MSBooster shows an error for non-specific HLA peptidomics - timsTOF data

[mshahbazy]

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]

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

Thanks,

Fengchao

[yangkl96]

Hi Moh,

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

Thanks,
Kevin

[mshahbazy]

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 <#1616 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALLIZTMAL5RQ4GG3EAXFQG3ZGHNAVAVCNFSM6AAAAABI52APL6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJVGE2TMMZUGQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[yangkl96]

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]

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 <#1616 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALLIZTPLVDHYJIU3MMP6RDLZGNOPFAVCNFSM6AAAAABI52APL6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJWGE2TKMRUHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[yangkl96]

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]

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.