-
Some pipelines need to filter PSMs taking into account the Search Engine provisioning (which search engines have identified the corresponding spectrum), we see two cased here:
- [x] Filter Peptide…
-
**Is your feature request related to a problem? Please describe.**
With biological samples we want to avoid matching identifications between files, where we might genuinely not have the protein in on…
-
Hi,
I have discovered a bug with Philosopher.
Console Information:
INFO[21:32:23] Executing Filter v5.1.0
INFO[21:32:23] Processing peptide identification files
INFO[2…
-
Peptides FDRs do not correspond to protein FDRs.
Currently, large-scale studies often have dozens or hundreds of LC-MS runs that are being accumulated. Repeated measurements lead to an accumulation o…
-
```
Eric posted this message to the list. You need to read the attached pdf
containing images for it to make sense
***************************
2) Our next challenge was how to encode the TPP probab…
-
I am trying to direct-search HeLa raw file in DIA-NN 18. There is no searched data at the end. Below is the report.log which says
[25:57] Loading run D:\Jae_DIA_practice\1_200 ng HeLa digest (3 file…
-
@bgruening @CarlosHorro
Has anyone seen this issue in PeptideShaker before?
PeptideShaker Error: "An error occurred while loading the identification files."
Would be great if anyone associated…
-
Workflow
The search engine definitely plays the most important role in the peptide identification process. As illustrated below, what the search engine itself does is bascically first in silico diges…
-
**Describe the bug**
Upon using MaxQuant version 2.4.2.0 for peptide identification with the digestion parameter set as Unspecific and other parameters set to default, the resulting PSMs in the outpu…
-
I'm doing a check to see if we can id tmt-tagged peptides. Particularly interested in PTM-modified peptides as these haven't been quantifiable in the past. If I get good identification rate then we ca…