Modified peptide quantification

[zoe1985]

Dear Vadim,

I searched top-ABPP DIA files with FragPipe to collect a file fold named "diann-output". My question is whether the quantification of assigned modified peptides also is generated from "report.tsv" using DIANN Rpackages or iq R? I'm not sure following script:

df <- diann_load("diann-output.tsv")
pep<-diann_maxlfq(df[df$Q.Value <= 0.01 & df$PG.Q.Value <= 0.01,],
group.header="Modified.Sequence",
id.header = "Precursor.Id",
quantity.header = "Precursor.Normalised",
margin=-10)

Best,

Zoe

[vdemichev]

Hi Zoe,

Yes, the above should group precursors by Modified.Sequence and quantify the resulting modified sequences with MaxLFQ.

Best,
Vadim