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Hi.
@algom reported a weird calculation of protein ratios by ProteinQuantifier. ProteinQuantier seems to use *peptide abundances* for the calculation of protein ratios, independent of the method (`…
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Hello,
I am trying to use FragPipe 13.0 (MSFragger 3.0 + Philosopher 3.2.9) for label-free quantification using IonQuant (see image of settings below). Initially, I was processing two files for comp…
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Would be great if we can annotate this list:
```
PXD004732 -- ProteomeTools -- 104608
PXD000561 -- A draft map of the human proteome -- 97948
PXD002815 -- A human interactome in three quantitat…
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I'm currently running Philosopher on Linux via my universities Linux HPC Cluster
I'm having problems of getting the rest of the Philosopher workflow to work on my MSFragger output (I used the scri…
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Hi, further to [another issue](https://github.com/Nesvilab/philosopher/issues/139) I was discussing which I now believe to be resolved, I am using the TMT pipeline to analyse databases that I am downl…
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Hello MSFragger team,
I try to use MSFragger (through FragPipe) to search phosphorylation data from Bruker’s TimsTOF pro. However, all intensity values for proteins and peptides are 0 in the search…
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Hi there Alexey and team,
I tried to run a site-ID and TMT quant analysis on some files, which went well up until the TMT integrator part. Not sure what went wrong here - can you help?
Log is as…
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when i execute the example 6.12 in page 162 in the Supplementary Text and Figures of your paper "A multicenter study benchmarks software tools for label-free proteome quantification", when i run the …
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Hello
I am unable to run the label free with protein quantification pipeline with the MascotAdapterOnline (OpenMS 2.1.0 on KNIME 3.3.2 OS X El Capitan).
Although I have IDPosteriorErrorProbability…
ghost updated
4 years ago
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I have done a bit of user testing on 2.1.0 today. Apologies if these issues are covered in another Issue or PR somewhere - I don't think they are, but there has been a lot of activity recently so I ma…