Send to

Choose Destination
Anal Chem. 2007 Oct 1;79(19):7439-49. Epub 2007 Aug 25.

Comprehensive phosphorylation site analysis of individual phosphoproteins applying scoring schemes for MS/MS data.

Author information

Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.


We have developed novel scoring schemes for the identification of (phospho)peptides (PeptideScore) and for pinpointing phosphorylation sites (PhosphoSiteScore) using MS/MS data. These scoring schemes have been developed for the in-depth analysis of individual phosphoproteins, not for large-scale phosphoproteomic-type data. The scoring schemes are implemented into the new software tool Phosm, which provides a concise and comprehensive presentation of the results. For development and evaluation of these schemes, we have analyzed approximately 500 phosphopeptide MS/MS spectra, most of them nontryptic peptides. The novel scoring schemes turned out to be very powerful, even with CID MS/MS spectra of very low quality. Many phosphopeptides and phosphorylation sites that remained unassigned in our LC-MS/MS data sets with Mascot could be identified with Phosm. Especially the number of identified multiply phosphorylated peptides could be significantly increased. The applied scoring parameters are described, and the scoring for several selected examples of phosphopeptides is discussed in detail. Furthermore, a new and simple nomenclature for all types of phosphorylated fragment ions is introduced in this publication.

[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for American Chemical Society
Loading ...
Support Center