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Improve the tandem mass spectra identification and reduce false negative rate using peptide LC retention time.
Author(s) -
Zhang Ling,
Yang Ruifeng,
Sun Wei,
Shao Chen,
Zhang Zhengguo,
Gao Youhe
Publication year - 2007
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.21.5.a265-d
Subject(s) - retention time , peptide , chromatography , false positive rate , false discovery rate , chemistry , tandem mass spectrometry , elution , tandem , mass spectrum , identification (biology) , mass spectrometry , liquid chromatography–mass spectrometry , database search engine , retention rate , analytical chemistry (journal) , search engine , computer science , biochemistry , biology , artificial intelligence , materials science , composite material , gene , computer security , botany , information retrieval
To reduce false positive rate, researchers commonly raise the threshold in tandem mass spectra identification, which leads to high false negative rate and greatly reduces proteomics research efficiency. Here we use peptide retention time to improve peptide identification. From at least 3 LC‐MS/MS experiments, the peptides from high quality spectra assignments with their LC retention times were collected in an Empirical Peptide Retention Time (EPRT) database. For a new experiment, peptides with substandard MS 2 spectra but similar elution time as in the EPRT database were accepted as positive identifications. For peptides without EPRT data, a peptide from two or more substandard spectra with similar elution time in different experiments was also accepted as positive. By this method, the positive identification could increase by 10–40%. The new identifications, most of which were low abundant peptides, were estimated to have false positive rate as low as 2.3% by known protein mixture experiment or reverse database searching methods. This method could be used in any standardized separation systems. As retention time of more peptides was collected in the EPRT database, the efficiency of peptide identification could be further improved.