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Automated Peptide Mass Fingerprint (PMF) file submission

Automated Peptide Mass Fingerprint (PMF) file submission. Adam Cornish. Mass Spectrometry. Matrix Assisted Laser Desorption Ionization with tandem time of flight MALDI-TOF/TOF Spectra produced PMF produced. Mascot. Probability-based search algorithm Searches databases NCBInr SwissProt

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Automated Peptide Mass Fingerprint (PMF) file submission

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  1. Automated Peptide Mass Fingerprint (PMF) file submission Adam Cornish

  2. Mass Spectrometry • Matrix Assisted Laser Desorption Ionization with tandem time of flight • MALDI-TOF/TOF • Spectra produced • PMF produced

  3. Mascot • Probability-based search algorithm • Searches databases • NCBInr • SwissProt • MSDB - Proteomics Department at the Hammersmith Campus of Imperial College London • ABRF_PRG – Association of Biomolecular Research Facilities: Protein Research Group

  4. Submission Script • Utilizes multiple modules: • Cwd • Used to get the current directory • HTTP::Request::Common qw(POST) • Used to POST information to the site • LWP::UserAgent • Facilitates submission • LWP::Simple • Requests information from the site • LWP::ConnCache • Keeps the connection open to speed up submission

  5. Structure • Grabs the PMF file • Submits it to Mascot • Waits for the result • Parses the returned data • Creates an easy to analyze HTML file

  6. Example Output

  7. Future Work • Implementation of ithreads • Allows for parallel submission of files • Ability to natively sort the data based on the columns • e.g. sort based on Score

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