tvpham
commented
1 year 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:
- taking the first entry, either protein ID or gene ID
- for identical proteins or genes, take: the first row, mean/median values, the one with the lowest number of NAs
Thang
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