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make advanced:
-ignore_charge
change default:
-mz_reference In my experience, mapping using the 'precursor' instead of the 'peptide' (theoretical mass) is inferior. I would vote for 'peptide' as …
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Hi,
I used ThermoRawFileParser to convert raw files to mzML. The output works fine with search engine.
However, when i use [IsobaricAnalyzer](http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentat…
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I use the command line to process the MSFragger,but the result files which genarated by MSFragger were not be understand when I want to found the identified PSM, peptides and proteins. another questio…
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I wonder if the pGlyco2 can identifi glycopeptide deglycosylated by PNGase F in 18O-water. there are Deamidated_18O(1)[Q] but no Deamidated_18O(1)[N] in the step of Identification.Thank you!
when I…
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I was looking through the tsv file and noticed that in some cases, with default settings, it was possible to find one spectra being assigned to multiple peptide interpretations. I also noticed that th…
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* Showed that depth cutoffs work to improve FDR for peptide identification in 10 cell lines paper
* Apply cutoff to both alleles in heterozygous variations?
* Heterozygous variation is included if a…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/yourusername/yourpackagename
Confirm the followin…
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Hello,
In a larger run of quandenser with files from three runs in two labs (alignments previous shared in issue #5) I hit a snag with a percolator run:
```
Percolator version 3.02.1, Build Dat…
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I was trying to run the demo with a huge document text and it shows me ```There was an error generating a question :(``` is there any limitation for the document text ? when i run the same with this r…
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Hi,
Is it possible to add the modification below to SearchGUI in a future release? It is the result of using TMT and SILAC together in the same experiment (hyperplexing). Just the lysine +8 modific…