Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS

Journal of Proteome Research

Volumn 5, Issue 8, 2006, Pages 2009-2018

  Faca, Vitor ^a   Coram, Marc ^a   Phanstiel, Doug ^a   Glukhova, Veronika ^a   Zhang, Qing ^a   Fitzgibbon, Matthew ^a   McIntosh, Martin ^a   Hanash, Samir ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Acrylamide isotope labeling; Human serum; LTQ FTICR

Indexed keywords

ACRYLAMIDE; CARBON 13; CYSTEINE; PLASMA PROTEIN;

ARTICLE; HUMAN; INFRARED SPECTROSCOPY; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; REVERSED PHASE LIQUID CHROMATOGRAPHY;

ACRYLAMIDES; ALGORITHMS; ALKYLATION; AMINO ACID SEQUENCE; BLOOD PROTEINS; CARBON RADIOISOTOPES; CHROMATOGRAPHY, LIQUID; CYSTEINE; DEUTERIUM; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA;

EID: 33747158479     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr060102+     Document Type: Article

References (19)

1. Ong, S. E.; Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1, 252-262.
2. Sechi, S.; Oda, Y. Quantitative proteomics using mass spectrometry. Curr. Opin. Chem. Biol. 2003, 7, 70-77.
3. Julka, S.; Regnier, F. Quantification in proteomics through stable isotope coding: a review. J. Proteome Res. 2004, 3, 350-363.
4. Wang, H.; Clouthier, S. G.; Galchev, V.; Misek, D. E.; Duffner, U.; Min, C. K.; Zhao, R.; Tra, J.; Omenn, G. S.; Ferrara, J. L.; Hanash, S. M. Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Mol. Cell. Proteomics 2005, 4, 618-625.
5. Zhang, H.; Yan, W.; Aebersold, R. Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr. Opin. Chem. Biol. 2004, 8, 66-75.
6. Kenyon, G. L.; Bruice, T. W. Novel sulfhydryl reagents. Methods Enzymol. 1977, 47, 407-430.
7. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
8. Sechi, S.; Chait, B. T. Modification of cysteine residues by alkylation. A tool in peptide mapping and protein identification. Anal. Chem. 1998, 70, 5150-5158.
9. Sechi, S. A method to identify and simultaneously determine the relative quantities of proteins isolated by gel electrophoresis. Rapid Commun. Mass. Spectrom. 2002, 16, 1416-1424.
10. Shen, M.; Guo, L.; Wallace, A.; Fitzner, J.; Eisenman, J.; Jacobson, E.; Johnson, R. S.; Isolation and isotope labeling of cysteine- and methionine-containing tryptic peptides: application to the study of cell surface proteolysis. Mol. Cell. Proteomics 2003, 2, 315-324.
11. Patterson, S. D. From electrophoretically separated protein to identification: strategies for sequence and mass analysis. Anal. Biochem. 1994, 221, 1-15.
12. Rauch, A; Bellew, M.; Eng, J.; Fitzgibbon, M.; Holzman, T.; Hussey, P.; Igra, M.; Maclean, B.; Lin, C. W.; Detter, A.; Fang, R.; Faca, V.; Gafken, P.; Zhang, H.; Whiteaker, J.; States, D.; Hanash, S.; Paulovich, A.; McIntosh, M. W. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res. 2006, 5, 112-121.
13. Nesvizhskii, A. I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75, 4646-4658.
14. Haab, B. B.; Geierstanger, B. H.; Michailidis, G.; Vitzthum, F.; Forrester, S.; Okon, R.; Saviranta, P.; Brinker, A.; Sorette, M.; Perlee, L.; Suresh, S.; Drwal, G.; Adkins, J. N.; Omenn, G. S. Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: systematic variation between sample types and calibration of mass spectrometry data. Proteomics 2005, 5, 3278-3291.
15. Bellew, M.; Coram, M.; Fitzgibbon, M.; Igra, M.; Randolph, T.; Wang, P.; May, D.; Eng, J.; Fang, R.; Lin, C.; Chen, J.; Goodlett, D.; Whiteaker, J.; Paulovich, A.; McIntosh, M. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 2006, in press.
16. Molloy, M. P.; Donohoe, S.; Brzezinski, E. E.; Kilby, G. W.; Stevenson, T. I.; Baker, J. D.; Goodlett, D. R.; Gage, D. A. Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling. Proteomics 2005, 5, 1204-1208.
17. Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. 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.
18. Arnott, D.; Kishiyama, A.; Luis, E. A.; Ludlum, S. G.; Marsters, J. C., Jr.; Stults, J. T. Selective detection of membrane proteins without antibodies: a mass spectrometric version of the Western blot. Mol. Cell. Proteomics 2002, 1, 148-156.
19. Zhang, R.; Sioma, C. S.; Thompson, R. A.; Xiong, L.; Regnier, F. E. Controlling deuterium isotope effects in comparative proteomics. Anal. Chem. 2002, 74, 3662-3669.