Discovering Undetected Peptide Modifications

Shimadzu Scientific Instruments introduced PTM Finder™ software, which 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 toward 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.