Shimadzu Scientific's PTM Finder software uses data mining to investigate post-translational modifications in complex protein samples, including data for hypothetical, novel modifications.
The software is designed to integrate with Shimadzu's Axima line of Maldi mass spectrometers.
With PTM Finder software, users can identify peptide sequences carrying one or more modifications using MS/MS data.
The software facilitates consecutive Mascot searches using all the functionality of MS/MS Ion Search.
Peptides that do not match any proteins during the searches are directed towards a 'PTM Define' module, where users define their own hypothetical modifications and screen the remaining MS/MS data for specific shifts in fragment masses, neutral losses and/or diagnostic ions.
Such searches are quick and thorough, as they are performed based on a reduced database of protein sequences.
Users can easily import amino-acid sequences with a simple copy/paste function or use the proteins derived from the initial Mascot search results, giving more flexibility to search for PTMs whether or not they know the protein they are using.
