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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Modified peptide quantification #1249

Open zoe1985 opened 2 weeks ago

zoe1985 commented 2 weeks ago

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 commented 1 week ago

Hi Zoe,

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

Best, Vadim