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### Installation Type
Docker
### pVACtools Version / Docker Image
latest
### Python Version
_No response_
### Operating System
Ubuntu
### Describe the bug
When running pvacseq to make predict…
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e.g. it would be nice to have Infos like mass and charge in there as well
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Hi everyone
I am new to FlashFLQ and I try to use it to quantify my proteomics data. The identification was done with sage and MS2 Rescore. I tried to generate the generic table for FlashLFQ with the…
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Hiya!
Thanks for such a wonderful package. I'm working with a lot of peptides that I order from GenScript. A lot of these have modifications or are non-natural amino acids (see [here](https://www.g…
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Hi @theGreatHerrLebert , Thansks for your great work! I followed the README documentation but got PSM all scored as 1. So, how do I calculate and get the posterior error, spectrum q, peptide q, protei…
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```
In the current specification it's stated (page 26): "The protein's accession
the peptide is associated with. In case no protein section is present in the
file or the peptide was not assigned to …
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Greetings, dear colleagues,
I am a 5th-year student at Lomonosov Moscow State University.
I have **one question about OnionNet**: is it possible to use this neural network to predict "protein-pep…
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We are simulating DIA data (using synthedia https://github.com/mgleeming/synthedia/) and putting it through FragPipe. When we simulate "perfect" fragmentation of spectras, it fail at PeptideProphet an…
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A script that converts a peptide file into a GTF/GFF file. The input for it should be a GFF/GTF file, a fasta file, and a tab delimited file.
The output:
A GFF file of mapped peptides. It should show…
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definition:
intersection_of: CHEBI:16670 ! peptide
intersection_of: has_role CHEBI:33281 ! antimicrobial agent
Example of use:
GO:0002775 ! antimicrobial peptide production [DEF: "The synthesis or …