Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks.
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.
Shinoda
Kosaku
K
Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan.
Sugimoto
Masahiro
M
Yachie
Nozomu
N
Sugiyama
Naoyuki
N
Masuda
Takeshi
T
Robert
Martin
M
Soga
Tomoyoshi
T
Tomita
Masaru
M
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
D029968:Escherichia coli Proteins