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PRIDE-Archive / xi-mzidentml-converter

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update crosslinking submission guidelines #47

Closed colin-combe closed 5 months ago

colin-combe commented 5 months ago

from last meeting, the page at https://www.ebi.ac.uk/pride/markdownpage/crosslinking needed some updates (in bold, 4 things, 2 re. escaping angled brackets):

  1. The accession attribute of target elements MUST be a valid uniprot accession, if it is a natural protein that has an accession number. That is, the value of the accession attribute for elements should match the regular expression: [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z]0-9{1,2}
  2. Every <DBSequence> element that describes a target protein MUST include the protein sequence in a <Seq> subelement. Limitations of Support
    • Information in mzIdentML files on scores and the passing of thresholds at higher levels of consolidation (unique peptide; crosslink level; PPI) are not processed by https://github.com/PRIDE-Archive/xi-mzidentml-converter, only the PSM level scores/threshold passes.
    • Doesn’t read linked FASTA files, hence item (6) above.
    • Doesn’t support the “combined spectra file type” from mzIdentML 1.2.0
ypriverol commented 5 months ago

Solved in PR https://github.com/PRIDE-Archive/pride-web/pull/342