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%.