SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping

Journal of Proteomics

Volumn 91, Issue , 2013, Pages 164-171

  Betancourt, Lázaro H ^a   De Bock, Pieter Jan ^b,c   Staes, An ^b,c   Timmerman, Evy ^b,c   Perez Riverol, Yasset ^a   Sanchez, Aniel ^a   Besada, Vladimir ^a   Gonzalez, Luis Javier ^a   Vandekerckhove, Joël ^b,c   Gevaert, Kris ^b,c  

^a CENTER FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Cuba)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c GHENT UNIVERSITY   (Belgium)

Author keywords

Cation exchange; Proteomics; Reversible alpha amino group and lysine modification; Selective peptide isolation

Indexed keywords

BUFFER; PROTEOME;

ACYLATION; AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CATION EXCHANGE; EMBRYO CELL; FIBROBLAST; PH; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTON TRANSPORT; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY;

CATION EXCHANGE; PROTEOMICS; REVERSIBLE ALPHA-AMINO GROUP AND LYSINE MODIFICATION; SELECTIVE PEPTIDE ISOLATION;

ANIMALS; CATIONS; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COMPUTATIONAL BIOLOGY; FIBROBLASTS; HUMANS; LYSINE; MICE; PEPTIDE MAPPING; PEPTIDES; PROTEOMICS; TRYPSIN;

EID: 84881487283     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.06.033     Document Type: Article

References (39)

1. Gil J., Betancourt L.Z., Sardinas G., Yero D., Niebla O., Delgado M., et al. Proteomic study via a non-gel based approach of meningococcal outer membrane vesicle vaccine obtained from strain CU385: a road map for discovering new antigens. Hum Vaccin 2009, 5:347-356.
2. Di P.S., Hennrich M.L., Heck A.J., Mohammed S. Recent advances in peptide separation by multidimensional liquid chromatography for proteome analysis. J Proteomics 2012, 75:3791-3813.
3. Messana I., Cabras T., Iavarone F., Vincenzoni F., Urbani A., Castagnola M. Unraveling the different proteomic platforms. J Sep Sci 2013, 36:128-139.
4. Vaudel M., Sickmann A., Martens L. Current methods for global proteome identification. Expert Rev Proteomics 2012, 9:519-532.
5. Shi R., Kumar C., Zougman A., Zhang Y., Podtelejnikov A., Cox J., et al. Analysis of the mouse liver proteome using advanced mass spectrometry. J Proteome Res 2007, 6:2963-2972.
6. Fournier M.L., Gilmore J.M., Martin-Brown S.A., Washburn M.P. Multidimensional separations-based shotgun proteomics. Chem Rev 2007, 107:3654-3686.
7. Motoyama A., Yates J.R. Multidimensional LC separations in shotgun proteomics. Anal Chem 2008, 80:7187-7193.
8. Boersema P.J., Divecha N., Heck A.J., Mohammed S. Evaluation and optimization of ZIC-HILIC-RP as an alternative MudPIT strategy. J Proteome Res 2007, 6:937-946.
9. Phillips H.L., Williamson J.C., van Elburg K.A., Snijders A.P., Wright P.C., Dickman M.J. Shotgun proteome analysis utilising mixed mode (reversed phase-anion exchange chromatography) in conjunction with reversed phase liquid chromatography mass spectrometry analysis. Proteomics 2010, 10:2950-2960.
10. Graumann J., Hubner N.C., Kim J.B., Ko K., Moser M., Kumar C., et al. Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins. Mol Cell Proteomics 2008, 7:672-683.
11. Malmstrom J., Lee H., Nesvizhskii A.I., Shteynberg D., Mohanty S., Brunner E., et al. Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. J Proteome Res 2006, 5:2241-2249.
12. Heller M., Ye M., Michel P.E., Morier P., Stalder D., Junger M.A., et al. Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides. J Proteome Res 2005, 4:2273-2282.
13. Uwaje N.C., Mueller N.S., Maccarrone G., Turck C.W. Interrogation of MS/MS search data with an pI filter algorithm to increase protein identification success. Electrophoresis 2007, 28:1867-1874.
14. Dwivedi R.C., Spicer V., Harder M., Antonovici M., Ens W., Standing K.G., et al. Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal Chem 2008, 80:7036-7042.
15. Manadas B., English J.A., Wynne K.J., Cotter D.R., Dunn M.J. Comparative analysis of OFFGel, strong cation exchange with pH gradient, and RP at high pH for first-dimensional separation of peptides from a membrane-enriched protein fraction. Proteomics 2009, 9:5194-5198.
16. Leitner A., Lindner W. Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics. Proteomics 2006, 6:5418-5434.
17. Olsen J.V., Andersen J.R., Nielsen P.A., Nielsen M.L., Figeys D., Mann M., et al. HysTag-a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain. Mol Cell Proteomics 2004, 3:82-92.
18. Wang H., Qian W.J., Chin M.H., Petyuk V.A., Barry R.C., Liu T., et al. Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment. J Proteome Res 2006, 5:361-369.
19. 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.
20. Gevaert K., Van D.J., Goethals M., Thomas G.R., Hoorelbeke B., Demol H., et al. Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins. Mol Cell Proteomics 2002, 1:896-903.
21. Gevaert K., Goethals M., Martens L., Van D.J., Staes A., Thomas G.R., et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 2003, 21:566-569.
22. Staes A., Impens F., Van D.P., Ruttens B., Goethals M., Demol H., et al. Selecting protein N-terminal peptides by combined fractional diagonal chromatography. Nat Protoc 2011, 6:1130-1141.
23. Van D.P., Staes A., Bronsoms S., Helsens K., Colaert N., Timmerman E., et al. Complementary positional proteomics for screening substrates of endo- and exoproteases. Nat Methods 2010, 7:512-515.
24. Betancourt L., Gil J., Besada V., Gonzalez L.J., Fernandez-de-Cossio J., Garcia L., et al. SCAPE: a new tool for the Selective CApture of PEptides in protein identification. J Proteome Res 2005, 4:491-496.
25. Sanchez A., Gonzalez L.J., Betancourt L., Gil J., Besada V., Fernandez-de-Cossio J., et al. Selective isolation of multiple positively charged peptides for 2-DE-free quantitative proteomics. Proteomics 2006, 6:4444-4455.
26. Sanchez A., Sun W., Wang L., Ma J., Betancourt L., Gil J., et al. Selective isolation-detection of two different positively charged peptides groups by strong cation exchange chromatography and matrix-assisted laser desorption/ionization mass spectrometry: application to proteomics studies. Eur J Mass Spectrom 2010, 16:693-702. [Chichester, Eng].
27. Betancourt L.H., Sanchez A., Perez Y., Fernandez de C.J., Gil J., Toledo P., et al. Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: evaluation in proteomic studies using peptide-centric database searches. J Proteomics 2011, 74:2210-2213.
28. Frese C.K., Altelaar A.F., Hennrich M.L., Nolting D., Zeller M., Griep-Raming J., et al. Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. J Proteome Res 2011, 10:2377-2388.
29. Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., et al. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A 2004, 101:12130-12135.
30. Taouatas N., Altelaar A.F., Drugan M.M., Helbig A.O., Mohammed S., Heck A.J. Strong cation exchange-based fractionation of Lys-N-generated peptides facilitates the targeted analysis of post-translational modifications. Mol Cell Proteomics 2009, 8:190-200.
31. Nesvizhskii A.I., Vitek O., Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 2007, 4:787-797.
32. Boersema P.J., Mohammed S., Heck A.J. Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal Bioanal Chem 2008, 391:151-159.
33. Hubner N.C., Ren S., Mann M. Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 2008, 8:4862-4872.
34. Pernemalm M., Lehtio J. A novel prefractionation method combining protein and peptide isoelectric focusing in immobilized pH gradient strips. J Proteome Res 2013, 12:1014-1019.
35. Ritorto M.S., Cook K., Tyagi K., Pedrioli P.G., Trost M. Hydrophilic strong anion exchange (hSAX) chromatography for highly orthogonal peptide separation of complex proteomes. J Proteome Res 2013, 12:2449-2457.
36. Nagaraj N., Wisniewski J.R., Geiger T., Cox J., Kircher M., Kelso J., et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 2011, 7:548.
37. Beck M., Schmidt A., Malmstroem J., Claassen M., Ori A., Szymborska A., et al. The quantitative proteome of a human cell line. Mol Syst Biol 2011, 7:549.
38. Michalski A., Cox J., Mann M. More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC-MS/MS. J Proteome Res 2011, 10:1785-1793.
39. Perez-Riverol Y., Sanchez A., Ramos Y., Schmidt A., Muller M., Betancourt L., et al. In silico analysis of accurate proteomics, complemented by selective isolation of peptides. J Proteomics 2011, 74:2071-2082.