title: Preprocessing significantly improves the peptide/protein identification sensitivity of high-resolution isobarically labeled tandem mass spectrometry data.
abstract: Isobaric labeling techniques coupled with high-resolution mass spectrometry have been widely employed in proteomic workflows requiring relative quantification. For each high-resolution tandem mass spectrum (MS/MS), isobaric labeling techniques can be used not only to quantify the peptide from different samples by reporter ions, but also to identify the peptide it is derived from. Because the ions related to isobaric labeling may act as noise in database searching, the MS/MS spectrum should be preprocessed before peptide or protein identification. In this article, we demonstrate that there are a lot of high-frequency, high-abundance isobaric related ions in the MS/MS spectrum, and removing isobaric related ions combined with deisotoping and deconvolution in MS/MS preprocessing procedures significantly improves the peptide/protein identification sensitivity. The user-friendly software package TurboRaw2MGF (v2.0) has been implemented for converting raw TIC data files to mascot generic format files and can be downloaded for free from https://github.com/shengqh/RCPA.Tools/releases as part of the software suite ProteomicsTools. The data have been deposited to the ProteomeXchange with identifier PXD000994.
authors.affiliation: From the ‡Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China; §Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee 37232-6848;
authors.forename: Quanhu
authors.initials: Q
authors.lastname: Sheng
authors.affiliation: From the ‡Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China;
authors.forename: Rongxia
authors.initials: R
authors.lastname: Li
authors.affiliation: ¶Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark.
authors.forename: Jie
authors.initials: J
authors.lastname: Dai
authors.affiliation: From the ‡Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China;
authors.forename: Qingrun
authors.initials: Q
authors.lastname: Li
authors.affiliation: From the ‡Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China;
authors.forename: Zhiduan
authors.initials: Z
authors.lastname: Su
authors.affiliation: §Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee 37232-6848;
authors.forename: Yan
authors.initials: Y
authors.lastname: Guo
authors.affiliation: From the ‡Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China;
authors.forename: Chen
authors.initials: C
authors.lastname: Li
authors.affiliation: §Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee 37232-6848; zr@sibs.ac.cn yu.shyr@vanderbilt.edu.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shyr
authors.affiliation: From the ‡Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200031, China; zr@sibs.ac.cn yu.shyr@vanderbilt.edu.
authors.forename: Rong
authors.initials: R
authors.lastname: Zeng
mesh_terms: D000818:Animals; D030562:Databases, Protein; D007477:Ions; D007553:Isotope Labeling / Q000379:methods*; D008970:Molecular Weight; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D011506:Proteins / Q000378:metabolism*; D051381:Rats; D057386:Search Engine; D013223:Statistics as Topic; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D007477:Ions; D010455:Peptides; D011506:Proteins