622 / 658
8
Comprehensive Peptide Searching Work ow to Maximize Protein Identi cations
creases the
least two
Conclusion
A comprehensive workflow strategy identified almost twice
as many high-confidence peptides compared to the
standard search strategy.
The comprehensive workflow helped increase the number
of high-confidence protein identifications and high-
confidence protein group identifications by approximately
90% and 75%, respectively, compared to the standard
search approach.
The comprehensive workflow identifies more high-
confidence peptides with multiple PTMs.
The percentage of matched spectra improves significantly
when using the comprehensive search workflow in
Proteome Discoverer software.
References
1. Khoury GA, Baliban RC, Floudas CA. Proteome-wide post-
translational modification statistics: frequency analysis and
curation of the swiss-prot database. Sci Rep. 2011 Sep
13;1.
2. Schandorff S, Olsen JV, Bunkenborg J, Blagoev B, Zhang
Y, Andersen JS, Mann M. A mass spectrometry-friendly
database for cSNP identification. Nat Methods. 2007 Jun;
4(6):465-6.
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