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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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Add a protein inference function #6

Closed jgriss closed 6 years ago

jgriss commented 6 years ago

For example iPQF

jgriss commented 6 years ago

Protein inference can be fine-grained in PeptideShaker using these options: https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI#protein-inference

We should evaluate whether these can be used for our purpose.

veitveit commented 6 years ago

iPQF can be used in MSnbase (but is used to summarize if I remember correctly). I vote for leaving other protein inference options (e.g. parsimony) for later.

veitveit commented 6 years ago

See discussion in #15