Chromatographic retention time prediction for posttranslationally modified peptides

Proteomics

Volumn 12, Issue 8, 2012, Pages 1151-1159

  Moruz, Luminita ^a   Staes, An ^b,c   Foster, Joseph M ^d   Hatzou, Maria ^a   Timmerman, Evy ^b,c   Martens, Lennart ^b,c   Käll, Lukas ^a,e  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c GHENT UNIVERSITY   (Belgium)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

Bioinformatics; Machine learning; Posttranslational modification; Retention time prediction; Reversed phase liquid chromatography

Indexed keywords

PEPTIDES AND PROTEINS;

ALGORITHM; ARTICLE; BIOINFORMATICS; CHROMATOGRAPHIC RETENTION TIME PREDICTION; COMPUTER PROGRAM; CORRELATION ANALYSIS; LIQUID CHROMATOGRAPHY; PRIORITY JOURNAL; PROTEIN MODIFICATION;

ALGORITHMS; ANIMALS; CHROMATOGRAPHY, LIQUID; HUMANS; INTERNET; MASS SPECTROMETRY; PEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SOFTWARE; TIME FACTORS;

EID: 84860866233     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201100386     Document Type: Article

References (41)

1. Ozlu, N., Akten, B., Timm, W., Haseley, N. et al., Phosphoproteomics. Wiley Interdiscip. Rev.: Syst. Biol. Med. 2010, 2, 255-276.
2. Dwek, R. A., Glycobiology: toward understanding the function of sugars. Chem. Rev. 1996, 96, 683-720.
3. Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J. et al., Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 2009, 27, 633-641.
4. Young, N. L., Plazas-Mayorca, M. D., Garcia, B. A., Systems-wide proteomic characterization of combinatorial post-translational modification patterns. Expert Rev. Proteomics 2010, 7, 79-92.
5. Hoffman, M. D., Sniatynski, M. J., Kast, J., Current approaches for global post-translational modification discovery and mass spectrometric analysis. Anal. Chim. Acta 2008, 627, 50-61.
6. Wilson-Grady, J. T., Villén, J., Gygi, S. P., Phosphoproteome analysis of fission yeast. J. Proteome Res. 2008, 7, 1088-1097.
7. Zhai, B., Villén, J., Beausoleil, S. A., Mintseris, J. et al., Phosphoproteome analysis of drosophila melanogaster embryos. J. Proteome Res. 2008, 7, 1675-1682.
8. Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L. et al., Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 2009, 325, 834-840.
9. Wollscheid, B., Bausch-Fluck, D., Henderson, C., O'Brien, R. et al., Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat. Biotechnol. 2009, 27, 378-386.
10. Zielinska, D. F., Gnad, F., Wisniewski, J. R., Mann, M., Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 2010, 141, 897-907.
11. Manzano, C., Abraham, Z., López-Torrejón, G., Del Pozo, J., Identification of ubiquitinated proteins in Arabidopsis. Plant Mol. Biol. 2008, 68, 145-158.
12. Ducret, A., Oostveen, I. V., Eng, J. K., Yates, J. R. et al., High throughput protein characterization by automated reverse-phase chromatography/electrospray tandem mass spectrometry. Protein Sci. 1998, 7, 706-719.
13. Domon, B., Broder, S., Implications of new proteomics strategies for biology and medicine. J. Proteome Res. 2004, 3, 253-260.
14. Gstaiger, M., Aebersold, R., Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat. Rev. Genet. 2009, 10, 617-627.
15. Larsen, M. R., Trelle, M. B., Thingholm, T. E., Jensen, O. N., Mass spectrometry for proteomics analysis. Biotechniques 2006, 40, 790-798.
16. Bertsch, A., Jung, S., Zerck, A., Pfeifer, N. et al., Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics. J. Proteome Res. 2010, 9, 2696-2704.
17. Palmblad, M., Ramstrom, M., Markides, K., Hakansson, P. et al., Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry. Anal. Chem. 2002, 74, 5826-5830.
18. Strittmatter, E. F., Kangas, L. J., Petritis, K., Mottaz, H. M. et al., Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J. Proteome Res. 2004, 3, 760-769.
19. Krokhin, O. V., Craig, R., Spicer, V., Ens, W. et al., An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS. Mol. Cell. Proteomics 2004, 3, 908-919.
20. Klammer, A. A., Yi, X., MacCoss, M. J., Noble, W. S., Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions. Anal. Chem. 2007, 79, 6111-6118.
21. Pfeifer, N., Leinenbach, A., Huber, C., Kohlbacher, O., Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach. J. Proteome Res. 2009, 8, 4109-4115.
22. Krokhin, O. V., Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. Anal. Chem. 2006, 78, 7785-7795.
23. Petritis, K., Kangas, L. J., Yan, B., Monroe, M. E. et al., Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal. Chem. 2006, 78, 5026-5039.
24. Pfeifer, N., Leinenbach, A., Huber, C., Kohlbacher, O., Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics. BMC Bioinformatics 2007, 8, 468.
25. Palmblad, M. Retention Time Prediction and Protein Identification, Humana Press, Totowa, NJ 2006, pp. 195-208.
26. Kim, J., Petritis, K., Shen, Y., Camp, D. G., II et al., Phosphopeptide elution times in reversed-phase liquid chromatography. J. Chromatogr A 2007, 1172, 9-18.
27. Gorshkov, A. V., Tarasova, I. A., Evreinov, V. V., Savitski, M. M. et al., Liquid chromatography at critical conditions: comprehensive approach to sequence-dependent retention time prediction. Analy. Chem. 2006, 78, 7770-7777.
28. Perlova, T. Y., Goloborodko, A. A., Margolin, Y., Pridatchenko, M. L. et al., Retention time prediction using the model of liquid chromatography of biomacromolecules at critical conditions in LC-MS phosphopeptide analysis. Proteomics 2010, 10, 3458-3468.
29. Moruz, L., Tomazela, D., and Käll, L., Training, selection, and robust calibration of retention time models for targeted proteomics. J. Proteome Res. 2010, 9, 5209-5216.
30. Gevaert, K., Goethals, M., Martens, L., Van Damme, J. et al., Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 2003, 21, 566-569.
31. Staes, A., Van Damme, P., Helsens, K., Demol, H. et al., Improved recovery of proteome-informative, protein n-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics 2008, 8, 1362-1370.
32. Staes, A., Impens, F., Van Damme, P., Ruttens, B. et al., Selecting protein N-terminal peptides by COmbined FRActional DIagonal Chromatography (COFRADIC). Nat. Protocols 2011, 6, 1130-1141.
33. Gevaert, K., Van Damme, J., Goethals, M., Thomas, G. R. et al., Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis. Mol. Cell. Proteomics 2002, 1, 896-903.
34. Van Damme, P., Staes, A., Bronsoms, S., Helsens, K. et al., Complementary positional proteomics for screening substrates of endo- and exoproteases. Nat. Methods 2010, 7, 512-515.
35. Gevaert, K., Ghesquière, B., Staes, A., Martens, L. et al., Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies. Proteomics 2004, 4, 897-908.
36. Perkins, D. N., Pappin, D. J. C., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
37. Helsens, K., Colaert, N., Barsnes, H., Muth, T. et al., ms_lims, a simple yet powerful open source laboratory information management system for ms-driven proteomics. Proteomics 2010, 10, 1261-1264.
38. Steen, H., Jebanathirajah, J. A., Rush, J., Morrice, N., et al., Phosphorylation analysis by mass spectrometry. Mol. Cell. Proteomics 2006, 5, 172-181.
39. Kawakami, T., Tateishi, K., Yamano, Y., Ishikawa, T. et al., Protein identification from product ion spectra of peptides validated by correlation between measured and predicted elution times in liquid chromatography/mass spectrometry. Proteomics 2005, 5, 856-864.
40. Gallien, S., Duriez, E., Domon, B., Selected reaction monitoring applied to proteomics. J. Mass Spectrom. 2011, 46, 298-312.
41. Picotti, P., Lam, H., Campbell, D., Deutsch, E. W. et al., A database of mass spectrometric assays for the yeast proteome. Nat. Methods 2008, 5, 913-914.