Evaluation of search engines for phosphopeptide identification and quantitation

Xiaoyue Jiang1, Ryan Bomgarden2, Joseph Brown1, Rosa Viner1, Andreas R Huhmer1 1 Thermo Fisher Scientific, San Jose, CA; 2Thermo Fisher Scientific, Rockford, IL Poster Note 64779 Sensitive and Accurate Quantitation of Phosphopeptides Using TMT Isobaric Labeling Technique Sensitive and accurate…

Xiaoyue Jiang1, David Horn1, Michael Blank1, Devin Drew1, Bernard Delanghe2, Rosa Viner1, Andreas FR Huhmer1 1 Thermo Fisher Scientific, San Jose, CA, USA; 2Thermo Fisher Scientific, Bremen, Germany Key Words Protein coverage, post-translational modification (PTM), Proteome Discoverer, SEQUEST, Byonic, Mascot,…

The intelligent protein informatics platform Thermo Scientific Proteome Discoverer software Transform proteomics mass spectrometry data into insights Thermo Scientific™ Proteome Discoverer™ software enables comprehensive proteomics data processing workflows empowered by artificial intelligence. • Powerful and flexible framework: Optimized analysis for…

evaluated traditional non-cleavable and MS-cleavable crosslinkers for crosslinked peptide analysis using an Orbitrap Fusion Lumos mass spectrometer. For MS-cleavable crosslinkers, we also compared different types of fragmentation (CID, ETD) and levels of tandem mass spectrometry (MS2 vs. MS3). Our data…