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### Description of the bug
This command is failing:
```
#!/usr/bin/env bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an e…
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Hello Vadim and Team,
I am using a spectral library for modified histone peptides that I built in skyline. I have some questions regarding using this library...
1. What is the best way to conver…
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Hi,
First of all, thank you for such wonderful tool. I'm working with proteins translated from new ORFs and I predicted that the new protein interact with another protein, say for e.g. protein X. N…
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### Title
Proteomics Identification Ontology
### Short Description
The Proteomics Identification Ontology (PRIDE ontology) provides a model for describing, sharing and integrating of proteom…
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Dear @jorainer
following up on the conversation in the slack channel, here comes the issue in the `Spectra` package.
The idea was to be able to calculate HUPO-PSI-defined quality metrics (http…
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Hi Vadim and team,
I have done 3 plex dimethyl labeling on samples and am now trying to analyze them following the steps outlined in the plexDIA section. But as you can see below, after finished wi…
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I am encountering an issue with software v.1.0.2. It reports that 25 identified peptides were assigned to a protein, 4 of which are unique. I expected to see which peptides are shared and which are un…
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Related to PS issue 260.
Data to reproduce the issue can be found here: http://vedlegg.uib.no/?id=4ecd6fd34cc85e9f5eb518a12bb0a55a.
```
java.lang.IllegalArgumentException: Two modifications fou…
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I hope this message finds you well. I am reaching out with a few questions regarding the identification and quantification of proteins and peptides using DIANN.
I have noticed that the results obta…
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@tivdnbos proposed to me the idea of propagating counts from taxa that are situated higher in the taxonomy tree to nodes that are situated lower, in order to increase identification confidence of taxa…