Hi Vitek lab,
I was trying out the MSstatsLiP pipeline on DIA-NN data, but when using the DIANNtoMSstatsLiPFormat function, I encountered the following error:
Error in [.data.table(dn_input, , req_cols, with = FALSE) :
column not found: [FragmentQuantCorrected]
To resolve this, I tried adding the --export-quant option in DIA-NN to include fragment quantification columns, but it seems that the FragmentQuantCorrected column is still missing from the output. Do you know where this column should come from and how I can ensure it's included in the DIA-NN report?
Additionally, I was wondering if it's possible to adapt the MSstatsLiP pipeline to retain semi-tryptic peptides downstream. Currently, the standard pipeline filters for fully tryptic peptides only, but I'd like to include semi-tryptics as well.
Thanks in advance!
Kind regards,
Chloé
Hi Vitek lab,
I was trying out the MSstatsLiP pipeline on DIA-NN data, but when using the DIANNtoMSstatsLiPFormat function, I encountered the following error:
Error in
[.data.table(dn_input, , req_cols, with = FALSE) :column not found: [FragmentQuantCorrected]
To resolve this, I tried adding the --export-quant option in DIA-NN to include fragment quantification columns, but it seems that the FragmentQuantCorrected column is still missing from the output. Do you know where this column should come from and how I can ensure it's included in the DIA-NN report?
Additionally, I was wondering if it's possible to adapt the MSstatsLiP pipeline to retain semi-tryptic peptides downstream. Currently, the standard pipeline filters for fully tryptic peptides only, but I'd like to include semi-tryptics as well.
Thanks in advance!
Kind regards,
Chloé