I was wondering if anyone knew of an R package that could process bottoms-up proteomics that would essentially do what MaxQuant does, and didn't require MaxQuant outputs (or similar software) first? I basically want to be able to do the entire processing from the raw data within R studio.
I am sorry, I am not aware of any package.
Let's admit it, Maxquant is the de-facto standard for doing these things.
And honestly I'd have more trust in MaxQuant being developed over many years (~15) by a very experienced team of developers than some package developed somewhere else and you don't really know who did this.
I definitely agree it is the gold standard. It does a great job, but I am struggling to get it to work at my current company just due to some of their strict cybersecurity rules. So I was hoping for a work around. I haven't been able to find one either, so was just curious.
This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.
If you have a query related to it or one of the replies, start a new topic and refer back with a link.