prolfqua_MaxQuant output

[Heidelbergrabbit]

Dear Mr. Wolski, @wolski

I am reading your publication in JPR, 2023 regarding the R package prolfqua. It could be quite useful for my current work.

I have datasets from LFQ bottom-up proteomics and a complete output folder from MaxQuant search, including evidence.txt, peptides.txt and proteinGroups.txt.
I have the latest version of prolfqua (v1.2.5) installed. And R has a version number 4.4.0.

May I kindly request an online documentation, where you have a clear instruction step-by-step on how to import data from MaxQuant output? That would be very helpful for the large community who uses MaxQuant. Many thanks in advance!

[jjGG]

Hello @Heidelbergrabbit,

Sorry for only answering your email now, somehow the issues are not forwarded to us.
There are some vignettes in our package that directly also start with "proteinGroups.txt".

Please check these out. It should be super straight forward

best regards
j