Error generation while converting raw files

Skip to first unread message

giangiacomo beretta

Jan 19, 2021, 11:10:14 AMJan 19
to spctools-discuss
Hi, when I try to convert raw files, the conversion tool stops immediately reporting the following error:

Reader_Thermo::fillInMetadata] unable to parse instrument model; please report this error to the ProteoWizard developers with this information: model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to convert the file anyway, use the ignoreUnknownInstrumentError flag 

It appears that the system is not recognizing the instrument model that produced the raw files. Is there any option to overcome this issue?

Actually I have converted the same files with ProteoWizard without troubles.

Thanks in advance!


David Shteynberg

Jan 19, 2021, 2:53:57 PMJan 19
to spctools-discuss
Dear Giangiacomo,

Thanks for trying the TPP and reporting the problem.  TPP uses the proteowizard's msconvert tools for this step.  You can remedy the problem by either upgrading to a newer version of proteowizard's msconvert tool or use  --ignoreUnknownInstrumentError option with your current version.  On the generate mzML page you can specify this option in the    "Enter additional options to pass directly to the command-line" text box, just enter the text  --ignoreUnknownInstrumentError 

Hope it works!


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
To view this discussion on the web visit

giangiacomo beretta

Jan 20, 2021, 4:30:48 AMJan 20
to spctools-discuss
Hi David! It works nicely, thank you ! 

Now I am experiencing another issue of mine :)

I run ProptideProphet on the XML fiel generated by XTandem. I need this file presuming that PP will add probabilities to the identified peptides as this is requested by SpectraST to generate the corresponding spectral library (this is actually my final goal).

However, when I try to do it, SpectraST reports: WARNING -- PEPXML IMPORT: Importing a .pep.xml file with no probabilities. PeptideProphet probably needs to be run on .pep.xml first.

Maybe probabilities are used for data processing but not appendend to the XML output file?

Thanks a lot in advance!


David Shteynberg

Jan 20, 2021, 7:24:47 PMJan 20
to spctools-discuss
I am not sure I know a tool called "ProptideProphet" ;) Perhaps you tried to run PeptideProphet but it generated no results for you?  When you run "Analyze Peptides" in the TPP interface, it should create a file called interact.pep.xml by default, that will contain probabilities among other information.  Did you run "Analyzed Peptides"?  Were there any messages reported by the analysis?

giangiacomo beretta

Jan 21, 2021, 3:09:22 AMJan 21
to spctools-discuss
Hi David, sorry for the mistypos!

Yes I run PeptideProphet under Analyze Peptides, and no relevant messages were generated :)

However, I forgot to mention that the problem is related to interact.pep.xml processing in SpectraST in its command line version (independent from TPP).

I am sorry, I did not notice that TPP includes an option for spectral library generation that works perfectly fine, and this is what I needed..! 

Just last question, is there any tool for visualisation/inpection of spectra in splib libraries ?

Lots of thanks,


Luis Mendoza

Jan 24, 2021, 1:26:36 PMJan 24
Hello Giangiacomo,

You can use the Lib2html tool to convert an splib into a webpage with clickable links to library spectra.  You can launch this tool from SpectraST Tools -> Convert Libraries to HTML. 

Hope this helps,

Reply all
Reply to author
0 new messages