title: Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks.
abstract: We developed a computational method to predict the retention times of peptides in HPLC using artificial neural networks (ANN). We performed stepwise multiple linear regressions and selected for ANN input amino acids that significantly affected the LC retention time. Unlike conventional linear models, the trained ANN accurately predicted the retention time of peptides containing up to 50 amino acid residues. In 834 peptides, there was a strong correlation (R2 = 0.928) between measured and predicted retention times. We demonstrated the utility of our method by the prediction of the retention time of 121,273 peptides resulting from LysC-digestion of the Escherichia coli proteome. Our approach is useful for the proteome-wide characterization of peptides and the identification of unknown peptide peaks obtained in proteome analysis.
authors.affiliation: Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan.
authors.forename: Kosaku
authors.initials: K
authors.lastname: Shinoda
authors.forename: Masahiro
authors.initials: M
authors.lastname: Sugimoto
authors.forename: Nozomu
authors.initials: N
authors.lastname: Yachie
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Sugiyama
authors.forename: Takeshi
authors.initials: T
authors.lastname: Masuda
authors.forename: Martin
authors.initials: M
authors.lastname: Robert
authors.forename: Tomoyoshi
authors.initials: T
authors.lastname: Soga
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D002851:Chromatography, High Pressure Liquid / Q000706:statistics & numerical data*; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics*; D016014:Linear Models; D013058:Mass Spectrometry; D016571:Neural Networks, Computer; D040901:Proteomics / Q000379:methods*; D013997:Time Factors
chemical_list: D029968:Escherichia coli Proteins