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It happens not rarely, that the (Thermo) instruments software determines an incorrect charge state for a particular precursor.
It has been shown in the past, that this misassignment leads to a reduce…
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# Describe the problem
* **I'm submitting a:**
- [ ] problem running the software
- [x ] bug report
- [ ] feature request
- [ ] question
* **My MSFragger use case:**
- [X ] _Close…
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We are trying to locate all the proteomics data files we'll need for the C.gigas seed temperature x time series manuscript. As a reminder, this data is from [Rhonda's 2016 oyster seed experiment](http…
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Hi,
I have results from different search engines from two different database searches (one for human and other for yeast). I would like to merge and create one combined result file using peptidesha…
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# Describe the problem
* **I'm submitting a:**
- [ ] problem running the software
- [ ] bug report
- [ ] feature request
- [x] question
* **My MSFragger use case:**
- [ ] _Closed_…
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Hi,
There is a question confusing me for a long time. In Equation (1) in the supplementary of "Semi-supervised learning for peptide identification from shotgun proteomics datasets", there is a `m_{…
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# Describe the problem
* **I'm submitting a:**
- [ ] problem running the software
* **My MSFragger use case:**
- [ ] _Open_ search (large precursor mass tolerance)
** _put your genera…
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Greetings to the proteomics team
I am using the CLI version of PeptideShaker, and have used this command to create a PeptideShaker project from a SearchCLI result
```
java -cp ~/PeptideShaker-1.1…
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Hi,
I wonder whether it is possible to export the total ion current (TIC) from a RAW file with RawTools? Does it happen automatically, or do I have to specify an attribute at the command line?
…
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### Summary
- What does this package do? (explain in 50 words or less):
This package is used at our core facility to generate FASTA sequence databases from smaller fasta files. It also is used…