FragPipe v22 + DIA-NN 1.9 - Failed to generate skyline document

[emhumphries]

Hi Fengchao,
I'm trying to set up a DIA_SpecLib_Quant proteomic workflow using the latest versions of FragPipe and DIA-NN. The run finishes with DIA-NN output files however, I keep getting a skyline error that I can't seem to shake. I've tried Skyline 23.1 and Skyline daily 23.1.1.520 with no luck. I know the workflow was designed for DIA-NN 1.8.2 beta 27 so is the new version of FragPipe currently incompatible with DIA-NN 1.9?
Regards,
Erin

log_2024-06-14_12-25-07.txt
[2024/06/13 17:36:39] Creating spectral library from files:
[2024/06/13 17:36:39] library.tsv.skyline.speclib
Process java.lang.ProcessBuilder@34f7cfd9 returned non zero value. Message:
[2024/06/13 17:36:40] Error: ERROR: unable to determine DIA-NN report filename for 'library.tsv.skyline.speclib': the TSV report is required to read speclib files and must be in the same directory as the speclib and share some leading characters (e.g. somedata-tsv.speclib and somedata-report.tsv)

[fcyu]

Thanks for the issue report. It seems that DIA-NN 1.9 changed the speclib file name?

[2024/06/13 17:36:39]	Creating spectral library from files:
[2024/06/13 17:36:39]	library.tsv.skyline.speclib
Process java.lang.ProcessBuilder@34f7cfd9 returned non zero value. Message:

[2024/06/13 17:36:40]	Error: ERROR: unable to determine DIA-NN report filename for 'library.tsv.skyline.speclib': the TSV report is required to read speclib files and must be in the same directory as the speclib and share some leading characters (e.g. somedata-tsv.speclib and somedata-report.tsv)

Could you share the E:\FragPipe-v22-test\proteome_anotherattempt\filelist_skyline.txt?

Thanks,

Fengchao

[emhumphries]

Thanks Fengchao for your rapid response. Here it is :) filelist_skyline.txt

[fcyu]

Thanks for the prompt reply.

It seems that FragPipe got a new speclib file name that we/Skyline don't expect: --import-search-file=E:\FragPipe-v22-test\proteome_anotherattempt\library.tsv.skyline.speclib. I will investigate tomorrow and get back to you ASAP.

Best,

Fengchao