In silico analysis of accurate proteomics, complemented by selective isolation of peptides

Journal of Proteomics

Volumn 74, Issue 10, 2011, Pages 2071-2082

  Perez Riverol, Yasset ^a   Sánchez, Aniel ^a   Ramos, Yassel ^a   Schmidt, Alex ^b   Müller, Markus ^b   Betancourt, Lázaro ^a   González, Luis J ^a   Vera, Roberto ^a   Padron, Gabriel ^a   Besada, Vladimir ^a  

^a CENTER FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Cuba)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

Accurate mass proteomics; Isoelectric point; Retention time; Selective isolation of peptides

Indexed keywords

ACCURACY; AMINO ACID ANALYSIS; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; FALSE POSITIVE RESULT; HUMAN; ISOELECTRIC POINT; ISOLATION PROCEDURE; MASS SPECTROMETRY; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS;

AMINO ACID SEQUENCE; ANIMALS; CHROMATOGRAPHY, LIQUID; COMPUTER SIMULATION; DATABASES, PROTEIN; HUMANS; ISOELECTRIC POINT; MOLECULAR WEIGHT; PEPTIDES; PROTEINS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 80052022909     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.05.034     Document Type: Article

References (56)

1. Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
2. Peng J., Elias J.E., Thoreen C.C., Licklider L.J., Gygi S.P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2003, 2:43-50.
3. Perkins D.N., Pappin D.J., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20:3551-3567.
4. Colinge J., Masselot A., Giron M., Dessingy T., Magnin J. OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 2003, 3:1454-1463.
5. Craig R., Beavis R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20:1466-1467.
6. Yen C.Y., Russell S., Mendoza A.M., Meyer-Arendt K., Sun S., Cios K.J., et al. Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS spectra. Anal Chem 2006, 78:1071-1084.
7. Belov M.E., Anderson G.A., Wingerd M.A., Udseth H.R., Tang K., Prior D.C., et al. An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics. J Am Soc Mass Spectrom 2004, 15:212-232.
8. Lipton M.S., Pasa-Tolic L., Anderson G.A., Anderson D.J., Auberry D.L., Battista J.R., et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci U S A 2002, 99:11049-11054.
9. Zimmer J.S., Monroe M.E., Qian W.J., Smith R.D. Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev 2006, 25:450-482.
10. Pasa-Tolic L., Masselon C., Barry R.C., Shen Y., Smith R.D. Proteomic analyses using an accurate mass and time tag strategy. Biotechniques 2004, 37:621-624. 6-33, 36 passim.
11. Norbeck A.D., Monroe M.E., Adkins J.N., Anderson K.K., Daly D.S., Smith R.D. The utility of accurate mass and LC elution time information in the analysis of complex proteomes. J Am Soc Mass Spectrom 2005, 16:1239-1249.
12. Bellew M., Coram M., Fitzgibbon M., Igra M., Randolph T., Wang P., et al. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 2006, 22:1902-1909.
13. May D., Fitzgibbon M., Liu Y., Holzman T., Eng J., Kemp C.J., et al. A platform for accurate mass and time analyses of mass spectrometry data. J Proteome Res 2007, 6:2685-2694.
14. Leptos K.C., Sarracino D.A., Jaffe J.D., Krastins B., Church G.M. MapQuant: open-source software for large-scale protein quantification. Proteomics 2006, 6:1770-1782.
15. Cargile B.J., Stephenson J.L. An alternative to tandem mass spectrometry: isoelectric point and accurate mass for the identification of peptides. Anal Chem 2004, 76:267-275.
16. Summerfield S.G., Bolgar M.S., Gaskell S.J. Promotion and stabilization of b1 ions in peptide phenythiocarbamoyl derivatives: analogies with condensed-phase chemistry. J Mass Spectrom 1997, 32:225-231.
17. Brancia F.L., Butt A., Beynon R.J., Hubbard S.J., Gaskell S.J., Oliver S.G. A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics. Electrophoresis 2001, 22:552-559.
18. van der Rest G., He F., Emmett M.R., Marshall A.G., Gaskell S.J. Gas-phase cleavage of PTC-derivatized electrosprayed tryptic peptides in an FT-ICR trapped-ion cell: mass-based protein identification without liquid chromatographic separation. J Am Soc Mass Spectrom 2001, 12:288-295.
19. Sanchez A., Perez-Riverol Y., González L.J., Noda J., Betancourt L., Ramos Y., et al. Evaluation of phenylthiocarbamoyl-derivatized peptides by electrospray ionization mass spectrometry: selective isolation and analysis of modified multiply charged peptides for liquid chromatography-tandem mass spectrometry experiments. Anal Chem 2010, 82(20):8492-8501.
20. Chelius D., Shaler T.A. Capture of peptides with N-terminal serine and threonine: a sequence-specific chemical method for Peptide mixture simplification. BioconjugChem 2003, 14:205-211.
21. Gevaert K., Van Damme 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.
22. 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.
23. 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, 1079:187-196.
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., Gonzalez L.J., Ramos Y., Betancourt L., Gil J., Besada V., et al. Selective isolation of lysine-free tryptic peptides delimited by arginine residues: a new tool for proteome analysis. J Proteome Res 2006, 5:1204-1213.
27. The universal protein resource (UniProt). Nucleic Acids Res 2008, 36:D190-D195.
28. Grumbling G., Strelets V. FlyBase: anatomical data, images and queries. Nucleic Acids Res 2006, 34:D484-D488.
29. Colinge J., Masselot A., Carbonell P., Appel R.D. InSilicoSpectro: an open-source proteomics library. J Proteome Res 2006, 5:619-624.
30. Lehninger A., Nelson D., Cox M. Lehninger principles of biochemistry 2004, W. H. Freeman.
31. Krokhin O.V., Craig R., Spicer V., Ens W., Standing K.G., Beavis R.C., 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.
32. Keller A., Nesvizhskii A.I., Kolker E., Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 2002, 74:5383-5392.
33. Cargile B.J., Sevinsky J.R., Essader A.S., Stephenson J.L., Bundy J.L. Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics. J Biomol Tech 2005, 16:181-189.
34. Krijgsveld J., Gauci S., Dormeyer W., Heck A.J. In-gel isoelectric focusing of peptides as a tool for improved protein identification. J Proteome Res 2006, 5:1721-1730.
35. Essader A.S., Cargile B.J., Bundy J.L., Stephenson J.L. A comparison of immobilized pH gradient isoelectric focusing and strong-cation-exchange chromatography as a first dimension in shotgun proteomics. Proteomics 2005, 5:24-34.
36. McLaughlin T., Siepen J.A., Selley J., Lynch J.A., Lau K.W., Yin H., et al. PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. Nucleic Acids Res 2006, 34:D649-D654.
37. Siepen J.A., Keevil E.J., Knight D., Hubbard S.J. Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics. J Proteome Res 2007, 6:399-408.
38. Sanders W.S., Bridges S.M., McCarthy F.M., Nanduri B., Burgess S.C. Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinf 2007, 8(Suppl 7):S23.
39. 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.
40. Petritis K., Kangas L.J., Yan B., Monroe M.E., Strittmatter E.F., Qian W.J., et al. Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal Chem 2006, 78:5026-5039.
41. 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.
42. Krokhin O.V., Ying S., Cortens J.P., Ghosh D., Spicer V., Ens W., et al. Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS. Anal Chem 2006, 78:6265-6269.
43. Palmblad M., Ramstrom M., Bailey C.G., McCutchen-Maloney S.L., Bergquist J., Zeller L.C. Protein identification by liquid chromatography-mass spectrometry using retention time prediction. J Chromatogr B Analyt Technol Biomed Life Sci 2004, 803:131-135.
44. Shen Y., Zhao R., Belov M.E., Conrads T.P., Anderson G.A., Tang K., et al. Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal Chem 2001, 73:1766-1775.
45. Cargile B.J., Talley D.L., Stephenson J.L. Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pI predictability of peptides. Electrophoresis 2004, 25:936-945.
46. Krijgsveld J., Gauci S., Dormeyer W., Heck A.J. In-gel isoelectric focusing of peptides as a tool for improved protein identification. J Proteome Res 2006, 5:1721-1730.
47. Horth P., Miller C.A., Preckel T., Wenz C. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol Cell Proteomics 2006, 5:1968-1974.
48. 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.
49. Cargile B.J., Sevinsky J.R., Essader A.S., Eu J.P., Stephenson J.L. Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects. Electrophoresis 2008, 29:2768-2778.
50. Gauci S., van Breukelen B., Lemeer S.M., Krijgsveld J., Heck A.J. A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing. Proteomics 2008, 8:4898-4906.
51. 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, 21:660-666.
52. 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.
53. Horth P., Miller C.A., Preckel T., Wenz C. Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis. Mol Cell Proteomics 2006, 5:1968-1974.
54. Mallick P., Schirle M., Chen S.S., Flory M.R., Lee H., Martin D., et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 2007, 25:125-131.
55. 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.
56. Sanchez A., Perez-Riverol Y., Gonzalez L.J., Noda J., Betancourt L., Ramos Y., et al. Evaluation of phenylthiocarbamoyl-derivatized peptides by electrospray ionization mass spectrometry: selective isolation and analysis of modified multiply charged peptides for liquid chromatography-tandem mass spectrometry experiments. Anal Chem 2010, 82:8492-8501.