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smith-chem-wisc / FlashLFQ

Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics
GNU Lesser General Public License v3.0
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mzML quant error : Index was outside the bounds of the array. #132

Open patrick-willems opened 1 year ago

patrick-willems commented 1 year ago

Dear FlashLFQ team,

I generated a custom TSV file, according the guidelines, for FlashLFQ on mzML files, however the it keeps giving me the same error in command line and GUI:

ErrorReport.txt

My input file looks like this:

File Name Scan Retention Time Precursor Charge Base Sequence Full Sequence Peptide Monoisotopic Mass Protein Accession T03797_AurEl3_trap1_CMB-1380_1_GC1_1_4093.mzML 15.97326183 2 KTDKHVQKY KTDKHVQKY 1145.61931 sp|Q15911|ZFHX3_HUMAN T03797_AurEl3_trap1_CMB-1380_1_GC1_1_4093.mzML 16.21448326 2 DHGHHESRAY DHGHHESRAY 1207.51188 sp|P05187|PPB1_HUMAN;sp|P10696|PPBN_HUMAN T03797_AurEl3_trap1_CMB-1380_1_GC1_1_4093.mzML 16.2346611 2 DHGHHESRAY DHGHHESRAY 1207.51188 sp|P05187|PPB1_HUMAN;sp|P10696|PPBN_HUMAN T03797_AurEl3_trap1_CMB-1380_1_GC1_1_4093.mzML 16.45538521 2 AHHKFSETH AHHKFSETH 1092.51009 sp|O00767|SCD_HUMAN T03797_AurEl3_trap1_CMB-1380_1_GC1_1_4093.mzML 17.13763428 2 HHKGDKTSF HHKGDKTSF 1055.51484 sp|Q6PJ21|SPSB3_HUMAN

Maybe there is still a stupid mistake somewhere in my input or something?

Thanks!

Alexander-Sol commented 1 year ago

Hi Patrick.

Based on the error log you provided, it seems that the .mzml file is the problem. Could you provide some more details about the how the mzml file was generated and/or send the file?

patrick-willems commented 1 year ago

Thanks for the fast reply. It is a mzML that is automatically generated by MSFragger during a timsTOF .d search. I saw that there was some support for Bruker data, perhaps that could be an option?

I could share the mzML in a PM if you like.

Thanks

Alexander-Sol commented 1 year ago

We're still experiencing some problems reading in .d files, so no guarantees.

If you could share the .mzml (and the .d file as well, if possible) via PM, I'll try to find and fix the issue.

Alexander-Sol commented 1 year ago

You can reach me here: mm_support@chem.wisc.edu

patrick-willems commented 1 year ago

You can reach me here: mm_support@chem.wisc.edu

Ok thanks! Uploading now.

patrick-willems commented 1 year ago

Sorry to come back to this. Is there are any solution? I have also been trying to use the raw .d Bruker directories, but I get

"Error: No spectra files were found"

Although the .d files are named accordingly the File Name.

Thanks Patrick

Alexander-Sol commented 1 year ago

Thank you for your patience on this!

I took a look at the .mzML file you shared, and it appears that the file doesn't contain any MS1 scans. This would preclude analysis with FlashLFQ.

Does the .d file contain MS1 scans?

Thanks, Alex

patrick-willems commented 1 year ago

Thank you for the help! Sorry, I should have noticed this in the first place, I will try some other mzML conversion.

Alternatively, how can I make FlashLFQ read the .d file itself?

Thanks!