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as discussed in #2495, it would be much better to have a defined interface for common operations on `vector` or `vector`.
All occurences could (gradually) be replaced by the new classes (one for `vec…
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The creation of the peptide-level protein inference graph sometimes results in a null pointer.
Example:
1) in the ProteinInferencePeptideLevelDialog constructor the list retainedProteins contai…
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**Is your feature request related to a problem? Please describe.**
Currently just a few metrics are taken from the X!tandem search and plottet by the Shiny app.
**Describe the solution you'd like…
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Hi,
Can anybody help me to understand what the allowed level of FDR is ?
How can I perform the FDR filtering to allow the level of false positive results no more than 0.01 for both peptides and pr…
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Hi all!
I need some help with idXML files handling in pyopenms.
I use it like this:
prot_ids=[]
pep_ids=[]
oms=IdXMLFile().load("omssa.idXML", prot_ids, pep_ids)
Is there a way to access the …
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Dear pLink Team,
is there a way to specify 2 different mono-links for one cross-linker? I am asking as I would like to search hydrolyzed and ammonium quenched BS3 mono-links within one search.
B…
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Hi,
> I've recieved the following message - "Caution! PSM with sequence ******** could not be read; a peptide with the same modified sequence but with different monoisotopic mass has already been a…
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Hi;
We need terms for the following tools and their scores:
**MSFragger**
**PeptideProphet**
- peptideprophet probability
**ProteinProphet**
- proteinprophet score
- protein group …
prvst updated
5 years ago
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See the section "Reducing redundancy in proteomes" in the [UniProt april 2015 release notes](http://www.uniprot.org/help/2015/04/01/release) to find the explanation why the number of proteins in TrEMB…
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In processing metagenomics data sets, I would systematically avoid the use of the `-e` option, since we start from DNA reads (not peptides identified by mass spec). However, it seems that generally th…