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tvpham / iq

An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
BSD 3-Clause "New" or "Revised" License
19 stars 9 forks source link

How #12

Open heylookabed opened 9 months ago

heylookabed commented 9 months ago

Hello Thang.

I've noticed that the output of the final file (post-rollup) contains the same protein in multiple permutations.

Example P28661;P28661-3 P28661;P28661-2;P28661-4 P28661;P28661-2;P28661-3;P28661-6

From my experience of using MaxQuant, I recall there was an appended table of razor peptides and unique peptides that helped consolidate the redundant entries. What is your recommended course of action for doing so in iq? If you could provide any insight as to how to consolidate or choose the best entry per identifier it would be immensely helpful.

Thanks in advance.

Joseph I. Wang

tvpham commented 8 months ago

Hi Joseph,

I am afraid I do not have any recommendation at the moment. We are looking a little bit into razor/unique peptides as well because the current version of DIA-NN, for example, reports the entries in alphabetical manner, which is not ideal I guess.

For downstream analysis, I have seen people making a few practical choices:

Thang