crash FragPipe v19

[Angrist75]

I think Fragpipe cannot handle DIAs with windows, which are too wide. I am trying to repeat on my EvosepOne-FAIMS-Exploris 480 system the work of Erwin M. Schoof: "Enhancing single-cell proteomics through tailored Data-Independent Acquisition and micropillar array-based chromatography." Spectronaut 17, DIA-NN 1.8.2 beta 11 smoothly handle the files I generated with great agreement with the results of the paper mentioned earlier. In contrast, when I reprocess the files with FragPipe v19 using DIAspecLib_Quant the software closes unexpectedly without giving errors. If needed I can share the raws. Andrea

[fcyu]

I believe the data is from low resolution MS2. FragPipe might have slightly low sensitivity but it should not crash. Can you tell me the file name you used? I think I have all files from that publication downloaded.

Best,

Fengchao

[Angrist75]

sorry I misunderstood, the data are my own. they are not low resolution if you give me an address I will share them, or if there is any useful logs from FragPipe I can attach them in the next comment

[fcyu]

No worries. Here is the link to upload the files: https://www.dropbox.com/request/9wb5fgjearDLkFDLzNrN

You can also upload the log files starting with "log_".

Thanks,

Fengchao

[fcyu]

H @Angrist75 ,

I tried your data and FragPipe finished without any error. Please see my log file from log_2022-12-18_21-35-52.txt

BTW, one possible mistake is that the files are in raw format. To let DIA-NN read the file, you need to install Thermo MS File Reader as warned by FragPipe:

Best,

Fengchao

[Angrist75]

I'm afraid I discovered the problem and realized it was because of the settings of my Institute's antivirus software...Thanks for everything Andrea

[fcyu]

You are welcome.

Best,

Fengchao