Data Analysis Tools

A collection of computational tools and links

Online calculators, viewers, and downloadable utilities developed or hosted by the UWPR for analyzing mass spectrometry data.

Online Tools and Calculators

• MS/MS fragmentation calculator
• Protein sequence digestion calculator
• Isotope distribution calculator
• Elemental mass calculator
• Peptide motif finder
• Lorikeet spectrum viewer
• Koina (Prosit, ms2pip, AlphaPeptDeep) spectrum prediction viewer
• Limelight: A web app to visualize and share MS/MS data and results

Additional Tools and Downloads

• RawMeat is a nice Thermo raw file diagnostic tool developed by the now-defunct Vast Scientific. RawMeat requires Thermo’s MSFileReader library to be installed. MSFileReader can be downloaded by creating an account with Thermo Fisher Scientific. Once registered, you will find the software under “Other Software Releases”.
• Zip file of contaminant protein sequences based on the GPM’s cRAP database. Updated 2022/06/21 to current UniProt sequences. Separated into bovine, human, yeast, chicken, E. coli, and others.