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Many proteins are modified after translation and the identification of these modifications has become a hot area of study. Accordingly, any software tool designed to identify proteins from tandem mass spectrometry data, must have the functionality to consider post-translational modifications (PTMs). PEAKS provides a number of features designed specifically to help identify modified proteins.

PEAKS employs both de novo sequencing and database search technology to identify PTMs. To identify modifications, PEAKS provides:

• a library of the most common PTMs (including: carbamidomethylation, phosphorylation, oxidation)
• a user-defined system for the creation of custom PTMs

Simply specify the modification(s) of interest and PEAKS will consider this information when providing sequence candidates or identification of proteins from your tandem mass spectrometry spectra.

The PEAKS auto de novo algorithm derives sequences with PTMs. The PTMs are then removed and both partial and complete sequence matches (tags) are used to search the database to find protein candidates. The short list of proteins in the database is then searched for spectrum-sequence matches, looking for variations in mass to identify PTMs. When this search finds a match with a PTM, the algorithm evaluates the quality of the match, and provides the result with a final score.

• PEAKS can provide sequence candidates with modifications, even for proteins not present in a database.
• When trying to identify a protein with a single modification, PEAKS rapidly finds high quality results with minimal false positives. This is particularly evident with multiple instances of the same modification on a single peptide. Traditional database searching often has difficulty finding these modifications.
• When the type of modification is not readily apparent, or in situations where many different modifications are suspected, PEAKS can consider all modifications present in the PEAKS internal PTM library (approx. 30 PTMs) and any user defined modifications. Other protein identification tools limit the user to a fixed number (e.g. less than 10).

Ultimately PEAKS provides a thorough analysis of modified proteins, presenting high qualtiy sequence candidates and protein identification results quickly and with minimal ambiguity.