To facilitate identification of particular ubiquitylation sites in proteins by mass spectrometry (MS), we developed UbIdent, a new tool for calculating precise masses of peptides bearing modification.
UbIdent is initially developed using Borland Delphi framework. UbIdent searches a protein sequence for proteolysis sites, calculates precise peptide masses and generates a list of modified peptides. At the moment the search area is limited by a single sequence provided by user in a FASTA format.
Identification of ubiquitylation sites by MS is currently based on the search for signature peptides. Peptides containing modification do not undergo cleavage after modified lysine residue during trypsinolysis. Besides that, these tryptic peptides have specific ubiquitin-derived diglycine (GG-) tags on modified lysines, with an additional mass of 114.1 Da. However, it was recently demonstrated that ubiquitylation sites could be identified by other types of signature peptides containing LRGG-tag (383.2 Da) on internal lysine residues or canonical GG-tag on the C-terminus of ubiquitylated peptides. UbIdent calculates peptide masses taking into account all 3 possible types of signature peptides. This allows accurate identification of ubiquitylation sites from MS data, giving more results than standard search algorithms.
This work was in part supported by RFBR (grant No. 08-04-97107).