title: pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra.
abstract: Determining the monoisotopic peak of a precursor is a first step in interpreting mass spectra, which is basic but non-trivial. The reason is that in the isolation window of a precursor, other peaks interfere with the determination of the monoisotopic peak, leading to wrong mass-to-charge ratio or charge state. Here we propose a method, named pParse, to export the most probable monoisotopic peaks for precursors, including co-eluted precursors. We use the relationship between the position of the highest peak and the mass of the first peak to detect candidate clusters. Then, we extract three features to sort the candidate clusters: (i) the sum of the intensity, (ii) the similarity of the experimental and the theoretical isotopic distribution, and (iii) the similarity of elution profiles. We showed that the recall of pParse, MaxQuant, and BioWorks was 98-98.8%, 0.5-17%, and 1.8-36.5% at the same precision, respectively. About 50% of tandem mass spectra are triggered by multiple precursors which are difficult to identify. Then we design a new scoring function to identify the co-eluted precursors. About 26% of all identified peptides were exclusively from co-eluted peptides. Therefore, accurately determining monoisotopic peaks, including co-eluted precursors, can greatly increase peptide identification rate.
authors: Key Laboratory of Intelligent Information Processing-Institute of Computing Technology, Chinese Academy of Sciences, Beijing, P R China.
authors: Zuo-Fei
authors: ZF
authors: Yuan
authors: Chao
authors: C
authors: Liu
authors: Hai-Peng
authors: HP
authors: Wang
authors: Rui-Xiang
authors: RX
authors: Sun
authors: Yan
authors: Y
authors: Fu
authors: Jing-Fen
authors: JF
authors: Zhang
authors: Le-Heng
authors: LH
authors: Wang
authors: Hao
authors: H
authors: Chi
authors: You
authors: Y
authors: Li
authors: Li-Yun
authors: LY
authors: Xiu
authors: Wen-Ping
authors: WP
authors: Wang
authors: Si-Min
authors: SM
authors: He
mesh_terms: D000465:Algorithms; D006367:HeLa Cells / Q000737:chemistry; D006801:Humans; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D011498:Protein Precursors / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D057386:Search Engine; D012680:Sensitivity and Specificity; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*; D013997:Time Factors; D015003:Yeasts / Q000737:chemistry
chemical_list: D010455:Peptides; D011498:Protein Precursors