In PEAKS 6, we have introduced a new algorithm for PTM "blind search", PEAKS PTM. This algorithm can search for modified peptides with all 600+ PTMs in the Unimod database. To use this algorithm, simply select the option in the PEAKS Search dialog.
How is the "blind search" achieved? The secret is de novo sequencing. In usual PTM search algorithm, all possible modification forms of all database peptides satisfying the enzyme digestion rules are tried to match the spectra.
In PEAKS PTM, we only search for PTMs on the peptides when there is a tag match*. The algorithm also takes the PTM rarity into account to reduce the search space and false PTM assignment.
With PEAKS PTM algorithm selected, users only need to specify a very small number of variable PTMs in de novo and PEAKS DB to speed up the search and rely on PEAKS PTM to find other modifications presented in the sample.
*X. Han et al. PeaksPTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications. JPR 2011, 10(7): 2930-2936.
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