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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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MSBooster shows an error for non-specific HLA peptidomics - timsTOF data #1616

Closed mshahbazy closed 3 months ago

mshahbazy commented 3 months ago

log_2024-06-06_18-51-57_Bjoren_AB_run1-25_06062024_test01.txt

Dear MSFragger team,

I encountered an error when trying to use FragPipe to search a timsTOF DDA dataset for immunopeptidomics, as follows:

Loading predicted spectra Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping Cancelling 91 remaining tasks

The log is attached. Would you please let me know how I can resolve the issue?

Thanks and regards, Moh

fcyu commented 3 months ago

@yangkl96 , can you take a look when you have time?

Thanks,

Fengchao

yangkl96 commented 3 months ago

Hi Moh,

Do you have any noncanonical amino acids in your protein sequences?

Thanks, Kevin

mshahbazy commented 3 months ago

Hi Kevin,

Thanks for your reply.

No, only canonical amino acids. I used the standard reviewed Uniprot proteome database.

Best, Moh

On Sat, 8 June 2024, 2:23 am yangkl96, @.***> wrote:

Hi Moh,

Do you have any noncanonical amino acids in your protein sequences?

Thanks, Kevin

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/1616#issuecomment-2155156344, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALLIZTMAL5RQ4GG3EAXFQG3ZGHNAVAVCNFSM6AAAAABI52APL6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJVGE2TMMZUGQ . You are receiving this because you authored the thread.Message ID: @.***>

yangkl96 commented 3 months ago

Could you please share one pin file and the file at D:\MSFragger_Results\Asolina\Bjoren_AB_run1-25_06062024_test01\spectraRT_full.tsv? You can deposit them here

mshahbazy commented 3 months ago

Sure, I uploaded the requested files. I only uploaded one pin file; please let me know if you need any further items. Thanks for your help.

Best, Moh

On Sun, 9 Jun 2024 at 05:54, yangkl96 @.***> wrote:

Could you please share one pin file and the file at D:\MSFragger_Results\Asolina\Bjoren_AB_run1-25_06062024_test01\spectraRT_full.tsv? You can deposit them here https://www.dropbox.com/request/P3ZWJpvfjWVby357hjWK

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/1616#issuecomment-2156155249, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALLIZTPLVDHYJIU3MMP6RDLZGNOPFAVCNFSM6AAAAABI52APL6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJWGE2TKMRUHE . You are receiving this because you authored the thread.Message ID: @.***>

yangkl96 commented 3 months ago

Thanks for sharing those. Msfragger 4.1 made some changes incompatible with the old msbooster. Could you please upgrade to the newest fragpipe release?

mshahbazy commented 3 months ago

OK, I tried running it with MSFragger v4.0, and it seems to be compatible now with the version of MSBosster that I am using in FragPipe v21.1. Thanks for your help.