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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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DIA-NN undetected protein #911

Open Yukii0102 opened 8 months ago

Yukii0102 commented 8 months ago

Hi. I am using the software DIA-NN to perform proteomic analysis. I am checking protein expression using ".pg files", but the protein which I want to look up is not included in the file. Could you tell me the solution. Do you think if I try to run DIA-NN, the protein which I want to look up is detected?

vdemichev commented 8 months ago

Means it's just not detectable or does not pass the stringent FDR filter used for the pg_matrix. I would recommend to also check in the main report.

Yukii0102 commented 8 months ago

Thank you. 1 Is there any possibility to run DIA-NN again to obtain the desired protein? 2 if the protein which I want to look up is not included in DIA-NN "pg file", is there any alternative way to obtain it? I can only think of a method to calculate the peak area using Skyline, Peakview, etc. and give it as a relative ratio of the protein, so please let me know if there is another method.

vdemichev commented 8 months ago
  1. Use a more sensitive approach, e.g. a spectral library instead of lib-free search.
  2. Please always use the main report, not pg_ and other matrices.
Yukii0102 commented 8 months ago

Thank you. When you say use main report, do you mean pdf?

vdemichev commented 8 months ago

No, .tsv. Please see https://github.com/vdemichev/DiaNN?tab=readme-ov-file#output

Yukii0102 commented 8 months ago

I see. Thank you very much.