Protein group matrix of multiplexed samples

[joachims1956]

Hello,

Thanks lot for developing DIA-NN and curating the Github.

My question is about the DIA-NN output: I performed a DIA-NN analysis of multiplexed samples. Is there an option to get an output matrix that shows protein groups per each channel of multiplexed samples per sample?

Thank you very much in advance.

[vdemichev]

No, unfortunately not. But this is quitea simple R script to get channel-specific protein quantities. Just

• Add a 'Channel' column to the main report, which indicates the channel (extract from Precursor.Id)
• Add a 'Sample' column to the main report as paste0(df$Run, df$Channel)
• Add 'Precursor' column based on 'Precursor.Id', but stripped from the channel information
• Use 'iq' package but instead of 'Run' column supply the 'Sample' column to it and instead of 'Precursor.Id' - 'Precursor'