Proteomatic scripts (0.5.24)

• Miscellaneous:
  • Sets:
    • Difference
    • Exclusion
    • Intersection
    • Union
  • Annotate CSV rows
  • Check MD5 sums
  • Create archive
  • Duplicate CSV column
  • Extract CSV column
  • Highlight items
  • Join CSV tables
  • Merge CSV files
  • Split CSV file
  • Swap CSV columns
• Proteomics:
  • Comparison:
    • Compare OMSSA PSM lists
    • Compare PSM and modifications
    • Compare SEQUEST CSV results
  • Crosslinking:
    • Calculate fragment masses
    • Convert xQuest XML to CSV
    • Remove PSM scans from xQuest results
  • Identification:
    • BLAST:
      • Run BLAST
      • Write BLAST report
    • GPF:
      • Compile GPF index
      • Extract GPF peptides
      • Run GPF
    • OMSSA:
      • 1. Run:
        • Run OMSSA
      • 2. Filter PSM:
        • Analyze protein groups
        • Apply protein groups
        • Crop PSM list by hit distinctiveness
        • Determine protein groups
        • Filter by FDR
        • Filter by mass accuracy
        • Filter by score threshold
        • Sanitize PSM
      • 3. Report:
        • Extract identifications
        • Write HTML report
      • Miscellaneous:
        • Analyze PSM
        • Convert OMSSA CSV to mzIdentML
        • Convert PSM lists to AMS
        • PSM score histogram
    • PEAKS:
      • Convert PEAKS results to CSV
      • Patchy peptides
  • Localization:
    • Localize via spectral counts
  • Miscellaneous:
    • Apply protein groups to protein list
    • Calculate peptide mass
    • Check modification masses
    • Determine GFF feature lengths
    • Extract OMSSA results
    • Extract SEQUEST results
    • Merge SEQUEST CSV results
    • Simulate isotope envelope
    • Transpose DNA
    • Tryptic protein digestion
    • Y ions mass calculator
  • Protein databases:
    • Check FASTA databases
    • Chop FASTA databases
    • Convert FASTA to BLAST database
    • Create FASTA database
    • Create six frame translation
    • Create target/decoy database
    • Match peptides to FASTA databases
    • Merge FASTA databases
    • Prefix FASTA database
    • Unwrap FASTA database
  • Quantitation:
    • qTrace:
      • 1. Run:
        • Run qTrace
      • 2. Filter:
        • Add protein groups information
        • Add protein information
        • Compare ratios
        • Crop XHTML report
        • Determine ratios
        • Normalize protein levels
        • Pick most abundant bands
        • Require MS2 identifications
        • Require both sister peptides
  • Spectra:
    • Check spectra
    • Convert mzML to MGF
    • Match peaks
    • Merge MGF files
    • RAW to mzML
    • Strip mzML files