Table of Contents
International Journal of Proteomics
Volume 2012 (2012), Article ID 104681, 5 pages
Research Article

High Mass Accuracy Phosphopeptide Identification Using Tandem Mass Spectra

Sealy Center for Molecular Medicine, Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA

Received 27 April 2012; Accepted 18 June 2012

Academic Editor: Qiangwei Xia

Copyright © 2012 Rovshan G. Sadygov. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Phosphoproteomics is a powerful analytical platform for identification and quantification of phosphorylated peptides and assignment of phosphorylation sites. Bioinformatics tools to identify phosphorylated peptides from their tandem mass spectra and protein sequence databases are important part of phosphoproteomics. In this work, we discuss general informatics aspects of mass-spectrometry-based phosphoproteomics. Some of the specifics of phosphopeptide identifications stem from the labile nature of phosphor groups and expanded peptide search space. Allowing for modifications of Ser, Thr, and Tyr residues exponentially increases effective database size. High mass resolution and accuracy measurements of precursor mass-to-charge ratios help to restrict the search space of candidate peptide sequences. The higher-order fragmentations of neutral loss ions enhance the fragment ion mass spectra of phosphorylated peptides. We show an example of a phosphopeptide identification where accounting for fragmentation from neutral loss species improves the identification scores in a database search algorithm by 50%.