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Dear Compomics-team,
I would very much like to **understand how the "confidence" metric in peptideShaker is calculated**. PeptideShaker's graphs and metrics make a lot of sense and the explanations a…
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I think the fix for #100 changed the validator from failing valid files to passing invalid files?
I think the validator is now passing files where there are 4 SpectrumIdentificationItems containin…
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Is there any tool which can be used to visualize the pepXML result of MSFragger?
Bo
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Hi @hbarsnes @CarlosHorro
the galaxy guy again :)
I just ran with peptideshaker into a similar problem as with searchgui. The program writes some data in the home directory, which again does n…
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@sureshhewabi One of the things we need to guarantee in the following implementations is that we return the Set of PTMs for all the identified peptides, not the ones defined for search parameters. Th…
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# Describe the problem
Hey! I generated my human fasta database by getting all the protein sequences from uniprot (~200 mb, ~500,000 sequences) + common contaminants. I then create a reverse decoy …
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# Describe the problem
Hello
I get the error message: " workspace not found" after finishing calculating spectral count. I saw an open issue about the same problem but fail to find the solution.
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@yaaminiv
Based on your .pynb post from when you did this, I should only be looking at proteins that have more than one peptide?
https://github.com/RobertsLab/project-oyster-oa/blob/master…
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# Describe the problem
* **I'm submitting a:**
- [x] problem running the software
- [x] bug report
- [ ] feature request
- [ ] question
* **My MSFragger use case:**
- [x] _Closed_…
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Same as: https://github.com/prvst/philosopher/issues/23
# Describe the problem
* **I'm submitting a:**
- [x] problem running the software
- [x] bug report
- [ ] feature request
- [ ]…