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Hello,
I tried to install and run ms2rescore together with percolator on a peptideshaker output.
I used conda environment and installed percolator using conda and ms2rescore using pip.
When I cal…
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Hello,
I'm trying to run MS2Rescore on the mzid and mgf files exported from PEAKS (using the export option for third party PRIDE / scaffold). However, I got the error below. Really appreciate your …
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My operating system: Ubuntu 20.04
My MZmine version: MzMine 3.0.11-beta
Dear developers,
while testing MzMine 3, I encountered a bug while trying to run the ADAP chromatogram builder algorithm on…
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Currently, crux percolator produces pepxml by parsing the Percolator text files and then calling psm-convert on them. Instead, we should use Percolator's built-in support for pepxml output. In the p…
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Hi,
i think there's a mistake in the definition of SpectraDataType in the .xsd file -
https://github.com/HUPO-PSI/mzIdentML/blob/master/schema/mzIdentML1.2.0.xsd#L1094-L1105
It should also cont…
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Similarly to parsing of search engine scores, we can search for all cvParams under [MS:1002354](https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1…
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Dear IonQuant developers,
we recently came about the task to quantify old search results on the basis of precursor intensities. As the database search was quite exhaustive and took several weeks in…
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Hey,
I stumbled across some issues when using the mzid files generated by Comet (2023.01 rev. 2 (7c9150d)). Therefore I tried to validate them using the PSI validator and got a lot of `cvc-identity-c…
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I experience an error when trying to open a specific mzid file.
https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/02/PXD039808/
File: Brain_Regions_LFQ.mzid
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I am trying to convert msgf+ output to `.pin` prior to using percolator.
I ran the following command: `msgf2pin -o TEAB.orthoalltime.pin -v 5 msgf.target.mzid msgf.decoy.mzid`. However, this throw…