search

compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
47 stars 19 forks source link

Can filtered results be loaded into PeptideShaker? #441

Closed danielgeiszler closed 3 years ago

danielgeiszler commented 3 years ago

Hi,

I already have filtered and validated PSM lists and I was hoping to take advantage of some of your visualization tools. Is there any way to load fully processed PSM lists into PeptideShaker? And if not, is this something you’re planning on supporting in the future?

hbarsnes commented 3 years ago

I'm afraid this is not supported at the moment as all of the loaded results have to be processed and unified before being displayed.

May I ask where the data you want to load comes from? Would it be an option to redo the filtering in PeptideShaker?

And are there any visualization options in PeptideShaker that you are particular interested in?

danielgeiszler commented 3 years ago

This is from FragPipe. Unfortunately, we need to use the Prophets for the filtering here.

There wasn't anything in particular, I was just poking around to see what was available and convenient, and it looked like there was a lot of functionality here.

Thanks for your time and the fast response! Cheers.