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ByrumLab / ProteoViz

Interactive tool for Phosphoproteomics
Apache License 2.0
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Is it possible to use Proteoviz with Proetome Discoverer output from the orbitrap? #8

Open zincfingers89 opened 7 months ago

zincfingers89 commented 7 months ago

Im looking to analyse my TMT data, my university proteomics core have used proteome discoverer and sent me the output of this. Can I still use Proteoviz for downstream analysis or does it have to be MaxQuant?

If so how do I generate the "protein groups" and "sample_metadata" files from the Proteome Discovered output?

mirshahvalady commented 6 months ago

the problem with PD output is rather the position of phospho sites that are provided within phosphopeptides and not relative to the protein! I am having the same problem and there is no easy way around!

ByrumLab commented 6 months ago

@mirshahvalady . Yes, it depends on the database that was used in the search and the start stop positions in the file. Sometimes the position will need to be modified in the code so they align correctly. We have been working more on the newer R package 'proteoDA' instead of this one. I'm not sure when I'll be able to update this version with new functions.

ByrumLab commented 6 months ago

@zincfingers89 For TMT data, I would recommend the proteoDA R package instead of proteoViz. There is a tutorial how to setup your database search output in order to run it through the full analysis using ByrumLab/proteoDA.