Since protein abundance analysis often confirms trends we identified from scRNA-seq analysis, the methods and goals are often similar.
However there are quite a few nuances. For instance, I didn’t do QC in this walkthrough but protein QC is very different from RNA QC because it makes different assumptions; one such being that mass spec readouts aren’t at single-cell resolution in the same way that single-cell RNA is. So even thinking about what “low quality” means in either context is different.
Thanks for the tutorial. It is very informative!
So, proteomics does not seem to be very different from analysing RNASeq data, is that right? The methods seem similar.
Since protein abundance analysis often confirms trends we identified from scRNA-seq analysis, the methods and goals are often similar.
However there are quite a few nuances. For instance, I didn’t do QC in this walkthrough but protein QC is very different from RNA QC because it makes different assumptions; one such being that mass spec readouts aren’t at single-cell resolution in the same way that single-cell RNA is. So even thinking about what “low quality” means in either context is different.
Very Vcc familiar.