Comet V2023.01 does not work with mzML files converted from Thermo raw files.

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June Wang

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Mar 20, 2023, 11:47:34 PM3/20/23
to Comet ms/ms db search support
Hello everyone,

On the newest version of Comet, it fails to load mzML files converted from Thermo raw files 
I got this error.  Load spectra:No index list offset found. File will not be read.ERROR: Failure reading input file XXX.mzML.
However, there is no problem in the Comet V202101 I have used before. I have no idea why I got this error in the Comet V2023.01. Is there anyone who have the same problem? Thanks in advance.

Best,
June


June Wang

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Mar 20, 2023, 11:58:57 PM3/20/23
to Comet ms/ms db search support
I would add that I use the Linux version of Comet.

Jimmy Eng

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Mar 21, 2023, 1:04:57 PM3/21/23
to Comet ms/ms db search support
Hi June.

Thanks for reporting this issue and yes, I can replicate what you observe.  In Comet v2019.01.4, I added support to Comet's version of the MSToolkit file parsing library to read mzML and mzXML files without scan indexes.  This functionality was present thru Comet v2022.01.1.  However in Comet v2022.01.2, I updated to the latest MSToolkit code and unfortunately my local changes to MSToolkit were lost which results in the behavior you're seeing.  I will add that functionality back with the next release and submit the code changes to the MSToolkit dev to incorporate into his repository (which I apparently haven't done).  

Until I can address this, you'll have to use mzML files with the scan index present for Comet 2022.01.2 thru 2023.01.1 to be able to search them.  These are your current options if you want to use the latest Comet:
  • Use msconvert to generate the mzML from the raw file again, making sure the "Write index" checkbox is checked in MSConvertGUI which it should be checked by default.  
  • Or you can take your existing mzML file and add the scan index to it.  I can't seem to get msconvert to take in an mzML file and successfully write out a new mzML file but it works with mzML in to mzXML out.  Alternately I can send you a binary of a add-scan-index tool from the TPP which will add the scan index to any mzML/mzXML file.  If you would like this, let me know and I'll send you a download link to the linux binary.
Jimmy 

Jimmy Eng

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Mar 30, 2023, 4:56:23 PM3/30/23
to Comet ms/ms db search support
June, this issue is addressed in the 2023.01.2 release available now.
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