title: The proteomic analysis improved by cleavage kinetics-based fractionation of tryptic peptides.
abstract: Selective enrichment of specific peptides is an effective way to identify low abundance proteins. Fractionation of peptides prior to mass spectrometry is another widely used approach to reduce sample complexity in order to improve proteome coverage.In this study, we designed a multi-stage digestion strategy to generate peptides with different trypsin cleavage kinetics. It was found that each of the collected peptide fractions yielded many new protein identifications compared to the control group due to the reduced complexity. The overlapping peptides identified between adjacent fractions were very low, indicating that each fraction had different sets of peptides. The multi-stage digestion strategy separates tryptic peptides with different cleavage kinetics while RPLC separates peptides with different hydrophobicity. These two separation strategies were highly orthogonal, and showed an effective multidimensional separation to improve proteome coverage.
authors.affiliation: Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.|University of Chinese Academy of Sciences, Beijing, P. R. China.
authors.forename: Yanbo
authors.initials: Y
authors.lastname: Pan
authors.affiliation: Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.|University of Chinese Academy of Sciences, Beijing, P. R. China.
authors.forename: Jiawei
authors.initials: J
authors.lastname: Mao
authors.affiliation: Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.|University of Chinese Academy of Sciences, Beijing, P. R. China.
authors.forename: Zhenzhen
authors.initials: Z
authors.lastname: Deng
authors.affiliation: Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.|University of Chinese Academy of Sciences, Beijing, P. R. China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Dong
authors.affiliation: Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.|University of Chinese Academy of Sciences, Beijing, P. R. China.
authors.forename: Yangyang
authors.initials: Y
authors.lastname: Bian
authors.affiliation: Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.
authors.forename: Mingliang
authors.initials: M
authors.lastname: Ye
authors.affiliation: Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P. R. China.
authors.forename: Hanfa
authors.initials: H
authors.lastname: Zou
mesh_terms: D000595:Amino Acid Sequence; D002852:Chromatography, Ion Exchange / Q000379:methods; D056148:Chromatography, Reverse-Phase / Q000379:methods; D006367:HeLa Cells; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis* / Q000378:metabolism; D020543:Proteome / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods; D014357:Trypsin / Q000378:metabolism
chemical_list: D010455:Peptides; D020543:Proteome; D014357:Trypsin
keywords: Fractionation of peptides; Mass spectrometry; Proteomic analysis; Technology; Trypsin digestion kinetics