Xiaoyue Jiang1, David Horn1, Ryan Bomgarden2 ,Tara Schroeder3, Rosa Viner1, Andreas FR Huhmer1
Purpose: To compare different fragmentation methods including HCD, CID, EThcD for phosphopeptide identification. The performance of search engine platforms for
phosphopeptide identification and quantitation were evaluated and optimized.
Methods: Enriched and multiplexed quantitative phosphopeptides were analyzed by mass spectrometry (MS) and searched using the SequestHT, Byonic and Mascot nodes in Proteome Discoverer software and the Andromeda search engine in MaxQuant software .
Results: Search engines performed differently for multiple fragmentation methods on the same sample. The quantitation accuracy was comparable across search engines. Novel search workflows were designed in Proteome Discoverer to maximize identification and to optimize quantitation accuracy
1Thermo Fisher Scientific, San Jose, CA
2Thermo Fisher Scientific, Rockford, IL
3Thermo Fisher Scientific, Somerset, NJ