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pParse: A method for accurate determination of monoisotopic peaks in high‐resolution mass spectra
Author(s) -
Yuan ZuoF ei,
Liu Chao,
Wang HaiPeng,
Sun RuiXiang,
Fu Yan,
Zhang JingFen,
Wang LeHeng,
Chi Hao,
Li You,
Xiu LiYun,
Wang WenPing,
He SiMin
Publication year - 2011
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201100081
Subject(s) - monoisotopic mass , elution , chemistry , mass spectrum , chromatography , similarity (geometry) , analytical chemistry (journal) , resolution (logic) , mass spectrometry , artificial intelligence , computer science , image (mathematics)
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.