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Hi, I wanted to use the 'addIdentificationData' to combine the mzID file data with the mzML data stored as msexp following the vignette's example. However, errors showed up and I could not perform thi…
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### Describe the question or discussion
Hi,
Is there a small example file using the PSI-MS ontology? I'm interested in how the `binary data array` class is populated, specifically for `m/z array…
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As a follow-up to #1635 and with some wisdom from Nico given in related issue #1636, there are several conflicts between the license labels and license URLs. Most of these are due to the lack of speci…
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Hi,
First of all, thanks a lot for this great library!
I recently found that pyteomics can't open mzId files created using [PeptideShaker](https://github.com/compomics/peptide-shaker). Iterating…
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Hello,
I have been trying to use searchgui to search previous data and hunting for new modifications that possibly hidden in those spectrum. I was using a GUI of version 4.1.0 for Windows. The erro…
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**Describe the question or problem**
I'm unsure if this is a bug or if I just need help. I am unable to convert the mzid files generated by MS-GF+ into pepXML files using idconvert.
**Details**
R…
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We are lacking this for ms, and it looks like the others use the old style sourceforge URLs
cc @germa @ontoden
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This replaces https://github.com/OBOFoundry/OBOFoundry.github.io/issues/257#issuecomment-264242016
I started working through the list; consolidated with @weasteam's list
* [x] xl.owl - now xlmo…
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Hello,
I am trying to generate the mzId file from the psdb project file using the following command
java -cp PeptideShaker-2.0.0.jar eu.isas.peptideshaker.cmd.MzidCLI -in FULLPATH/FILE.psdb -con…
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Currently, I do not see an official strategy on the OBO website that describes under which conditions an ontology, once accepted, can be removed again from the OBO foundry active ontology list, i.e. `…