Shimadzu Scientific Instruments PTM Finder software

PTM Finder software uses data mining to investigate post-translational modification in complex protein samples, including data for hypothetical, novel modifications. The software is designed to integrate with the Axima range of Maldi mass spectrometers.

Users can identify peptide sequences carrying one or more modifications using MS/MS data and 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 hypothetical modifications and screen the remaining MS/MS data for specific shifts in fragment masses, neutral losses and/or diagnostic ions. Such searches, performed based on a reduced database of protein sequences, are quick and thorough.

Users can import amino acid sequences with a copy/paste function or use the proteins derived from the initial Mascot search results, allowing searches for PTMs whether or not the protein being used is known.