Evaluation of protein quantification using standard peptides containing single conservative amino acid replacements

Journal of Mass Spectrometry

Volumn 47, Issue 2, 2012, Pages 188-194

  Remily Wood, Elizabeth R ^a   Koomen, John M ^a,b  

^a Molecular Oncology   (United States)

^b Experimental Therapeutics   (United States)

Author keywords

epidermal growth factor receptor; immunoglobulins; multiple reaction monitoring; peptide standards; quantitative mass spectrometry

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTORS; FRAGMENTATION PATTERNS; IMMUNOGLOBULINS; INTERNAL STANDARDS; ION SIGNALS; ISOTOPE-LABELED STANDARD; LUNG CANCER CELLS; METHYLENE GROUPS; MULTIPLE MYELOMA; MULTIPLE REACTION MONITORING; PROTEIN QUANTIFICATION; REACTION MONITORING; SIDE-CHAINS;

AMINO ACIDS; ASSAYS; ISOTOPES; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; STANDARDS;

PEPTIDES;

AMINO ACID; EPIDERMAL GROWTH FACTOR RECEPTOR; IMMUNOGLOBULIN M; STABLE ISOTOPE;

AMINO ACID SUBSTITUTION; ARTICLE; EVALUATION; HUMAN; INTERMETHOD COMPARISON; ISOTOPE LABELING; PERFORMANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; SINGLE CONSERVATIVE AMINO ACID REPLACEMENT; STANDARD;

AMINO ACID SUBSTITUTION; AMINO ACIDS; CELL LINE, TUMOR; HUMANS; IMMUNOGLOBULIN M; LUNG NEOPLASMS; MASS SPECTROMETRY; MULTIPLE MYELOMA; PEPTIDES; PROTEINS; RECEPTOR, EPIDERMAL GROWTH FACTOR; REFERENCE STANDARDS;

EID: 84857485723     PISSN: 10765174     EISSN: 10969888     Source Type: Journal    
DOI: 10.1002/jms.2053     Document Type: Article

References (33)

1. J. R. Barr, V. L. Maggio, D. G. Patterson Jr., G. R. Cooper, L. O. Henderson, W. E. Turner, S. J. Smith, W. H. Hannon, L. L. Needham, E. J. Sampson,. Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-1. Clin. Chem. 1996, 42, 1676-1682.
2. D. R. Barnidge, E. A. Dratz, T. Martin, L. E. Bonilla, L. B. Moran, A. Lindall,. Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards. Anal. Chem. 2003, 75, 445-451.
3. K. Bluemlein, M. Rasler,. Monitoring protein expression in whole-cell extracts by targeted label- and standard-free LC-MS/MS. Nat. Protoc. 2011, 6, 859-869.
4. H. Zhang, Q. Liu, L. J. Zimmerman, A. L. Ham, R. J. C. Slebos, J. Rahman, T. Kikuchi, P. P. Massion, D. P. Carbone, D. Billheimer, D. C. Leibler,. Methods for protein and peptide quantification by liquid chromatography-multiple reaction monitoring mass spectrometry. Mol. Cell. Proteomics 2011, 10, M110.006593.
5. H. John, M. Walden, S. Schäfer, S. Genz, W. G. Forssmann,. Analytical procedures for quantification of peptides in pharmaceutical research by liquid chromatography-mass spectrometry. Anal. Bioanal. Chem. 2004, 378, 883-897.
6. M. Vogeser, C. Seger,. Pitfalls associated with the use of liquid chromatography-tandem mass spectrometry in the clinical laboratory. Clin. Chem. 2010, 56, 1234-1244.
7. A. N. Kettenbach, J. Rush, S. A. Gerber,. Absolute quantification of proteins and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat. Protoc. 2011, 6, 175-186.
8. M. H. Elliott, D. S. Smith, C. E. Parker, C. Borchers,. Current trends in quantitative proteomics. J. Mass Spectrom. 2009, 44, 1637-1660.
9. L. Anderson, C. L. Hunter,. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 2006, 5, 573-588.
10. Y. Chen, M. Gruidl, E. Remily-Wood, R. Z. Liu, S. Eschrich, M. Lloyd, A. Nasir, M. M. Bui, E. Huang, D. Shibata, T. Yeatman, J. M. Koomen,. Quantification of b-catenin signaling components in colon cancer cell lines, tissue sections, and microdissected tumor cells using reaction monitoring mass spectrometry. J. Proteome Res. 2010, 9, 4215-4227.
11. A. Wolf-Yadlin, S. Hautaniemi, D. A. Lauffenburger, F. M. White,. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 5860-5865.
12. L. L. Jin, J. Tong, A. Prakash, S. M. Peterman, J. R. St-Germain, P. Taylor, S. Trudel, M. F. Moran,. Measurement of protein phosphorylation stoichiometry by selected reaction monitoring mass spectrometry. J. Proteome Res. 2010, 9, 2752-2761.
13. K. Lanckmans, S. Sarre, I. Smolders, Y. Michotte,. Use of a structural analogue versus a stable isotope labeled internal standard for the quantification of angiotensin IV in rat brain dialysates using nano-liquid chromatography/tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2007, 21, 1187-1195.
14. E. Stokvis, H. Rosing, J. H. Beijnen,. Stable isotopically labeled internal standards in quantitative bioanalysis using liquid chromatography/mass spectrometry: necessity or not? Rapid Commun. Mass Spectrom. 2005, 19, 401-407.
15. I. Fu, E. J. Woolf, B. K. Matuszewski,. Effect of the sample matrix on the determination of indinavir in human urine by HPLC with turbo ion spray tandem mass spectrometric detection. J. Pharm. Biomed. Anal. 1998, 18, 347-357.
16. Sancho J. V., Pozo O. J., Lõpez F. J., Hernández F.,. Different quantitation approaches for xenobiotics in human urine samples by liquid chromatography/electrospray tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2002, 16, 639-645.
17. K. Kito, K. Ota, T. Fujita, T. Ito,. A synthetic approach towards accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes. J. Proteome Res. 2007, 6, 792-800.
18. L. Prokai, A. D. Zharikova, T. Janáky, K. Prokai-Tatrai,. Exploratory pharmacokinetics and brain distribution study of a neuropeptide FF antagonist by liquid chromatography/ atmospheric pressure ionization tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2000, 14, 2412-2418.
19. A. J. Oosterkamp, E. Gelpí, J. Abian,. Quantitative peptide bioanalysis using column-switching nano liquid chromatography/mass spectrometry. J. Mass Spectrom. 1998, 33, 976-983.
20. W. Y. Feng, K. K. Chan, J. M. Covey,. Electrospray LC-MS/MS quantitation, stability, and preliminary pharmacokinetics of bradykinin antagonist polypeptide B201 (NSC 710295) in the mouse. J. Pharm. Biomed. Anal. 2002, 28, 601-612.
21. S. Hatziieremia, N. Kostomitsopoulos, V. Balafas, C. Tamvakopoulos,. A liquid chromatographic/tandem mass spectroscopic method for quantification of the cyclic peptide melanotan-II. Plasma and brain tissue concentrations following administration in mice. Rapid Commun. Mass Spectrom. 2007, 21, 2431-2438.
22. D. Winter, J. Seidler, D. Kugelstadt, B. Derrer, B. Kappes, W. Lehmann,. Minimally permutated peptide analogs as internal standards for relative and absolute quantitification of peptides and proteins. Proteomics 2010, 10, 1510-1514.
23. R. L. Beardsley, J. P. Reilly,. Quantitation using enhanced signal tags: a technique for comparative proteomics. J. Proteome Res. 2003, 2, 15-21.
24. IPIP Download available at http://proteome.moffitt.org/
25. L. Carpino, G. Han,. 9-Fluorenylmethoxycarbonyl amino-protecting group. J. Org. Chem. 1972, 37, 3404-3409.
26. E. R. Remily-Wood, R. Z. Liu, Y. Xiang, Y. Chen, C. E. Thomas, N. Rajyaguru, L. M. Kaufman, J. E. Ochoa, L. Hazlehurst, J. Pinilla-Ibarz, J. Lancet, G. Zhang, E. Haura, D. Shibata, T. Yeatman, K. S. Smalley, W. S. Dalton, E. Huang, E. Scott, G. C. Bloom, S. A. Eschrich, J. K. Koomen,. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics Clin. Appl. 2011, 5, 383-396.
27. B. MacLean, D. M. Tomazela, N. Shulman, M. Chambers, G. L. Finney, B. Frewen, R. Kern, D. L. Tabb, D. C. Liebler, M. J. MacCoss,. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26, 966-968.
28. L. J. Foster, C. L. de Hoog, M. Mann,. Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 5813-5818.
29. S. E. Ong, B. Blagoev, I. Kratchmarova, D. B. Kristensen, H. Steen, A. Pandey, M. Mann,. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
30. H. Keshishian, T. Addona, M. Burgess, E. Kuhn, S. A. Carr,. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 2007, 6, 2212-2229.
31. N. L. Anderson, N. G. Anderson, L. R. Haines, D. B. Hardie, R. W. Olafson, T. W. Pearson,. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Proteome Res. 2004, 3, 235-244.
32. J. Jiang, C. E. Parker, J. R. Fuller, T. H. Kawula, C. H. Borchers,. An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularensis. Anal. Chim. Acta 2007, 605, 70-99.
33. M. Sasaki, S. Takeda, T. Kato, K. Matsuba,. Antigenicities of stem bromelain. Contribution of three-dimensional structure and individual amino acid residues. J. Biochem. 1980, 87, 817-824.