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ping @bernt-matthias
A Galaxy Australia user sent a report of MS Fragger Adapter failing with this stdout
```
Input file '/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar' coul…
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* link to support ticket: [#2023042860000704](https://otrsdict.ugent.be/otrs/index.pl?Action=AgentTicketZoom;TicketID=119018)
* website: https://github.com/Nesvilab/FragPipe
* installation docs: htt…
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**- Upload your log file**
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the…
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MSFragger now supports the "cut before amino acid" function since 3.4 (https://github.com/Nesvilab/MSFragger/issues/9), which is not supported by MSFraggerAdapter yet and it will be good to have this …
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Hello,
I am encountering an error where I get the message "'mv' is not recognized as an internal or external command, operable program or batch file" in the peptide prophet portion of my workflow. …
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the default peptide length in DIANN is 7-30.
Clearly, this is an overall suitable r…
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Dear Fragpipe team,
We are comparing identification and quantitation numbers in spectral data acquired in DIA mode from TimsTOF Ultra and Thermo Astral.
Samples are N-terminally enriched extract…
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Dear all,
I tried to install msfragger node for pd 3 following the instructions (https://www.nesvilab.org/PD-Nodes/) but unfortunately it doesn't appear as software in workflows . the version of PD i…
asogg updated
6 months ago
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We have been waiting for PD 3.0 compatibility for over a year but Thermo has gone ahead and released version 3.1 of their software in September.
Do you plan to release a PD 3.1 compatible MsFragger…
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I had some questions regarding training a new scoring model:
1. As I understand it, there's no direct way to specify fragment tolerance, as it it's automatically learned during the training phase, …