Wednesday, January 30, 2019

DIA -- An almost perfect tutorial!

Have you finally seen that bit of evidence that said "hey -- DIA would be the way to do this project?" but are not really sure how to get started?


This is a great way to get started. I've gone back and forth on the title of this post. I'm going with "almost perfect" for 2 reasons.

1) This is great if you've got a QE HF/HF-X. There are loads of them out there.
2) It is very focused on the leading (and expensive) software package.

I know. I know. I've got 60+ videos on an expensive software package over there -->. I'm a clumsy insomniac in a glass house full of elderly half-blind rescue dogs who juggle their time between being tripping hazards and barking at invisible things.  That's obviously a metaphor or an analogy for "I don't have room to criticize"...I don't know which.

And this is a 48 year old bichon with orange/purple dreadlocks who showed more energy in this adorable attempted escape from the veterinarian than she has in the last 4 months here combined.

Still -- this is a GREAT guide. If you've got a high field orbitrap you don't have to tinker with anything. If you've got a D30 Orbitrap (QE Classic/Plus) you can start with this and adjust the cycle times and window widths and you are good to go! My dumb calculator might help. It is fair to note, however, that there are several other DIA software packages out there. I have my favorite (Pinnacle, but I'm biased, I used to work with the guy who wrote it and it's got a very government-friendly price tag). I used a VERY early version of SpectroNaut and -- for real -- it was awesome.

So I'm leaving the title as it is.


  1. Cool, thanks for sharing! We've been guiding users on how to do DIA proteomics for over a year (Proteome Software), including helping set up workflows:

  2. You seem to have missed this tutorial;

    C. Ludwig, L. Gillet, G. Rosenberger, S. Amon, B.C. Collins, R. Aebersold, Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial, Molecular Systems Biology. 14 (2018) e8126. doi:10.15252/msb.20178126.

    It handles the topic in a manufacturer agnostic approach.