title: Locus-specific Retention Predictor (LsRP): A Peptide Retention Time Predictor Developed for Precision Proteomics.
abstract: The precision prediction of peptide retention time (RT) plays an increasingly important role in liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics. Owing to the high reproducibility of liquid chromatography, RT prediction provides promising information for both identification and quantification experiment design. In this work, we present a Locus-specific Retention Predictor (LsRP) for precise prediction of peptide RT, which is based on amino acid locus information and Support Vector Regression (SVR) algorithm. Corresponding to amino acid locus, each peptide sequence was converted to a featured locus vector consisting of zeros and ones. With locus vector information from LC-MS/MS data sets, an SVR computational process was trained and evaluated. LsRP finally provided a prediction correlation coefficient of 0.95~0.99. We compared our method with two common predictors. Results showed that LsRP outperforms these methods and tracked up to 30% extra peptides in an extraction RT window of 2 min. A new strategy by combining LsRP and calibration peptide approach was then proposed, which open up new opportunities for precision proteomics.
authors.affiliation: Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, School of Basic Medical, Fudan University, Shanghai, 200032, P. R. China.
authors.forename: Wenyuan
authors.initials: W
authors.lastname: Lu
authors.affiliation: Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Liu
authors.affiliation: Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, School of Basic Medical, Fudan University, Shanghai, 200032, P. R. China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Liu
authors.affiliation: Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, School of Basic Medical, Fudan University, Shanghai, 200032, P. R. China.
authors.forename: Weiqian
authors.initials: W
authors.lastname: Cao
authors.affiliation: Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, School of Basic Medical, Fudan University, Shanghai, 200032, P. R. China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, School of Basic Medical, Fudan University, Shanghai, 200032, P. R. China.|Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China.
authors.forename: Pengyuan
authors.initials: P
authors.lastname: Yang
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D010455:Peptides / Q000032:analysis / Q000737:chemistry* / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides