Everything looks fine but Philosopher reports "No PSM was found in data set."

[Golden-proteogenomics]

Hello,

Thank you for your support and help with the MSFragger user. I have completed several data search work, but there is still a problem that is described as follow： “INFO[12:45:11] Executing Filter v1.5.1
INFO[12:45:11] Processing peptide identification files
FATA[12:45:47] No PSM was found in data set.
Process 'ReportFilter' finished, exit code: 1

Process returned non-zero exit code, stopping” log_2019-10-12_16-05-43.txt

Attachment is the log file for this running and . The software version I use are MSFragger-20190628.jar and the FragPipe v9.4.

[anesvi]

I think you should upgrade to the latest versions of the tools and rerun before we can help

There were many bug fixes

Sent from my iPhone

On Oct 12, 2019, at 4:10 AM, Golden-proteogenomics notifications@github.com wrote:

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Hello,

Thank you for your support and help with the MSFragger user. I have completed several data search work, but there is still a problem that is described as follow： “INFO[12:45:11] Executing Filter v1.5.1 INFO[12:45:11] Processing peptide identification files FATA[12:45:47] No PSM was found in data set. Process 'ReportFilter' finished, exit code: 1

Process returned non-zero exit code, stopping” log_2019-10-12_16-05-43.txthttps://github.com/Nesvilab/MSFragger/files/3720355/log_2019-10-12_16-05-43.txt

Attachment is the log file for this running and . The software version I use are MSFragger-20190628.jar and the FragPipe v9.4.

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[prvst]

Try the following MSFragger parameters using the exact syntax (i.e. use gluc, not GluC), and run again.

search_enzyme_name = gluc
search_enzyme_cutafter = DE
search_enzyme_butnotafter = P

[fcyu]

It was due to one or more interact-*.pep.xml having no PSM. Has been fixed.