Analyzing Metaproteomic Data

[Aarthie Senathirajah]

Hi I'm currently trying to analyze the raw files from this metaproteomic dataset of the human gut microbiome. Which uses maxquant usually but i would like to use Comet. 

Firstly I am getting this error when trying to convert the raw file into mzml 

processing file: c:/TPP/data/TMT_Microbiome\Xu_20210512_IRIstudy_Concentration_TMT_Plate1_D.raw [Reader_Thermo::fillInMetadata] unable to parse instrument model; please report this error to the ProteoWizard developers with this information: model(Orbitrap Exploris 480) name(Orbitrap Exploris Slot #162); if want to convert the file anyway, use the ignoreUnknownInstrumentError flag

Which I'm not sure how to solve.. Any help would be great! 

[Luis Mendoza]

Hello,

The version of msconvert that is shipped with TPP is a couple of years old and does not know about that instrument.  You have three options to convert your files:

1. Download and install a newer version of ProteoWizard, run the conversion, and use that mzML file in Comet.  This is likely the simplest and most expedient.

2. Use the command-line to convert the file, using the --ignoreUnknownInstrumentError flag, for example:

  msconvert.exe --ignoreUnknownInstrumentError c:\TPP\data\TMT_Microbiome\Xu_20210512_IRIstudy_Concentration_TMT_Plate1_D.raw

3. We will be releasing a new version of TPP later this week.  If you are able to wait, then just update to the new version, which includes a more recent version of msconvert.   This is recommended as long as you can wait a few days to process your data.

Hope this helps,

--Luis

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/ed16c06b-a6c5-4f68-ac69-d96c5b95092fn%40googlegroups.com.