research and Development, St. Louis Laboratories, Pfizer Inc., St. Louis, Missouri 63017
| | - Yurong Lai
- Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Pfizer Global Research and Development, St. Louis Laboratories, Pfizer Inc., St. Louis, Missouri 63017
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327
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Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, Zhang J, Brentnall TA. Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res 2009; 8:787-97. [PMID: 19105742 PMCID: PMC2657955 DOI: 10.1021/pr800538n] [Citation(s) in RCA: 313] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent advance in technology for mass spectrometry-based targeted protein quantification has opened new avenues for a broad range of proteomic applications in clinical research. The major breakthroughs are highlighted by the capability of using a "universal" approach to perform quantitative assays for a wide spectrum of proteins with minimum restrictions and the ease of assembling multiplex detections in a single measurement. The quantitative approach relies on the use of synthetic stable isotope labeled peptides or proteins, which precisely mimic their endogenous counterparts and act as internal standards to quantify the corresponding candidate proteins. This report reviews recently developed platform technologies for emerging applications of clinical proteomics and biomarker development.
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Affiliation(s)
- Sheng Pan
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA.
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328
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Hennekinne JA, Brun V, De Buyser ML, Dupuis A, Ostyn A, Dragacci S. Innovative application of mass spectrometry for the characterization of staphylococcal enterotoxins involved in food poisoning outbreaks. Appl Environ Microbiol 2009; 75:882-4. [PMID: 19074605 PMCID: PMC2632143 DOI: 10.1128/aem.01924-08] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 12/01/2008] [Indexed: 11/20/2022] Open
Abstract
Staphylococcal poisoning is a common food-borne disease for which immunoassays to detect enterotoxins were developed, but these assays often lead to false diagnoses due to interferences or lack of specificity. Absolute quantitative mass spectrometry was for the first time successfully applied to an investigation of a staphylococcal outbreak due to coconut pearls.
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329
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Ye X, Blonder J, Veenstra TD. Targeted proteomics for validation of biomarkers in clinical samples. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 8:126-35. [PMID: 19109305 DOI: 10.1093/bfgp/eln050] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The rapid rise and application of proteomic technologies has resulted in an exponential increase in the number of proteins that have been discovered and presented as 'potential' biomarkers for specific diseases. Unfortunately, the number of biomarkers approved for use by the Food and Drug Administration has not risen in likewise manner. While there are a number of reasons for this discrepancy, this glut of 'potential' biomarkers also indicates the need for validation methods to confirm or refute their utility in clinical diagnostics. For this reason, the emphasis on developing methods to target and measure the absolute quantity of specific proteins and peptides in complex proteomic samples has grown.
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Affiliation(s)
- Xiaoying Ye
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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330
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Fortin T, Salvador A, Charrier JP, Lenz C, Lacoux X, Morla A, Choquet-Kastylevsky G, Lemoine J. Clinical quantitation of prostate-specific antigen biomarker in the low nanogram/milliliter range by conventional bore liquid chromatography-tandem mass spectrometry (multiple reaction monitoring) coupling and correlation with ELISA tests. Mol Cell Proteomics 2008; 8:1006-15. [PMID: 19068476 DOI: 10.1074/mcp.m800238-mcp200] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteomics discovery leads to a list of potential protein biomarkers that have to be subsequently verified and validated with a statistically viable number of patients. Although the most sensitive, the development of an ELISA test is time-consuming when antibodies are not available and need to be conceived. Mass spectrometry analysis driven in quantitative multiple reaction monitoring mode is now appearing as a promising alternative to quantify proteins in biological fluids. However, all the studies published to date describe limits of quantitation in the low microg/ml range when no immunoenrichment of the target protein is applied, whereas the concentration of known clinical biomarkers is usually in the ng/ml range. Using prostate-specific antigen as a model biomarker, we now provide proof of principle that mass spectrometry enables protein quantitation in a concentration range of clinical interest without immunoenrichment. We have developed and optimized a robust sample processing method combining albumin depletion, trypsin digestion, and solid phase extraction of the proteotypic peptides starting from only 100 microl of serum. For analysis, mass spectrometry was coupled to a conventional liquid chromatography system using a 2-mm-internal diameter reverse phase column. This mass spectrometry-based strategy was applied to the quantitation of prostate-specific antigen in sera of patients with either benign prostate hyperplasia or prostate cancer. The quantitation was performed against an external calibration curve by interpolation, and results showed good correlation with existing ELISA tests applied to the same samples. This strategy might now be implemented in any clinical laboratory or certified company for further evaluation of any putative biomarker in the low ng/ml range of serum or plasma.
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Affiliation(s)
- Tanguy Fortin
- R&D Proteomique, bioMérieux SA, 69280 Marcy l'Etoile, France
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331
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Yi J, Liu Z, Craft D, O’Mullan P, Ju G, Gelfand CA. Intrinsic Peptidase Activity Causes a Sequential Multi-Step Reaction (SMSR) in Digestion of Human Plasma Peptides. J Proteome Res 2008; 7:5112-8. [DOI: 10.1021/pr800396c] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jizu Yi
- BD Diagnostics, and BD Medical, One Becton Drive, Franklin Lakes, New Jersey 07417
| | - Zhaoxia Liu
- BD Diagnostics, and BD Medical, One Becton Drive, Franklin Lakes, New Jersey 07417
| | - David Craft
- BD Diagnostics, and BD Medical, One Becton Drive, Franklin Lakes, New Jersey 07417
| | - Patrick O’Mullan
- BD Diagnostics, and BD Medical, One Becton Drive, Franklin Lakes, New Jersey 07417
| | - Gang Ju
- BD Diagnostics, and BD Medical, One Becton Drive, Franklin Lakes, New Jersey 07417
| | - Craig A. Gelfand
- BD Diagnostics, and BD Medical, One Becton Drive, Franklin Lakes, New Jersey 07417
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332
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Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008; 4:222. [PMID: 18854821 PMCID: PMC2583086 DOI: 10.1038/msb.2008.61] [Citation(s) in RCA: 1057] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 09/15/2008] [Indexed: 12/01/2022] Open
Abstract
Systems biology relies on data sets in which the same group of proteins is consistently identified and precisely quantified across multiple samples, a requirement that is only partially achieved by current proteomics approaches. Selected reaction monitoring (SRM)-also called multiple reaction monitoring-is emerging as a technology that ideally complements the discovery capabilities of shotgun strategies by its unique potential for reliable quantification of analytes of low abundance in complex mixtures. In an SRM experiment, a predefined precursor ion and one of its fragments are selected by the two mass filters of a triple quadrupole instrument and monitored over time for precise quantification. A series of transitions (precursor/fragment ion pairs) in combination with the retention time of the targeted peptide can constitute a definitive assay. Typically, a large number of peptides are quantified during a single LC-MS experiment. This tutorial explains the application of SRM for quantitative proteomics, including the selection of proteotypic peptides and the optimization and validation of transitions. Furthermore, normalization and various factors affecting sensitivity and accuracy are discussed.
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Affiliation(s)
- Vinzenz Lange
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Bruno Domon
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
- Institute for Systems Biology, Seattle, WA, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
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333
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Quantitative analysis of highly homologous proteins: the challenge of assaying the “CYP-ome” by mass spectrometry. Anal Bioanal Chem 2008; 392:1123-34. [DOI: 10.1007/s00216-008-2407-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 08/18/2008] [Accepted: 09/11/2008] [Indexed: 11/25/2022]
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334
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Dupuis A, Hennekinne JA, Garin J, Brun V. Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks. Proteomics 2008; 8:4633-6. [DOI: 10.1002/pmic.200800326] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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335
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Paulovich AG, Whiteaker JR, Hoofnagle AN, Wang P. The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline. Proteomics Clin Appl 2008; 2:1386-1402. [PMID: 20976028 DOI: 10.1002/prca.200780174] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The application of "omics" technologies to biological samples generates hundreds to thousands of biomarker candidates; however, a discouragingly small number make it through the pipeline to clinical use. This is in large part due to the incredible mismatch between the large numbers of biomarker candidates and the paucity of reliable assays and methods for validation studies. We desperately need a pipeline that relieves this bottleneck between biomarker discovery and validation. This paper reviews the requirements for technologies to adequately credential biomarker candidates for costly clinical validation and proposes methods and systems to verify biomarker candidates. Models involving pooling of clinical samples, where appropriate, are discussed. We conclude that current proteomic technologies are on the cusp of significantly affecting translation of molecular diagnostics into the clinic.
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336
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Bennett N, Letourneur F, Ragno M, Louwagie M. Sorting of the v-SNARE VAMP7 in Dictyostelium discoideum: A role for more than one Adaptor Protein (AP) complex. Exp Cell Res 2008; 314:2822-33. [DOI: 10.1016/j.yexcr.2008.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 06/11/2008] [Accepted: 06/16/2008] [Indexed: 01/31/2023]
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337
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Duriez E, Fenaille F, Tabet JC, Lamourette P, Hilaire D, Becher F, Ezan E. Detection of ricin in complex samples by immunocapture and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Proteome Res 2008; 7:4154-63. [PMID: 18651759 DOI: 10.1021/pr8003437] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ricin, the toxin component of Ricinus communis is considered as a potential chemical weapon. Several complementary techniques are required to confirm its presence in environmental samples. Here, we report a method combining immunocapture and analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the accurate detection of different species of R. communis. Liquid environmental samples were applied to magnetic particles coated with a monoclonal antibody directed against the B-chain of the toxin. After acidic elution, tryptic peptides of the A- and B-chains were obtained by accelerated digestion with trypsin in the presence of acetonitrile. Of the 20 peptides observed by MALDI-TOF MS, three were chosen for detection ( m/ z 1013.6, m/ z 1310.6 and m/ z 1728.9, which correspond to peptides 161-LEQLAGNLR-169, 150-YTFAFGGNYDR-160, and 233-SAPDPSVITLENSWGR-248, respectively). Their selection was based on several parameters such as detection sensitivity, specificity toward ricin forms and absence of isotopic overlap with unrelated peptides. To increase assay reproducibility, stable isotope-labeled peptides were incorporated during the sample preparation phase. The final assay has a limit of detection estimated at approximately 50 ng/mL ( approximately 0.8 nM) of ricin in buffer. No interference was observed when the assay was applied to ricin-spiked milk samples. In addition, several varieties of R. communis or from different geographical origins were also shown to be detectable. The present assay provides a new tool with a total analytical time of approximately 5 h, which is particularly relevant in the context of a bioterrorist incident.
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Affiliation(s)
- Elodie Duriez
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France
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338
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Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M. MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics 2008; 7:2270-8. [PMID: 18641041 PMCID: PMC2577205 DOI: 10.1074/mcp.m700504-mcp200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.
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Affiliation(s)
- Daniel B Martin
- Institute for Systems Biology, Seattle, Washington 98103, USA
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339
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Heudi O, Barteau S, Zimmer D, Schmidt J, Bill K, Lehmann N, Bauer C, Kretz O. Towards Absolute Quantification of Therapeutic Monoclonal Antibody in Serum by LC−MS/MS Using Isotope-Labeled Antibody Standard and Protein Cleavage Isotope Dilution Mass Spectrometry. Anal Chem 2008; 80:4200-7. [DOI: 10.1021/ac800205s] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Olivier Heudi
- DMPK/Bioanalytics, and Biotechnology Development, Novartis Pharma AG, CH-4002 Basel Switzerland
| | - Samuel Barteau
- DMPK/Bioanalytics, and Biotechnology Development, Novartis Pharma AG, CH-4002 Basel Switzerland
| | - Dieter Zimmer
- DMPK/Bioanalytics, and Biotechnology Development, Novartis Pharma AG, CH-4002 Basel Switzerland
| | - Joerg Schmidt
- DMPK/Bioanalytics, and Biotechnology Development, Novartis Pharma AG, CH-4002 Basel Switzerland
| | - Kurt Bill
- DMPK/Bioanalytics, and Biotechnology Development, Novartis Pharma AG, CH-4002 Basel Switzerland
| | - Natalie Lehmann
- DMPK/Bioanalytics, and Biotechnology Development, Novartis Pharma AG, CH-4002 Basel Switzerland
| | - Christian Bauer
- DMPK/Bioanalytics, and Biotechnology Development, Novartis Pharma AG, CH-4002 Basel Switzerland
| | - Olivier Kretz
- DMPK/Bioanalytics, and Biotechnology Development, Novartis Pharma AG, CH-4002 Basel Switzerland
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340
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Dubois M, Fenaille F, Clement G, Lechmann M, Tabet JC, Ezan E, Becher F. Immunopurification and Mass Spectrometric Quantification of the Active Form of a Chimeric Therapeutic Antibody in Human Serum. Anal Chem 2008; 80:1737-45. [DOI: 10.1021/ac7021234] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mathieu Dubois
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - François Fenaille
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Gilles Clement
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Martin Lechmann
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Jean-Claude Tabet
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Eric Ezan
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - François Becher
- CEA, Service de Pharmacologie et d'Immunoanalyse, 91191 Gif-sur-Yvette, France, INRA, Laboratoire d'Immuno-Allergie Alimentaire, 91191 Gif sur Yvette, France, Institute of Drug Metabolism and Pharmacokinetic, Merck KGaA, Merck Serono, 85567 Grafing, Germany, and Laboratoire de Synthèse, Structure et Fonction de Molécules Bioactives, CNRS UMR 7613, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris Cedex 05, France
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