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Hi I am trying to combine peptide identification results from Mascot and MaxQuant. The consensusID paper claims that it supports all search engines. But from the online documentation, it seems that Ma…
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Trying to run OpenPepXLLF in openms 2.5.0. I am getting the following error when I do a crosslink search. I am running OpenMS 2.5.0 from the released binaries installed in a docker image based on U…
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The more I work with MSFragger, the more I think I can appreciate the quality of the results obtained. Being a long time MaxQuant user though, I am missing the Viewer functionality that serves as a co…
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## Issue:
mzLib takes 30 mins to build in AppVeyor
## Possible solution:
Split mzLib down the middle into two different namespaces:
1. **mzLib.Fundamentals**: Chemistry, Chromatography, MassS…
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Is there a way to output the PSM info/features used by the NNClassifier? Perhaps in Percolator's `.pin` format or `pepXML`/`mzIdentML`?
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* imports:
* imports to obo format files will not work in OWL toolchains
* always use official OBO PURLs in imports. For example, you are using PATO, see products here: http://obofoundry.…
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Hey all!
I am trying to process all ontologies in the OBO foundry at the moment, and I have a problem with xlmod because no owl version is provided. If I helped you to provide one, would you mind a…
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Collection of issues that I discovered while working on the SAX parser for mzIdentML (mzid):
- In mzid, the "SpectrumIdentification" element can contain multiple "SearchDatabase" elements, to represen…
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The idXML schema contains an attribute "spectrum_reference" of "PeptideIdentification" elements, that can store the "Integer reference number of the identified spectrum (or feature)". This should be s…
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Hi,
we would like to use the pyteomics mzident parser for our metaproteomic software Prophane. We require the following infomation about protein groups (“ProteinAmbigousGroup”):
* the protein acces…