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### Describe the new term or terms you would like to add.
Hi Joshua (@mobiusklein),
assuming I've correctly understood how the new MS:1003372 and MS:1003373 terms are meant to work,
and bearing …
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Hi Julian,
I am wondering if PIA can adapt imaging MS data like imzML. This format is used for new bruker MALDI-TOF and it seems there is no way to transfer the imzML file into other format that ca…
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[small.mzid.gz](https://github.com/percolator/percolator/files/10268548/small.mzid.gz)
When trying to run msgf2pin, I get a memory error, as follows. (I've attached a zipped and renamed version of …
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### Describe the question or discussion
minor mistake made by me for term MS:1003333
```
[Term]
id: MS:1003333
name: regular expression for encoding identifications based on multiple spectra.
de…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/SimoneTiberi/IsoBayes
Confirm the following by ed…
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Hi Peptide-Shaker team,
I am getting the following error:
Cannot invoke "com.compomics.util.pride.CvTerm.getOntology()" because "cvTerm" is null.`
I recently got back to this tool and I am re…
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I use the peptide-shaker with command line to analyze mzid files that are generated by MS Amanda2.0 standalone version. I place all identification files, spectrum files, and fasta file in the same dir…
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### Describe the question or discussion
Hi,
@lutzfischer and I had a go at updating/fixing the regex syntax for MS:1002505 (regular expression for modification localization scoring).
We propose…
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When reading in multiple search files to crux percolator, there may be a problem of PSMs have the same scan number but from different search files. We should handle this by tracking which file the PS…
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Greetings!
In your manual you are writing "XMAS currently supports evidence files generated with the search engines XlinkX for Proteome
Discoverer (PD), Xi, and pLink, in csv, tsv, txt, and xlsx f…