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A tool to evaluate correspondence between extraction ion chromatographic peaks and peptide‐spectrum matches in shotgun proteomics experiments
Author(s) -
Ruse Cristian I.,
Peacock Samantha,
Ghiban Cornel,
Rivera Keith,
Pappin Darryl J.,
Leopold Peter
Publication year - 2013
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.201300022
Subject(s) - database search engine , shotgun proteomics , chromatography , chemistry , orbitrap , leverage (statistics) , ion trap , mass spectrometry , ion , decoy , quadrupole ion trap , peptide , shotgun , proteomics , fragmentation (computing) , analytical chemistry (journal) , search engine , computer science , artificial intelligence , biochemistry , receptor , organic chemistry , information retrieval , gene , operating system
Chromatographed peptide signals form the basis of further data processing that eventually results in functional information derived from data‐dependent bottom‐up proteomics assays. We seek to rank LC / MS parent ions by the quality of their extracted ion chromatograms. Ranked extracted ion chromatograms act as an intuitive physical/chemical preselection filter to improve the quality of MS / MS fragment scans submitted for database search. We identify more than 4900 proteins when considering detector shifts of less than 7 ppm. High quality parent ions for which the database search yields no hits become candidates for subsequent unrestricted analysis for PTMs. Following this rational approach, we prioritize identification of more than 5000 spectrum matches from modified peptides and confirmed the presence of acetylaldehyde‐modified H is/ L ys. We present a logical workflow that scores data‐dependent selected ion chromatograms and leverage information about semianalytical LC / LC dimension prior to MS. Our method can be successfully used to identify unexpected modifications in peptides with excellent chromatography characteristics, independent of fragmentation pattern and activation methods. We illustrate analysis of ion chromatograms detected in two different modes by RF linear ion trap and electrostatic field orbitrap.