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Hi,
Is it possible to export PeptideShaker PSM scoring in a pepXML format and also to export the protein scores as something similar to the prot.xml output like with PeptideProphet and ProteinProphet?…
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(Collect change requests for the CV here.)
[Term]
id: PI:00216
name: sequest:PeptideRank
def: "The SEQUEST result 'Rank' in out file (peptide)." [ref:ref]
is_a: PI:00153 ! search engine specific …
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This post concerns the identification of the search database in analysisXML.
Search sequence databases will include:
* complete public databases
* private databases
* custom built sequence datab…
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Drop any issues with instance docs in this issue
```
Original issue reported on code.google.com by `andrewro...@googlemail.com` on 16 Oct 2008 at 3:57
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Hello,
the packaged linux64 Myrimatch software generates a segmentation fault upon execution:
> /home/jflucier/apps/compomics/SearchGUI-2.0.5/resources/MyriMatch/linux/linux_64bit/myrimatch
> Segmen…
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> What steps will reproduce the problem?
SearchGUI exports the Myrimatch output results in the mzIdentML format by
default.
> What is the expected output? What do you see instead?
Myrimatch also…
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ProteinQuantifier writes in its output not the complete protein name. That makes it for biologists difficult to interpret the results (unlike in other software packages).
For example, in the fasta da…
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> What steps will reproduce the problem?
We tried to use peptide shaker to load these files:
http://mingwangbeta.ucsd.edu/public/jakob/20150529_Fuji_MR_JH_Biofilm00H.mgf
http://mingwangbeta.ucsd…
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Hey Marc and Harald,
i somehow fail to load some data into PeptideShaker (more details below). tried PS 1.7.5 and 1.7.4, both the same result. It was a rather open search of a QC sample, so with vari…
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What steps will reproduce the problem?
1. java -cp mzTabCLI.jar uk.ac.ebi.pride.jmztab.MZTabCommandLine -convert
inFile=/some/absolute/path/input.mzid format=MZIDENTML -outFile
/some/absolute/pa…