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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 …
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Until now, these files only seem accessible when in the same folder and thus one cannot use pkg_resources to access them when being somewhere else.
I suspect that this is due to a missing general s…
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- [x] I think the source names are not correct in https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD002088/sdrf.tsv
they differ between fractions
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Dear all,
after mentioning a few times that there are some issues with non-consistent vocabulary usage I finally read all sdrf tables and compared all labels/column-names (using my R package wrProt…
wraff updated
2 years ago
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The Label-free and TMT example URLs do not work (https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD008934/sdrf.tsv and https://raw.githubusercontent.com/bigbio/p…
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**Wrangler responsible for this dataset/lab:**
Primary: Ami
Secondary: Enrique
**Description of the task:**
GSE116222: EpithelialDiversityHealthInflammation
https://docs.google.com/spre…
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I am running the UPS data set with the --add_decoy option:
```
nextflow run nf-core/proteomicslfq -r 1.0.0 -profile docker --input https://raw.githubusercontent.com/bigbio/proteomics-metadata-standa…
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@daichengxin :
Can you add to each SDRF in my fork https://github.com/ypriverol/proteomics-metadata-standard the field
`Technology Type` with the value: `proteomic profiling by mass spectr…