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- Describe the issue or question:
Hello,
Thank you for offering wonderful software! We were doing a TMT run and it seems to have stopped with 1 remaining task, with a message of can't find the refer…
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I am running Philosopher on a set of TMT10-MS3 proteomic samples from a single experiment. I have augmented my human proteome reference FASTA with custom sequences (I generated decoys for all sequence…
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Hello,
We were testing a coupling of methods on an Exploris. For some of the output files I get problems running the philosopher pipeline (in particular an error with Protein Prophet which does not…
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### Description of bug
I have been running Philosopher 4.0.0 since August, and I was unable to reproduce a run that I had generated about a month ago due to
1. Philosopher not reading in the sp…
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When I am running Philosopher (version 3.4.13) on a set of TMT10-MS3 samples, I am reaching the "label-free quantification step" and experiencing the following error message:
```
...
time="10:23:…
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Hi NesviLab (and other proteomics enthusiasts),
Thanks for your efforts in software development. Earlier, FragPipe workflow has performed really great with my label free data analysis!
Now, I'm…
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There is no TMT6 workflow option in the drop down menu.
Is it ok to select TMT10 in the drop down workflow option menu, then in the Quant (Isobaric) tab select TMT-6 in the drop down menu for Label t…
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@hayse1 thanks for pipeline [wiki](https://github.com/Nesvilab/philosopher/wiki/Pipeline-mode-for-TMT-analysis)
Philosopher 3.4.13 installed Ubuntu 18.04 (via *.deb file)
Following instructions …
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- quant isobaric fail because no reporter ions were detected. the parameters are the default for TMT10-MS3 workflow . I don't know what and if my parameters are wrong.
- log file
[log_2021-09…
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Hi,
I'm trying to search an MS3-TMT file. Error is below. I generated the mzml using MSConvert but perhaps incorrectly. Also using runstart IC. MS2-TMT files processed fine.
Thanks,
Matt
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