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Hi,
TMT-Integrator keeps crashing with the following error (I've also uploaded the log file):
_Exception in thread "main" java.lang.NumberFormatException: empty String
at java.base/jdk.interna…
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I utilized MSFragger-PD for performing an open search on a set of 12 files, totaling 23 GB in size. Remarkably, the close search of these identical files using SEQUESTA completes within approximately …
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**Describe the bug**
I'm trying to run the philosopher TMT analysis pipeline on a 11plex LC-MS/MS data with the following setting in the philosopher.yml file.
-----------------------------------…
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Hi,
I'm trying to label the TMT channels to the mzML files with the command labelquant, and get the following errors for v3.3.12 and v4.4.0
~/Programs/philosopher_v3.3.12/philosopher labelquant …
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The error information is as following:
tail -n 20 philosopher.PipelineModel.log
time="08:25:44" level=info msg="Restoring peptide results"
time="08:27:42" level=info msg="collecting data from ind…
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Hello,
I have been using the isobaric quant tool in FragPipe 17 and now version 18, and I wanted to report an unexpected result when using different "ratio to abundance" conversion options. I have r…
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In the `labelquant` help doc, there are
```
Usage:
philosopher labelquant [flags]
Flags:
--annot string annotation file with custom names for the TMT channels
--bestpsm …
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## Bug report
(Please follow this template replacing the text between parentheses with the requested information)
### Expected behavior and actual behavior
The tests for docker fail without …
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I'm using philosopher.yml for TMT quantification. I noticed that even though I don't apply any normalisation or correction the TMT abundances on peptide level differ from the abundances on protein lev…