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- Describe the issue or question:
I am trying to run diaumpire via fragpipe only but with it being the only tab checked in fragpipe, but it only runs check centroid.
We have found that the diaumpire…
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Hi All,
I'm trying to run `parse_sdrf convert-openms` on my SDRF file, but I'm getting an error that I don't fully understand, particularly since the validation tool doesn't indicate any obvious is…
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### Description of the bug
Hi, thanks for the all useful docs and work so far!
I am currently trying to run DIA data through quantms. We are primarily interested in Phosphoproteomics but I would …
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Tasks:
- [ ] @daichengxin can you update the documentation with how the tool can be run from the command line.
- [ ] @ypriverol make a PR to proteomicsLFQ with the tool to automatically generate…
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### Description of the bug
I am trying to run quantms on a DIA dataset - acquired on an Exploris 480, with raw files converted to mzML.
I am using N E X T F L O W ~ version 23.10.0
with
```
…
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Hey there!
Me again ...
If I am understanding the code correctly, when reading the DIA-NN report, it tries to match the data in the experimental design and changes the extension to mzML. Since I a…
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*Instructions:* When making a request, replace the text < between chevrons > after first reading the instructions. The instructions can be removed. Do not change any other text, and please try to com…
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- Describe the issue or question:
I recently updated the whole FragPipe workflow ( all tools updated for V21.0, 8jan 2024).
Standaard DDA search runs repeatedly into error message after PeptideProp…
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Hi all @jpfeuffer @timosachsenberg @enriquea @dai:
We have recently generated data for almost 100 datasets, differentially expression analyses (DE), and absolute/baseline expression analyses (AE). …
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Currently, for proteomics labelled quantification analysis, the ontology does not include reagent for TMTpro 16-plex labelling. They are
TMT133N
TMT133C
TMT134N
The errors that I've received in …