Development of MRM-based assays for the absolute quantitation of plasma proteins

Methods in Molecular Biology

Volumn 1023, Issue , 2013, Pages 53-82

  Kuzyk, Michael A ^a   Parker, Carol E ^a   Domanski, Dominik ^a   Borchers, Christoph H ^a,b  

^a UNIVERSITY OF VICTORIA   (Canada)

^b UNIVERSITY OF VICTORIA   (Canada)

Author keywords

Assay development; Diagnostics; Internal standards; Mass spectrometry; MRM; Multiple reaction monitoring; Plasma; Quantitation; Selected reaction monitoring; SIS peptides; SRM; Stable isotope labeling

Indexed keywords

EDETIC ACID; PEPTIDE; PLASMA PROTEIN;

AMINO ACID ANALYSIS; ANALYTIC METHOD; ARTICLE; BIOPHYSICS; CAPILLARY ZONE ELECTROPHORESIS; CONTROLLED STUDY; ENZYME DEGRADATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ION PAIR CHROMATOGRAPHY; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETER; MOLECULAR WEIGHT; MULTIPLE REACTION MONITORING; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEIN PURIFICATION; PROTEIN TARGETING; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SELECTED REACTION MONITORING; SENSITIVITY AND SPECIFICITY; TANDEM MASS SPECTROMETRY; TRIPLE QUADRUPOLE MASS SPECTROMETRY;

EID: 84883189721     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4614-7209-4_4     Document Type: Article

References (29)

1. Wei J, Sun J, Yu W, Jones A, Oeller P, Keller M, Woodnutt G, Short JM (2005) Global proteome discovery using an online three-dimensional LC-MS/MS. J Proteome Res 4:801-808
2. Kondrat RW, McClusky GA, Cooks RG (1978) Multiple reaction monitoring in mass spectrometry/ mass spectrometry for direct analysis of complex mixtures. Anal Chem 50:2017-2021
3. Anderson NL, Anderson NG (2002) The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 1:845-867
4. Anderson L (2005) Candidate-based proteomics in the search for biomarkers of cardiovascular disease. J Physiol 563:23-60
5. Ackermann BL, Berna MJ (2007) Coupling immunoaf finity techniques with MS for quantitative analysis of low-abundance protein biomarkers. Expert Rev Proteomics 4:175-186
6. Kamiie J, Ohtsuki S, Iwase R, Ohmine K, Katsukura Y, Yanai K, Sekine Y, Uchida Y, Ito S, Terasaki T (2008) Quantitative atlas of membrane transporter proteins: Development and application of a highly sensitive simultaneous LC/MS/MS method combined with novel in-silico peptide selection criteria. Pharm Res 25:1469-1483
7. Barnidge DR, Goodmanson MK, Klee GG, Muddiman DC (2004) Absolute quantification of the model biomarker prostate-specific antigen in serum by LC-MS/MS using protein cleavage and isotope dilution mass spectrometry. J Proteome Res 3:644-652
8. Kuhn E, Wu J, Karl J, Liao H, Zolg W, Guild B (2004) Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics 4:1175-1186
9. Zhang F, Bartels MJ, Stott WT (2004) Quantitation of human glutathione S-transferases in complex matrices by liquid chromatography/tandem mass spectrometry with signature peptides. Rapid Commun Mass Spectrom 18:491-498
10. Kirkpatrick DS, Gerber SA, Gygi SP (2005) The absolute quantification strategy: A general procedure for the quantification of proteins and post-translational modi fications. Methods 35:265-273
11. Kuzyk M, Smith D, Yang J, Cross T, Jackson A, Hardie D, Anderson L, Borchers C (2009) MRM-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol Cell Proteomics 8:1860-1877
12. Walsh GM, Lin S, Evans DM, Khosrovi-Eghbal A, Beavis RC, Kast J (2009) Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring. J Proteomics 72:838-852
13. Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R (2007) Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 12:125-131
14. Skyline-SRM/MRM-Builder (2009) https:// brendanx-uw1.gs.washington.edu/ labkey/ wiki/home/software/Skyline/page. view?name=default . Accessed 15 Aug 2009
15. MacLean B, Tomazela D, Finney G, Chambers M, Shulman N, Prakash A, Peterman S, Maccoss MJ (2009) Automated creation and re finement of complex scheduled SRM methods for targeted proteomics. Presented at the 57th ASMS conference on mass spectrometry and allied topics, Philadelphia, PA, 31 May to 4 June 2009
16. Prakash A, Tomazela DM, Frewen B, MacLean B, Merrihew G, Peterman S, MacCoss. MJ (2009) Expediting the development of targeted SRM assays: Using data from shotgun proteomics to automate method development. J Proteome Res 8:2733-2739
17. MRMpilot. https://products.appliedbiosystems. com/ab/en/US/adirect/ab? cmd=cat Navigate2&catID=605354&tab=DetailInfo . Accessed 15 Aug 2009
18. Sherwood C, Eastham A, Peterson A, Eng JK, Shteynberg D, Mendoza L, Deutsch E, Risler J, Lee LW, Tasman N, Aebersold RL, Lam H, Martin DB (2009) MaRiMba: A software application for spectral library-based MRM transition list assembly. J Proteome Res 8:4396-4405
19. Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ, Bessant C (2009) MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol Cell Proteomics 8:696-705
20. Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M (2009) MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics 7:2270-2278
21. Xu Y, Lazar IM (2009) MRM screening/biomarker discovery with linear ion trap MS: A library of human cancer-specific peptides. BMC Cancer 9:96
22. Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R (2008) A database of mass spectrometric assays for the yeast proteome. Nat Methods 5:913-914
23. MIDAS-work flow-designer. https://products. appliedbiosystems.com/ab/en/ US/adirect/ ab?cmd=catNavigate2&catID=604874& tab=DetailInfo . Accessed 15 Aug 2009
24. Janecki DJ, Bemis KG, Tegeler TJ, Sanghani PC, Zhai L, Hurley TD, Bosron WF, Wang M (2007) A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme. Anal Biochem 369:18-26
25. Green JM (1996) A practical guide to analytical method validation. Anal Chem 68: 305A-309A
26. Lin S, Shaler TA, Becker CH (2006) Quantification of intermediate- abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap. Anal Chem 78:5762-5767
27. Keshishian H, Addona T, Burgess M, Kuhn E, Carr SA (2007) Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 6:2212-2229
28. Yin H, Killeen K (2007) The fundamental aspects and applications of Agilent HPLCChip. J Sep Sci 30:1427-1434
29. Roepstorff P, Fohlman J (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom 11:601