CometAdapter
and I have some issues. When I search a light file with some variable modifications it works fine. But when I use a quite big file (for instance a 2.2GB mzML) and more that three variable modifications the search takes ages and does not finish. I tried the same search without using the CometAdapter
, I mean, by running the comet.linux.exe
and the search ends in 1h aprox. Do you have any idea on why the CometAdapter is taking so long? I can upload all the files in a Dropbox and the command line instructions I'm running if you want to debug it. Thanks!
Hi @jpfeuffer, I would like to ask some questions about the expected results of epifany. So both figure (please see pdf below) shows a component, the top row are peptides with their qvalue and pep, the bottom row is are the protein with their qvalue. The figure with the higher qvalue for protein is the one I ran with more decoy
I was wondering if it is supposed to happen that when I added more decoy, the qvalue increases.
I was also wondering that if all protein are supposed to be similar in qvalue?
Thank you
Hi, I am trying to run OpenSWATH on timsTOF DIA data. I converted DIA files with the latest MSConvert. I am using OpenMS docker image ghcr.io/openms/openms-executables:2.8.0
. When I ran OpenSWATH the first time, there was an error error message: Requested ion mobility extraction but no ion mobility array found.
. The problem seems to be due to header of IM array.
Currently, MSConvert writes array header as
<cvParam cvRef="MS" accession="MS:1003006" name="mean inverse reduced ion mobility array" value="" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
I changed the text to
<cvParam cvRef="MS" accession="MS:1003006" name="non-standard data array" value="Ion Mobility" unitCvRef="MS" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
so that value is Ion Mobility
as OpenMS parser looks for this keyword
https://github.com/OpenMS/OpenMS/blob/c2555c3278de34a5f261df9a0915f42a8bfada3c/src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h#L269
However, I am still getting the same error.
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FATAL: uncaught exception!
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last entry in the exception handler:
exception of type IllegalArgument occurred in line 332, function void OpenMS::ChromatogramExtractorAlgorithm::extractChromatograms(OpenSwath::SpectrumAccessPtr, std::vector<boost::shared_ptr<OpenSwath::OSChromatogram> >&, const std::vector<OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates>&, double, bool, double, const OpenMS::String&) of /OpenMS/src/openms/source/ANALYSIS/OPENSWATH/ChromatogramExtractorAlgorithm.cpp
error message: Requested ion mobility extraction but no ion mobility array found.
---------------------------------------------------
Does anyone what could be going wrong?
convertTDFtoMzML
, it doesn't include ion-mobility array in exported mzML. MSConvert outputs ion mobility array but with a different header "mean inverse reduced ion mobility array".