duplicated rows resulted in error

[ibphuangchen]

          > Hi Igatto, did you get a chance to look into the problems I describe in our previous discussion? Thanks!

Hi @lgatto - you comments make very good sense to me. I found the problem I had was that when using the mzR to open the identification file (.pep.xml), for whatever reason, it resulted into a data frame in which a peptide with N modifications (e.g. 57.02147 for cysteine and there are N cysteines in the peptide) will be duplicated with N rows; each row with only a single modification with a specific "modMass" and "modLocation", but in reality all these modifications should all be there for this peptide. Same thing with MSnbase::readMzIdData.

Originally posted by @ibphuangchen in https://github.com/lgatto/MSnbase/issues/584#issuecomment-1319310681

[lgatto]

Yes, this makes sense, and is expected. Several options from here on:

• you are only interested in looking at identification data, and you can focus on the data.frame with the multiple rows per peptides
• if you are interested in quantitation data, I don't think you will distinguish the different forms, and will thus have a single set of quantitation values, so prick either id results (noting that you have more)
• same for the raw data, pick one to simply get around that error
• or, see PSMatch and how to reduce such and identification result object.