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### Describe the question or discussion
I just came across a problem in my parser, as basically all PSM scores from search engines are defines as "is_a: MS:1001143 ! PSM-level search engine specific …
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Laurent, do you know what governs the choice of number for the acquisitionNum in the mzR header()?
As some of the native ID formats contains multiple integer values this is important to ensure correc…
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I would like to import the results obtained with Sage into the Trans Proteomic Pipeline (TPP). I want to create a spectral library from the results but I would need the Sage output as a pepXML file. W…
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This is a very minor but:
right now you export the time of the `` in mzid with the CVParam "retention time" (MS:1000894). The mzid-documentation recommends the usage of "scan start time" (MS:1000016)…
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in the definition of SearchModification on p.65 of the spec it says "MAY supply a *child* term of MS:1001471 (peptide modification details) only once".
Is that correct? E.g. a fragment may have mult…
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I was thinking that I would be able to import the results into IDpicker and export them as a MzidentML. I spoke to David T but he said it wasn't implemented, yet i found mention of it in a command lin…
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While trying to compile for a .mzid file ([output.mzid.zip](https://github.com/user-attachments/files/16161788/output.mzid.zip)), the NullPointerException below occurs. Apparently because the "start" …
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Hi,
xpath in the pyteomics mzIdentML reader is behaving differently for me from other xpath implementations?
I made a small example project to compare xpath behaviour from the pyteomics mzIdent…
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in Section 6.56, ProteinDetectionHypothesis (pg. 59) of mzIdentml 1.2.0 spec, under example CV params, it says:
> MAY supply a *child* term of MS:1001060 (quality estimation method details) one or …
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Hi,
section 6.83 of the mzIdentML 1.2.0 spec (pg.81) defines Threshold as:
> Depending on context:
1: The threshold(s) applied to determine that a result is significant. If multiple terms are use…