Protein processing and other modifications analyzed by diagonal peptide chromatography

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1764, Issue 12, 2006, Pages 1801-1810

  Gevaert, Kris ^a   Van Damme, Petra ^a   Ghesquière, Bart ^a   Vandekerckhove, Joël ^a  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

Author keywords

Diagonal chromatography; N glycosylation; Protein phosphorylation; Protein processing; Proteomics

Indexed keywords

AMINO ACID; CYSTEINE; METHIONINE; PEPTIDE;

AMINO TERMINAL SEQUENCE; CHROMATOGRAPHY; COMBINED FRACTIONAL DIAGONAL CHROMATOGRAPHY; HUMAN; HYDROPHOBICITY; IN VIVO STUDY; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN GLYCOSYLATION; PROTEIN ISOLATION; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW;

CARBON ISOTOPES; CHROMATOGRAPHY, LIQUID; GLYCOSYLATION; HUMANS; MASS SPECTROMETRY; PEPTIDE FRAGMENTS; PHOSPHORYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 33845413316     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2006.09.003     Document Type: Review

References (75)

1. O'Farrell P.H. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250 (1975) 4007-4021
2. Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues, a novel approach to testing for induced point mutations in mammals. Humangenetik 26 (1975) 231-243
3. Bjellqvist B., Ek K., Righetti P.G., Gianazza E., Gorg A., Westermeier R., and Postel W. Isoelectric focusing in immobilized pH gradients: principle, methodology and some applications. J. Biochem. Biophys. Methods 6 (1982) 317-339
4. Unlu M., Morgan M.E., and Minden J.S. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18 (1997) 2071-2077
5. Wilkins M.R., Gasteiger E., Sanchez J.C., Bairoch A., and Hochstrasser D.F. Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number. Electrophoresis 19 (1998) 1501-1505
6. Gygi S.P., Corthals G.L., Zhang Y., Rochon Y., and Aebersold R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. U S. A. 97 97 (2000) 9390-9395
7. Taylor S.W., Fahy E., and Ghosh S.S. Global organellar proteomics. Trends Biotechnol. 21 (2003) 82-88
8. Santoni V., Molloy M., and Rabilloud T. Membrane proteins and proteomics: un amour impossible?. Electrophoresis 21 (2000) 1054-1070
9. 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 Ii D.G., Khan A.H., Smith D.J., and Smith R.D. Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment. J. Proteome Res. 5 (2006) 361-369
10. Link A.J., Eng J., Schieltz D.M., Carmack E., Mize G.J., Morris D.R., Garvik B.M., and Yates III J.R. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17 (1999) 676-682
11. Washburn M.P., Wolters D., and Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19 (2001) 242-247
12. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17 (1999) 994-999
13. Zhang H., Yan W., and Aebersold R. Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr. Opin. Chem. Biol. 8 (2004) 66-75
14. Gevaert K., Van Damme P., Martens L., and Vandekerckhove J. Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?. Anal. Biochem. 345 (2005) 18-29
15. Gygi S.P., Rist B., Griffin T.J., Eng J., and Aebersold R. Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags. J. Proteome Res. 1 (2002) 47-54
16. Brown J.R., and Hartley B.S. Location of disulphide bridges by diagonal paper electrophoresis, the disulphide bridges of bovine chymotrypsinogen A. Biochem. J. 101 (1966) 214-228
17. Cruickshank W.H., Malchy B.L., and Kaplan H. Diagonal chromatography for the selective purification of tyrosyl peptides. Can. J. Biochem. 52 (1974) 1013-1017
18. Gevaert K., Van Damme J., Goethals M., Thomas G.R., Hoorelbeke B., Demol H., Martens L., Puype M., Staes A., and Vandekerckhove J. Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Mol. Cell. Proteomics 1 (2002) 896-903
19. Ellman G.L. Tissue sulfhydryl groups. Arch. Biochem. Biophys. 82 (1959) 70-77
20. Gevaert K., Ghesquiere B., Staes A., Martens L., Van Damme J., Thomas G.R., and Vandekerckhove J. Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies. Proteomics 4 (2004) 897-908
21. Gevaert K., Pinxteren J., Demol H., Hugelier K., Staes A., Van Damme J., Martens L., and Vandekerckhove J. A four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells. J. Proteome Res. 5 (2006) 1415-1428
22. Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., and Vandekerckhove J. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted n-terminal peptides. Nat. Biotechnol. 21 (2003) 566-569
23. Liu H., Sadygov R.G., and Yates J.R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76 (2004) 4193-4201
24. Durr E., Yu J., Krasinska K.M., Carver L.A., Yates J.R., Testa J.E., Oh P., and Schnitzer J.E. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat. Biotechnol. 22 (2004) 985-992
25. Gevaert K., and Vandekerckhove J. COFRADIC™: the Hubble telescope of proteomics. DDT: TARGETS 3 (2004) S16-S22
26. Seidah N.G., and Chretien M. Eukaryotic protein processing: endoproteolysis of precursor proteins. Curr. Opin. Biotechnol. 8 (1997) 602-607
27. Buhling F., Waldburg N., Reisenauer A., Heimburg A., Golpon H., and Welte T. Lysosomal cysteine proteases in the lung: role in protein processing and immunoregulation. Eur. Respir. J. 23 (2004) 608-620
28. Kim J.C., Spence R.A., Currier P.F., Lu X., and Denison M.R. Coronavirus protein processing and RNA synthesis is inhibited by the cysteine proteinase inhibitor E64d. Virology 208 (1995) 1-8
29. Zeitlin P.L., Gail D.B., and Banks-Schlegel S. Protein processing and degradation in pulmonary health and disease. Am. J. Respir. Cell Mol. Biol. 29 (2003) 642-645
30. Wilquet V., and De Strooper B. Amyloid-beta precursor protein processing in neurodegeneration. Curr. Opin. Neurobiol. 14 (2004) 582-588
31. Lopez-Otin C., and Overall C.M. Protease degradomics: a new challenge for proteomics. Nat. Rev., Mol. Cell Biol. 3 (2002) 509-519
32. Honer B., Shoeman R.L., and Traub P. Degradation of cytoskeletal proteins by the human immunodeficiency virus type 1 protease. Cell Biol. Int. Rep. 16 (1992) 603-612
33. Thiede B., Dimmler C., Siejak F., and Rudel T. Predominant identification of RNA-binding proteins in Fas-induced apoptosis by proteome analysis. J. Biol. Chem. 276 (2001) 26044-26050
34. Bredemeyer A.J., Lewis R.M., Malone J.P., Davis A.E., Gross J., Townsend R.R., and Ley T.J. A proteomic approach for the discovery of protease substrates. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 11785-11790
35. Tam E.M., Morrison C.J., Wu Y.I., Stack M.S., and Overall C.M. Membrane protease proteomics: isotope-coded affinity tag MS identification of undescribed MT1-matrix metalloproteinase substrates. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 6917-6922
36. Neher S.B., Villen J., Oakes E.C., Bakalarski C.E., Sauer R.T., Gygi S.P., and Baker T.A. Proteomic profiling of ClpXP Substrates after DNA damage reveals extensive instability within SOS regulon. Mol. Cell 21 (2006) 193-204
37. Deperthes D. Phage display substrate: a blind method for determining protease specificity. Biol. Chem. 383 (2002) 1107-1112
38. Duan Y., and Laursen R.A. Protease substrate specificity mapping using membrane-bound peptides. Anal. Biochem. 216 (1994) 431-438
39. St Hilaire P.M., Alves L.C., Sanderson S.J., Mottram J.C., Juliano M.A., Juliano L., Coombs G.H., and Meldal M. The substrate specificity of a recombinant cysteine protease from Leishmania mexicana: application of a combinatorial peptide library approach. ChemBioChem 1 (2000) 115-122
40. Gosalia D.N., Salisbury C.M., Maly D.J., Ellman J.A., and Diamond S.L. Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays. Proteomics 5 (2005) 1292-1298
41. Scholle M.D., Kriplani U., Pabon A., Sishtla K., Glucksman M.J., and Kay B.K. Mapping protease substrates by using a biotinylated phage substrate library. ChemBioChem 7 (2006) 834-838
42. Bell J.K., Goetz D.H., Mahrus S., Harris J.L., Fletterick R.J., and Craik C.S. The oligomeric structure of human granzyme A is a determinant of its extended substrate specificity. Nat. Struct. Biol. 10 (2003) 527-534
43. Harris J.L., Peterson E.P., Hudig D., Thornberry N.A., and Craik C.S. Definition and redesign of the extended substrate specificity of granzyme B. J. Biol. Chem. 273 (1998) 27364-27373
44. Waugh S.M., Harris J.L., Fletterick R., and Craik C.S. The structure of the pro-apoptotic protease granzyme B reveals the molecular determinants of its specificity. Nat. Struct. Biol. 7 (2000) 762-765
45. Kumazaki T., Nakako T., Arisaka F., and Ishii S. A novel method for selective isolation of C-terminal peptides from tryptic digests of proteins by immobilized anhydrotrypsin: application to structural analyses of the tail sheath and tube proteins from bacteriophage T4. Proteins 1 (1986) 100-107
46. Tsugita A., Takamoto K., Kamo M., and Iwadate H. C-terminal sequencing of protein. A novel partial acid hydrolysis and analysis by mass spectrometry. Eur. J. Biochem. 206 (1992) 691-696
47. Samyn B., Hardeman K., Van der Eycken J., and Van Beeumen J. Applicability of the alkylation chemistry for chemical C-terminal protein sequence analysis. Anal. Chem. 72 (2000) 1389-1399
48. Samyn B., Sergeant K., Castanheira P., Faro C., and Van Beeumen J. A new method for C-terminal sequence analysis in the proteomic era. Nat. Methods 2 (2005) 193-200
49. Kawasaki H., Imajoh S., and Suzuki K. Separation of peptides on the basis of the difference in positive charge: simultaneous isolation of C-terminal and blocked N-terminal peptides from tryptic digests. J. Biochem. (Tokyo) 102 (1987) 393-400
50. Kuhn K., Thompson A., Prinz T., Muller J., Baumann C., Schmidt G., Neumann T., and Hamon C. Isolation of N-terminal protein sequence tags from cyanogen bromide cleaved proteins as a novel approach to investigate hydrophobic proteins. J. Proteome Res. 2 (2003) 598-609
51. McDonald L., Robertson D.H., Hurst J.L., and Beynon R.J. Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat. Methods 2 (2005) 955-957
52. Prinz T., Muller J., Kuhn K., Schafer J., Thompson A., Schwarz J., and Hamon C. Characterization of low abundant membrane proteins using the protein sequence tag technology. J. Proteome Res. 3 (2004) 1073-1081
53. Martens L., Van Damme P., Van Damme J., Staes A., Timmerman E., Ghesquiere B., Thomas G.R., Vandekerckhove J., and Gevaert K. The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile. Proteomics 5 (2005) 3193-3204
54. Meuleman P., Libbrecht L., De Vos R., de Hemptinne B., Gevaert K., Vandekerckhove J., Roskams T., and Leroux-Roels G. Morphological and biochemical characterization of a human liver in a uPA-SCID mouse chimera. Hepatology 41 (2005) 847-856
55. Van Damme P., Martens L., Van Damme J., Hugelier K., Staes A., Vandekerckhove J., and Gevaert K. Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nat. Methods 2 (2005) 771-777
56. Staes A., Demol H., Van Damme J., Martens L., Vandekerckhove J., and Gevaert K. Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18. J. Proteome Res. 3 (2004) 786-791
57. Ji J., Chakraborty A., Geng M., Zhang X., Amini A., Bina M., and Regnier F. Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. J. Chromatogr., B Biomed. Sci. Appl. 745 (2000) 197-210
58. Shibue M., Mant C.T., and Hodges R.S. Effect of anionic ion-pairing reagent concentration (1-60 mM) on reversed-phase liquid chromatography elution behaviour of peptides. J. Chromatogr., A 1080 (2005) 58-67
59. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., and Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1 (2002) 376-386
60. Wu D., Ingram A., Lahti J.H., Mazza B., Grenet J., Kapoor A., Liu L., Kidd V.J., and Tang D. Apoptotic release of histones from nucleosomes. J. Biol. Chem. 277 (2002) 12001-12008
61. Perkins D.N., Pappin D.J., Creasy D.M., and Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20 (1999) 3551-3567
62. Shav-Tal Y., Lee B., Bar-Haim S., Vandekerckhove J., and Zipori D. Enhanced proteolysis of pre-mRNA splicing factors in myeloid cells. Exp. Hematol. 28 (2000) 1029-1038
63. Back S.H., Shin S., and Jang S.K. Polypyrimidine tract-binding proteins are cleaved by caspase-3 during apoptosis. J. Biol. Chem. 277 (2002) 27200-27209
64. Demontis S., Rigo C., Piccinin S., Mizzau M., Sonego M., Fabris M., Brancolini C., and Maestro R. Twist is substrate for caspase cleavage and proteasome-mediated degradation. Cell Death Differ. 13 (2006) 335-345
65. Saiardi A., Bhandari R., Resnick A.C., Snowman A.M., and Snyder S.H. Phosphorylation of proteins by inositol pyrophosphates. Science 306 (2004) 2101-2105
66. Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., and White F.M. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20 (2002) 301-305
67. Ballif B.A., Villen J., Beausoleil S.A., Schwartz D., and Gygi S.P. Phosphoproteomic analysis of the developing mouse brain. Mol. Cell. Proteomics 3 (2004) 1093-1101
68. Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., and Gygi S.P. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 12130-12135
69. Zolodz M.D., Wood K.V., Regnier F.E., and Geahlen R.L. New approach for analysis of the phosphotyrosine proteome and its application to the chicken B cell line, DT40. J. Proteome Res. 3 (2004) 743-750
70. Liu P., Feasley C.L., and Regnier F.E. Optimization of diagonal chromatography for recognizing post-translational modifications. J. Chromatogr., A 1047 (2004) 221-227
71. Gevaert K., Staes A., Van Damme J., De Groot S., Hugelier K., Demol H., Martens L., Goethals M., and Vandekerckhove J. Global phosphoproteome analysis on human HepG2 hepatocytes using reverse-phase diagonal liquid chromatography. Proteomics 5 (2005) 3589-3599
72. Blom N., Sicheritz-Ponten T., Gupta R., Gammeltoft S., and Brunak S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4 (2004) 1633-1649
73. Tarentino A.L., Gomez C.M., and Plummer T.H. Deglycosylation of asparagine-linked glycans by peptide:N-glycosidase F. Biochemistry 24 (1985) 4665-4671
74. Ghesquière B., Van Damme J., Martens L., Vandekerckhove J., and Gevaert K. Proteome-wide characterization of N-glycosylation events by diagonal chromatography. J. Proteome Res. 5 (2006) 2438-2447
75. Thomson R., Hodgman T.C., Yang Z.R., and Doyle A.K. Characterizing proteolytic cleavage site activity using bio-basis function neural networks. Bioinformatics 19 (2003) 1741-1747