Cysteinyl peptide capture for shotgun proteomics: Global assessment of chemoselective fractionation

Journal of Proteome Research

Volumn 9, Issue 10, 2010, Pages 5461-5472

  Lin, De ^a,b   Li, Jing ^a   Slebos, Robbert J C ^b,c   Liebler, Daniel C ^a,b  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c VANDERBILT INGRAM CANCER CENTER   (United States)

Author keywords

AUTHOR; KEYWORDS; PLEASE; SUBMIT

Indexed keywords

AMIDE; CYSTEINE; N [2 [2 [2 [2 [3 (1 HYDROXY 2 OXO 2 PHENYLETHYL)PHENOXY]ACETAMIDO]ETHOXY]ETHOXY]ETHYL] 5 (2 OXOHEXAHYDRO 1H THIENO[3,4 D]IMIDAZOL 4 YL)PENTANAMIDE; PEPTIDE DERIVATIVE; STREPTAVIDIN; THIOL DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CANCER CELL CULTURE; HUMAN; HUMAN CELL; HYDROLYSIS; ISOELECTRIC FOCUSING; LIQUID CHROMATOGRAPHY; NONHUMAN; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; PROTEOMICS; SACCHAROMYCES CEREVISIAE; TANDEM MASS SPECTROMETRY;

ANALYSIS OF VARIANCE; BIOTINYLATION; CELL LINE, TUMOR; CHEMICAL FRACTIONATION; CHROMATOGRAPHY, LIQUID; COLONIC NEOPLASMS; CYSTEINE; HUMANS; ISOELECTRIC FOCUSING; PEPTIDES; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TANDEM MASS SPECTROMETRY;

SACCHAROMYCES CEREVISIAE;

EID: 77957337489     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr1007015     Document Type: Article

References (46)

1. Motoyama, A.; Yates, J. R. Multidimensional LC separations in shotgun proteomics Anal. Chem. 2008, 80 (19) 7187-93
2. 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 (10) 994-9
3. Liu, T.; Qian, W. J.; Chen, W. N.; Jacobs, J. M.; Moore, R. J.; Anderson, D. J.; Gritsenko, M. A.; Monroe, M. E.; Thrall, B. D.; Camp, D. G., 2nd; Smith, R. D. Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: the human mammary epithelial cell proteome Proteomics 2005, 5 (5) 1263-73
4. Gygi, S. P.; Rist, B.; Griffin, T. J.; Eng, J.; Aebersold, R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags J. Proteome Res. 2002, 1 (1) 47-54
5. Wang, H.; Qian, W. J.; Chin, M. H.; Petyuk, V. A.; Barry, R. C.; Liu, T.; Gritsenko, M. A.; Mottaz, H. M.; Moore, R. J.; Camp, D. G., II; Khan, A. H.; Smith, D. J.; Smith, R. D. Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment J. Proteome Res. 2006, 5 (2) 361-9
6. Zhou, H.; Ranish, J. A.; Watts, J. D.; Aebersold, R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry Nat. Biotechnol. 2002, 20 (5) 512-5
7. Foettinger, A.; Leitner, A.; Lindner, W. Solid-phase capture and release of arginine peptides by selective tagging and boronate affinity chromatography J. Chromatogr., A 2005, 1079 (1-2) 187-96
8. Ji, J.; Chakraborty, A.; Geng, M.; Zhang, X.; Amini, A.; Bina, M.; Regnier, F. Strategy for qualitative and quantitative analysis in proteomics based on signature peptides J. Chromatogr., B: Biomed. Sci. Appl. 2000, 745 (1) 197-210
9. 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 (5) 315-24
10. Oda, Y.; Nagasu, T.; Chait, B. T. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome Nat. Biotechnol. 2001, 19 (4) 379-82
11. Zhou, H.; Watts, J. D.; Aebersold, R. A systematic approach to the analysis of protein phosphorylation Nat. Biotechnol. 2001, 19 (4) 375-8
12. Zhang, H.; Li, X. J.; Martin, D. B.; Aebersold, R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry Nat. Biotechnol. 2003, 21 (6) 660-6
13. Kaji, H.; Saito, H.; Yamauchi, Y.; Shinkawa, T.; Taoka, M.; Hirabayashi, J.; Kasai, K.; Takahashi, N.; Isobe, T. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins Nat. Biotechnol. 2003, 21 (6) 667-72
14. Qu, J.; Jusko, W. J.; Straubinger, R. M. Utility of cleavable isotope-coded affinity-tagged reagents for quantification of low-copy proteins induced by methylprednisolone using liquid chromatography/tandem mass spectrometry Anal. Chem. 2006, 78 (13) 4543-52
15. 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 (2) 148-56
16. Liu, T.; Qian, W. J.; Strittmatter, E. F.; Camp, D. G., 2nd; Anderson, G. A.; Thrall, B. D.; Smith, R. D. High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology Anal. Chem. 2004, 76 (18) 5345-53
17. Gevaert, K.; Ghesquiere, B.; Staes, A.; Martens, L.; Van Damme, J.; Thomas, G. R.; Vandekerckhove, J. Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies Proteomics 2004, 4 (4) 897-908
18. Raftery, M. J. Enrichment by organomercurial agarose and identification of cys-containing peptides from yeast cell lysates Anal. Chem. 2008, 80 (9) 3334-41
19. Lu, M.; Li, X. F.; Le, X. C.; Weinfeld, M.; Wang, H. Identification and characterization of cysteinyl exposure in proteins by selective mercury labeling and nano-electrospray ionization quadrupole time-of-flight mass spectrometry Rapid Commun. Mass Spectrom. 2010, 24 (11) 1523-32
20. Hong, F.; Sekhar, K. R.; Freeman, M. L.; Liebler, D. C. Specific patterns of electrophile adduction trigger Keap1 ubiquitination and Nrf2 activation J. Biol. Chem. 2005, 280 (36) 31768-75
21. Dennehy, M. K.; Richards, K. A.; Wernke, G. R.; Shyr, Y.; Liebler, D. C. Cytosolic and nuclear protein targets of thiol-reactive electrophiles Chem. Res. Toxicol. 2006, 19 (1) 20-9
22. Wong, H. L.; Liebler, D. C. Mitochondrial protein targets of thiol-reactive electrophiles Chem. Res. Toxicol. 2008, 21 (4) 796-804
23. Lin, D.; Saleh, S.; Liebler, D. C. Reversibility of Covalent Electrophile-Protein Adducts and Chemical Toxicity Chem. Res. Toxicol. 2008, 21, 2361-69
24. Borisov, O. V.; Goshe, M. B.; Conrads, T. P.; Rakov, V. S.; Veenstra, T. D.; Smith, R. D. Low-energy collision-induced dissociation fragmentation analysis of cysteinyl-modified peptides Anal. Chem. 2002, 74 (10) 2284-92
25. Hansen, K. C.; Schmitt-Ulms, G.; Chalkley, R. J.; Hirsch, J.; Baldwin, M. A.; Burlingame, A. L. Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography Mol. Cell. Proteomics 2003, 2 (5) 299-314
26. Kim, H. Y.; Tallman, K. A.; Liebler, D. C.; Porter, N. A. An azido-biotin reagent for use in the isolation of protein adducts of lipid-derived electrophiles by streptavidin catch and photo-release Mol. Cell. Proteomics 2009, 8 (9) 2080-9
27. Paulovich, A. G.; Billheimer, D.; Ham, A. J.; Vega-Montoto, L. J.; Rudnick, P. A.; Tabb, D. L.; Wang, P.; Blackman, R. K.; Bunk, D. M.; Cardasis, H. L.; Clauser, K. R.; Kinsinger, C. R.; Schilling, B.; Tegeler, T. J.; Variyath, A. M.; Wang, M.; Whiteaker, J. R.; Zimmerman, L. J.; Fenyo, D.; Carr, S. A.; Fisher, S. J.; Gibson, B. W.; Mesri, M.; Neubert, T. A.; Reginier, F. E.; Rodriguez, H.; Spiegelman, C.; Stein, S. E.; Tempst, P.; Liebler, D. C. A CPTAC inter-laboratory study characterizing a yeast performance standard for benchmarking LC-MS Platform performance Mol. Cell. Proteomics 2009, 9 (2) 242-54
28. Slebos, R. J.; Brock, J. W.; Winters, N. F.; Stuart, S. R.; Martinez, M. A.; Li, M.; Chambers, M. C.; Zimmerman, L. J.; Ham, A. J.; Tabb, D. L.; Liebler, D. C. Evaluation of Strong Cation Exchange versus Isoelectric Focusing of Peptides for Multidimensional Liquid Chromatography-Tandem Mass Spectrometry J. Proteome Res. 2008, 7, 5286-94
29. Cortes, H. J.; Pfeiffer, C. D.; Richter, B. E.; Stevens, T. S. Porous Ceramic Bed Supports for Fused-Silica Packed Capillary Columns Used in Liquid-Chromatography J. High Resol. Chromatogr. Chromatogr. Commun. 1987, 10 (8) 446-8
30. Licklider, L. J.; Thoreen, C. C.; Peng, J.; Gygi, S. P. Automation of nanoscale microcapillary liquid chromatography-tandem mass spectrometry with a vented column Anal. Chem. 2002, 74 (13) 3076-83
31. Tabb, D. L.; Fernando, C. G.; Chambers, M. C. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis J. Proteome Res. 2007, 6 (2) 654-61
32. Zhang, B.; Chambers, M. C.; Tabb, D. L. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency J. Proteome Res. 2007, 6 (9) 3549-57
33. Elias, J. E.; Haas, W.; Faherty, B. K.; Gygi, S. P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations Nat. Methods 2005, 2 (9) 667-75
34. Sheehan, J. C.; Wilson, R. M.; Oxford, A. W. Photolysis of Methoxy-Substituted Benzoin Ester-Photosensitive Protecting Group for Carboxylic Acids J. Am. Chem. Soc. 1971, 93 (26) 7222
35. Hansen, K. C.; Rock, R. S.; Larsen, R. W.; Chan, S. I. A method for photoinitating protein folding in a nondenaturing environment J. Am. Chem. Soc. 2000, 122 (46) 11567-8
36. Rock, R. S.; Chan, S. I. Synthesis and photolysis properties of a photolabile linker based on 3′-methoxybenzoin J. Org. Chem. 1996, 61 (4) 1526-9
37. Aoyagi, Y.; Iijima, A.; Williams, R. M. Asymmetric synthesis of [2,3-(13)C(2),(15)N]-4-benzyloxy-5,6-diphenyl-2,3,5,6-tetrahydro-4H-oxazin e-2-one via lipase TL-mediated kinetic resolution of benzoin: general procedure for the synthesis of [2,3-(13)C(2),(15)N]-L-alanine J. Org. Chem. 2001, 66 (24) 8010-4
38. Cargile, B. J.; Sevinsky, J. R.; Essader, A. S.; Stephenson, J. L., Jr.; Bundy, J. L. Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics J. Biomol. Tech. 2005, 16 (3) 181-9
39. Sprung, R. W., Jr.; Brock, J. W.; Tanksley, J. P.; Li, M.; Washington, M. K.; Slebos, R. J.; Liebler, D. C. Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis Mol. Cell. Proteomics 2009, 8 (8) 1988-98
40. Gao, J.; Opiteck, G. J.; Friedrichs, M. S.; Dongre, A. R.; Hefta, S. A. Changes in the protein expression of yeast as a function of carbon source J. Proteome Res. 2003, 2 (6) 643-9
41. Liu, H.; Sadygov, R. G.; Yates, J. R., 3rd A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76 (14) 4193-201
42. Old, W. M.; Meyer-Arendt, K.; Aveline-Wolf, L.; Pierce, K. G.; Mendoza, A.; Sevinsky, J. R.; Resing, K. A.; Ahn, N. G. Comparison of label-free methods for quantifying human proteins by shotgun proteomics Mol. Cell. Proteomics 2005, 4 (10) 1487-502
43. Ghaemmaghami, S.; Huh, W. K.; Bower, K.; Howson, R. W.; Belle, A.; Dephoure, N.; OShea, E. K.; Weissman, J. S. Global analysis of protein expression in yeast Nature 2003, 425 (6959) 737-41
44. Coghlan, A.; Wolfe, K. H. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae Yeast 2000, 16 (12) 1131-45
45. Gygi, S. P.; Corthals, G. L.; Zhang, Y.; Rochon, Y.; Aebersold, R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology Proc. Natl. Acad. Sci. U.S.A 2000, 97 (17) 9390-5
46. Zhang, B.; Kirov, S.; Snoddy, J. WebGestalt: an integrated system for exploring gene sets in various biological contexts Nucleic Acids Res. 2005, 33 (Web Server issue) W741-8