draw protein quantification table for spectral counting

bigbio / pmultiqc

A library for QC report based on MultiQC framework

GNU General Public License v3.0

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draw protein quantification table for spectral counting #65

Closed daichengxin closed 2 years ago

daichengxin commented 2 years ago

A example report https://github.com/daichengxin/data-folder/tree/main/pmultiqc

jpfeuffer commented 2 years ago

Do we always draw a PSM table now? Or only for spectral counting? It might be a bit much for large LFQ datasets.

ypriverol commented 2 years ago

@jpfeuffer the idea is that for spectral counting analyses we don't have a way to see the peptide identifications or any peptide information. The peptide table is missing in the mzTab. I had the idea that for this analysis only show the psm table to enable users to find their peptides.

jpfeuffer commented 2 years ago

Ok for this analysis it can be the default. For featurebased I would leave it out per default.

ypriverol commented 2 years ago

Yes, that is the idea:

[x] feature base (intensity) quantitation should be run as before with Protein and peptide Quantitation tables.
[x] spectral counting base quantitation analysis should be run with Protein quantitation and PSM tables (no quant information).