Sunday, May 19, 2013

Gas phase fractionation is back!

Every couple of days right now I hear something new about gas phase fractionation.  If this is a new concept to you, you're probably a relative new comer to the field.  This was big news for a while thanks to some really great papers around 2001-2003, then it kind of flickered out and we didn't hear much about it.  Until now.  For those of you going to ASMS, I'd expect to hear a lot about it!

Gas phrase fractionation is essentially the "binning" experiments that I mentioned in an entry a couple of months back.  You perform your normal MS1 scans, but you only look for ions for MS/MS if they fall within a particular mass range.  You then repeat the run on another mass range and another until you've covered them all. That's all there is to it.  It is much simpler than the "tiling" experiments that recently came out of the University of Wisconsin.

One of the driving forces behind this buzz is a company called NonLinear Dynamics.  They are driving this buzz because their software package, Progenesis is optimized to compile data from these experiments.  It seems like a really cool piece of software, with 3 dimensional peak integration and support for all vendor software.

Unfortunately for me, I don't have Progenesis, but they do offer a free trial that I think I'll jump on once I get caught up on the other 100 things I need to do.  Fortunately, for me, I do have SIEVE and Proteome Discoverer so I have no problem processing gas phase fractionated data.  Since SIEVE only looks at MS1 spectra and PD can be set up to only look at MS/MS spectra, neither packages care what internal instrument methods you are using.  I'm still excited to check out this package but I'm not in a huge rush.


  1. Hi Ben,

    Thanks for the mention of Progenesis LC-MS. Also worth noting is that since we first described how you can implement GPF with Progenesis, we've added a feature in the software that will automatically calculate the mass ranges for you, based on the number of bins you want.

    Anyway, please do download it and give it a try - it would be great to get your feedback on it.



  2. Thanks for checking the blog out.
    I'm looking forward to running Progenesis.
    And I might have to backtrack a little. With other label free quan software we're having difficulty processing this data.