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ProtProtocols / IsoProt

Protocol of the analysis of iTRAQ/TMT proteomics data including quantification, statistical analysis and maybe clustering
https://protprotocols.github.io
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Facilitate manual change of isotope corrections #89

Open veitveit opened 5 years ago

veitveit commented 5 years ago

Depending on the iTRAQ/TMT kit, this seems still to be an issue and we might need to provide an "easy" way to change this table.

jgriss commented 5 years ago

@veitveit This will require a new dynamic GUI element. Depending on the labeling techniques the correction matrix looks a bit different. Also, the way the information is supplied by companies and the input needed by Msnbase is a bit different.

veitveit commented 5 years ago

@jgriss I would opt to have the matrix in a file and to provide a link to it in the GUI. As easy solution, we could prepare templates for all labelling methods (based on MSnbase defaults) and then copy the respective ones to the OUT folder.

veitveit commented 5 years ago

@jgriss As this will not the only option people might want to change, I suggest to add a new layer of options which are controlled by a parameter file (e.g. number of threads). Then the interface will remain simple and easy to maintain. What do you think? For example putting everything in to an additional or the same json with the parameters?