(patent pending) University of Missouri Kansas City - School of Biological Sciences - 2005
Use this tool to impose statistically and biologically likely amino acid substitutions ("virtual polymorphism") on your amino acid sequence entry and make a database to re-interrogate your MS or MS/MS data. Simply paste single letter coded amino acid sequence of the protein you want to generate polymorphism in, and click the "VIRTMORPH" button. The database generator will produce a compiled list of peptides containing single substitutions, surrounded by native sequence, derived from your input sequence, encompassing two trypsin cleavable sites in both directions. Database output is in FASTA format, for compatibility with your\ protein identification program, (such as Mascot © Matrix Science, LTD, Sequest© Thermo-Electron, CO., etc.) Copy and paste the resulting database into your notepad or other text editor, save the file as "all files" or other text only format with the extension ".fasta". Search the new database for matches using your protein identification software, and validate matches as you would any other database match.
You may need to have a different file extension in order to be recognized as a fasta database, depending on the search program that you will use to search the new database. Consult your search program for instructions on importing and searching fasta formatted databases.