FragPipe workflow for Astral DIA data with an ~3GB database

[ygprot]

Hello,

I am planning to analyze 20 Astral DIA files (>20 GB each) using a ~3 GB FASTA database containing over 8 million protein sequences.

Is a database of this size practical to use with FragPipe? Which FragPipe workflow and MSFragger settings would you recommend?

Thank you!

[fcyu]

You will need to use the database split option in the MSFragger tab. The current version does not support DIA data, please wait for the next release.

Best,

Fengchao

[ygprot]

How about a ~800MB database of >2.5M proteins? Will that work with the current version?

[fcyu]

I am not sure. You can have a try using the DIA_SpecLib_Quant workflow.

Best,

Fengchao