Can I use Maxquant DDA files to generate a DIA spectra library? js2126  2023-05-02 07:55

I was just wondering if it is possible to use files from a Maxquant DDA analysis (having gone through the Maxquant’s andromeda search engine) to builds a spectral library for a DIA analysis in Skyline. We generated our DDA and DIA data on a Thermo Q-Exactive instrument.

Many thanks,

Nick Shulman responded:  2023-05-02 08:22
Yes, the scenario you describe is very similar to what is covered by the "Basic Data Independent Acquisition" tutorial:

As an alternative to the steps outlined in the tutorial, there are a couple of other ways of accomplishing the same thing:
1. On Skyline's Start Page, there is a button "Import DIA Peptide Search" which is a different way to get started.

2. Alternatively, in Skyline, you can use the menu item "File > Import > Peptide Search", and on the first page of the Import Peptide Search wizard choose "Search results (build library directly)" in the "Start from" dropdown and choose "DIA" for the "Workflow" down at the bottom.

-- Nick