Tuesday, September 5, 2017

Okay...so what about SUB-nanogram proteomics?

My library hasn't listed this one yet (in press on Sept 1) but based on the abstract I really need to grab it when it lists here! 

In this study they look at tons of variables.

What instrument is best at the lowest loads?
What nanoLC column lengths provide the greatest sensitivity (and - I'll assume -- gradient optimization as well)
And -- what algorithms will provide the greatest sensitivity.

They conclude (as anyone else has that is doing lots of this) MaxQuant "match between runs" (similar functions are applicable under different names in Minora, PeakJuggler, and IonStar) provides massive increases in peptide identification sensitivity!

After optimizing all these parameters these authors run a bunch of samples to prove they got it right!


  1. Hi Ben,
    Will there be a "match between runs" in PD especially when we are using SEQUEST? Not sure if other search modules such as Amanda has it. It is a useful feature that I think PD developers are neglecting.


    1. Prahlad,
      Thanks for the comment and YES! There are two ways to get the equivalent in PD.
      PD 2.2 has it in the LFQ algorithms and it works great!
      PD 2.1 has a node from IMP, called PeakJuggler that has it. It is also available in the free versions of PD, IMP-PD.

    2. Oh yeah -- and I think if you get the Open-MS community nodes then you can essentially use the same feature. I need more time with those...