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Hi,
I tried to set up the pipeline for running msfragger and philosopher. When I do this, I stops after the Protein Inference step. If I then modify the parameter.yml file and set only one step to …
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Hi!
I am running into the same issue as #274. I am runnning philosopher with Comet, PeptideProphet, ProteinProphet, which all proceed without issue. When it gets up to FDR filtering, I get the error…
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Hello,
when running FragPipe in headless mode (analyzing a TMT experiment), I get weird TMT channel names. I put an example here: https://oc.embl.de/index.php/s/9iEiAtMw6j0hSMK
In the annotatio…
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Dear FragPipe team,
I've been analyzing a TMT data set with FragPipe enabling the Quant (isobaric) option. When plotting the density of normalized log2 intensities from the tmt-report, I observe a…
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- Describe the issue or question:
Hello,
I am struggling with an issue with FragPipe v16.0 while quantifies PSMs in TMT-10 dataset. It seems the tool is not able to generate the "Purity" column in…
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Hi,
I get this error while running from filter step in the pipeline; (attached my parameter file). Could you help me solve it?
I said no to database search and peptide valdation, as untill thi…
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Hi,
I tried to set up the pipeline for running msfragger and philosopher. When I do this, I stops after the Protein Inference step. If I then modify the parameter.yml file and set only one step to …
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Hey,
I wanted to get the MS1 peak intensities of all peptide precursors in a couple of samples run on a Thermo orbitrap.
I've run the default alphapept work flow and was looking at the results in …
adder updated
2 years ago
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Dear @chambm
We tried to reproduce some results from previous analyses, which include TMT quantification, and we noticed major differences in the output. The major issue was the lack of any TMT qu…
prvst updated
3 years ago
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# Things that need to be done for the Alpha Release (v.0.4.0)
## Major
- [x] DIA library export
- [x] **Upgrade GPU FF to CPU**
- [x] **Include GPU CI/CD**
- [x] Test unspecific search again
…