Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments

Bioinformatics

Volumn 24, Issue 14, 2008, Pages 1590-1595

  Shinoda, Kosaku ^a,b   Tomita, Masaru ^a,b   Ishihama, Yasushi ^a,c  

^a KEIO UNIVERSITY   (Japan)

^b Keio University and Human Metabolome Technologies Inc   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ORGANIC SOLVENT; PEPTIDE;

ANALYTIC METHOD; ARABIDOPSIS; ARTICLE; ESCHERICHIA COLI; GENE CONVERSION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; LIQUID CHROMATOGRAPHY; MACHINE LEARNING; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS; SPECTROMETER; SYSTEMS THEORY; TANDEM MASS SPECTROMETRY;

ARABIDOPSIS;

EID: 47049091146     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn240     Document Type: Article

References (25)

1. Callister,S.J. et al. (2006) Application of the accurate mass and time tag approach to the proteome analysis of sub-cellular fractions obtained from Rhodobacter sphaeroides 2.4.1. Aerobic and photosynthetic cell cultures. J. Proteome Res., 5, 1940-1947.
2. Funahashi,K. (1989) On the approximate realization of continuous mappings by neural networks. Neural Netw., 2, 183-192.
3. Ishihama,Y. (2006) Method for detection of peptide sequence based on chromatography retention time, PCT/JP2006/315549.
4. Ishihama,Y. et al. (2002) Microcolumns with self-assembled particle frits for proteomics. J. Chromatogr. A, 979, 233-239.
5. Ishihama,Y. et al. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics, 9, 102.
6. Jaitly,N. et al. (2006) Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Anal. Chem., 78, 7397-7409.
7. Janikow,C.Z. and Michalewicz,Z. (1991) An experimental comparison of binary and floating point representations in genetic algorithms. In Proceedings of the Fourth International Conference on Genetic Algorithms Morgan Kaufmann, San Diego, CA, USA, pp. 31-36.
8. Jonathan,P. et al. (2000) On the use of cross-validation to assess performance in multivariate prediction. Stat. Comput., 10, 209-229.
9. Kerner,M.J. et al. (2005) Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell, 122, 209-220.
10. Krokhin,O.V. (2006) 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., 78, 7785-7795.
11. Nielsen,N.-P.V. et al. (1998) Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping. J. Chromatogr. A, 805, 17-35.
12. Norbeck,A.D. et al. (2005) The utility of accurate mass and LC elution time information in the analysis of complex proteomes. J. Am. Soc. Mass Spectrom., 16, 1239-1249.
13. Palmblad,M. et al. (2002) Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry. Anal. Chem., 74, 5826-5830.
14. Petritis,K. et al. (2003) Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. Anal. Chem., 75, 1039-1048.
15. Petritis,K. et al. (2006) Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal. Chem., 78, 5026-5039.
16. Rappsilber,J. et al. (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoco., 2, 1896-1906.
17. Saito,H. et al. (2006) Multiplexed two-dimensional liquid chromatography for MALDI and nanoelectrospray ionization mass spectrometry in proteomics. J. Proteome Res., 5, 1803-1807.
18. Shen,Y. et al. (2001) Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal. Chem., 73, 1766-1775.
19. Shinoda,K. et al. (2006) Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks. J. Proteome Res., 5, 3312-3317.
20. Smith,R.D. et al. (2002) An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2, 513-523.
21. Snyder,L.R. (1980) High Performance Liquid Chromatography: Advances and Perspectives. Academic Press, New York.
22. Stadalius,M.A. et al. (1984) Optimization model for the gradient elution separation of peptide mixtures by reversed-phase high-performance liquid chromatography: Verification of retention relationships. J. Chromatogr. A, 296, 31-59.
23. Strittmatter,E.F. et al. (2003) Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. J. Am. Soc. Mass Spectrom., 14, 980-991.
24. van Nederkassel,A.M. et al. (2006) A comparison of three algorithms for chromatograms alignment. J. Chromatogr. A, 1118 199-210.
25. Zimmer,J.S. et al., (2006) Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrum. Rev., 25, 450-482.