Improved Sequence Tag Generation Method for Peptide Identification in Tandem Mass Spectrometry
Xia Cao
Alexey I. Nesvizhskii
10.1021/pr800400q.s001
https://acs.figshare.com/articles/journal_contribution/Improved_Sequence_Tag_Generation_Method_for_Peptide_Identification_in_Tandem_Mass_Spectrometry/2910154
The sequence tag-based peptide identification methods are a promising alternative to the traditional database search approach. However, a more comprehensive analysis, optimization, and comparison with established methods are necessary before these methods can gain widespread use in the proteomics community. Using the InsPecT open source code base (Tanner et al., Anal. Chem. 2005, 77, 4626−39), we present an improved sequence tag generation method that directly incorporates multicharged fragment ion peaks present in many tandem mass spectra of higher charge states. We also investigate the performance of sequence tagging under different settings using control data sets generated on five different types of mass spectrometers, as well as using a complex phosphopeptide-enriched sample. We also demonstrate that additional modeling of InsPecT search scores using a semiparametric approach incorporating the accuracy of the precursor ion mass measurement provides additional improvement in the ability to discriminate between correct and incorrect peptide identifications. The overall superior performance of the sequence tag-based peptide identification method is demonstrated by comparison with a commonly used SEQUEST/PeptideProphet approach.
2008-10-03 00:00:00
precursor ion mass measurement
proteomics community
source code base
InsPecT search scores
control data sets
tandem mass spectra
SEQUEST
peptide identifications
database search approach
sequence tag generation method
Peptide Identification
semiparametric approach
charge states
mass spectrometers
Sequence Tag Generation Method
performance
multicharged fragment ion peaks