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**Describe the bug**
I'm trying to run the philosopher TMT analysis pipeline on a 11plex LC-MS/MS data with the following setting in the philosopher.yml file.
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It is possible to use `rawrr` to access the noise
values for a raw file collected in reduced profile mode?
From reading
the code in rawrr.cs, it seems that the noise is only read for
centroide…
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At the moment Sage offers just a small set of 250 named knots (`src/sage/knots/knot_table.py`) taken form the [Rolfsen table](http://katlas.math.toronto.edu/wiki/The_Rolfsen_Knot_Table). Proper name…
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Dear FragPipe team,
I've been analyzing a TMT data set with FragPipe enabling the Quant (isobaric) option. When plotting the density of normalized log2 intensities from the tmt-report, I observe a…
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Hi Mathieu,
I wanted to try the package out on my break on my entire bib database. I installed it via pip install (for the user) and ran it, but it didn't generate a result.
Hope it helps improv…
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Hi, I got this error when setting `isotope_error` with MSFraggerAdapter.
```
Invalid string parameter value '0,1,2' for parameter 'isotope_error' given! Valid values are: '0,1,2'
```
I checked…
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>> 3. Ok I'll file it if I get the example output working. I thought it might be because I'm putting waaaay too many unique Samples in there, but if you used it for the Fiebig study I guess they also …
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Greetings @levitsky,
Currently, I am trying to perform AA_Stat analysis using Open Search results. This Open Search was performed as per our discussion via email. The error is as following:
C:\U…
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Hi,
using the new philosopher 4.2.1, I have some problems with TMT16. Almost all proteins in the protein.tsv output have a quantification value of 0 for the different TMT channels.
When looking i…
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Dear all,
thanks for this very useful package!
Is there a way to extract the peak "charges" of MS1 spectras with rawrr::readSpectrum? It seems to only work for MS2 spectras at the moment.
Thanks a…