ProteoSAFe workflow - spectral library creation

Workflow to allow users to upload spectra and iteratively create a server-side searchable MGF spectral library.

An input metadata form is required with annotations to the spectra. This includes 19 fields specified in a tab separated format (tsv). Here is an example: chemstandards_meta.txt

MGF fields that need to be included:

  • SOURCE_FILE - name of uploaded file
  • SOURCE_SCAN - scan number of the extracted spectrum in the uploaded file
  • SOURCE_INDEX - index of the extracted spectrum in the uploaded file
  • SEQ - may not be an amino acid sequence, modified peptide sequences are represented as a "+number" or "-number" after the modified amino acid
  • NAME - Name of the peptide/compound (optional)
  • PROTEIN - Name of the protein the peptide comes from (optional)
  • MSLEVEL
  • ORGANISM**
  • MOLECULEMASS
    • Theoretical mass for the compound?
  • SMILES
    • "Not available" if unknown
  • INCHI
    • "Not available" if unknown
  • INCHIAUX
    • "Not available" if unknown
  • SPECTRUMQUALITY
    • 1-5 scale low - high
    • 0 - unknown
  • Fields that should be derived directly from the submitted spectrum file:
    • Peak lists between "BEGIN IONS" and "END IONS"
    • CHARGE - precursor charge
    • PRECURSOR - precursor M/Z
  • Fields that may be filled by user-defined protocol
    • ITOL** - Ion mass tolerance
    • ITOLU** - Ion mass tolerance units
    • TOL** - Precursor mass tolerance
    • TOLU** - Precursor mass tolerance units
    • SOURCE_INSTRUMENT**
  • System-added fields (Will be a tuple colon separated with the file name SUBMISSION_METADATA)
    • SUBMISSION_USER* - ProteoSAFe user name
    • SUBMISSION_ID* - ProteoSAFe task ID ( can be used for deletion )
    • SUBMISSION_DATE* - Date of ProteoSAFe submission

Possible additional fields (e.g., from MSP):

*Automatically populated by system
**Entered once and can be automatically set for subsequent uploads

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