No proteins found in pg_matrix.tsv file

[ABRai11]

Hi Vadim,

I am searching a plant DIA data in DIA-NN. I couldn't get any proteins in the pg_matrix file. However, there are proteins listed in the report.tsv file. Can you let me know what may be the reason?

Thanks.
Akhila

[vdemichev]

Hi Akhila,

Means either no proper protein annotation or nothing passed the FDR filters.
The main report can help see which one it is.

Best,
Vadim

[ABRai11]

Hi Vedim,
DIA_report.zip

Thank you for the reply. I have uploaded the results here. Could you please check?

[ABRai11]

Ok, then is the pg. quantity the abundance value?

[vdemichev]

PG.MaxLFQ

[ABRai11]

Ok, thanks. Btw may I know the difference.

[vdemichev]

PG.MaxLFQ is calculated using the MaxLFQ algorithm, please see the 2014 paper by the Cox lab on this

[ABRai11]

Ok, Sure. Thank you so much for clarifying.