Peptide retention prediction applied to proteomic data analysis.
A retention prediction model was developed for peptides separated in reversed-phase chromatography. The model was utilized to identify and exclude the false positive (FP) peptide identifications obtained via database search. The selected database included human proteins, as well as decoy sequences of random proteins. The FP peptide detection rate was defined either as number of retention time outliers, or random decoy sequence identifications. The FP rate for various MASCOT scores was calculated. The peptides identified in one-dimensional (1D) and two-dimensional (2D) liquid chromatography/mass spectrometry (LC/MS) experiments were validated by prediction models. Multi-dimensional LC was based on two orthogonal reversed-phase chromatography modes; prediction models were successfully applied for data filtering in both separation dimensions.
Waters Corporation, 34 Maple Street, Milford, MA 01757, USA. Martin_Gilar@waters.com
Martin
M
Gilar
Aleksander
A
Jaworski
Petra
P
Olivova
John C
JC
Gebler
D000465:Algorithms; D001774:Blood Chemical Analysis / Q000379:methods; D001798:Blood Proteins / Q000737:chemistry*; D002851:Chromatography, High Pressure Liquid / Q000379:methods; D003198:Computer Simulation; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008956:Models, Chemical; D010449:Peptide Mapping / Q000379:methods; D010455:Peptides / Q000737:chemistry*; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D001798:Blood Proteins; D010455:Peptides; D020543:Proteome