Saturday, May 19, 2012

PTMScan Direct

The front page of MCP is back online.  One reason that this is good is that you can read about PTMScan Direct.  This paper is from Cell Signaling and describes a really good combination of using antibody enrichment and mass spectrometry.
The PTMScan technology is based on mixtures of antibodies that can be used to pull down multiple important signaling pathway proteins all at once.  The pulldowns are then analyzed by LC-MS/MS (in the paper, they describe the use of an LTQ-Orbitrap Velos).  The antibody combinations can provide you with a rapid and thorough look into what pathways are involved in your system of interest.  The technology is fully compatible with both label free discovery methods, as well as SILAC for quantification.
My one small criticism with this absolutely brilliant paper is in the settings they used in their MS/MS analysis.  I was very surprised to see that they used an MS1 mass window of 50ppm with an MS/MS window of 1 Da.  These are considerably less strict than what I use and what I am used to seeing in the literature.  When our bionformatician informed me that our false discovery rate calculations benefited from using larger mass windows, I began using 10ppm and 0.5 Da with our Velos.  I don't think I could be convinced to widen my MS1 window 5-fold.  My only thought on why they used these settings is that the Sorceror system they used for analysis benefits dramatically from having a larger window, but at this point I'm just speculating.

In summary, this technique takes immunoaffinity pull-downs to a whole new level.  I expect this technology to be in high-demand, particularly in drug mechanism studies.  If you read one paper this month, this is the one I recommend.

1 comment:

  1. Dear Ben,

    I started following your blog recently. I really liked your take on happenings in proteomics world.

    I don't see any blogs after May 19th, Perhaps you would have enjoyed the ASMS'12 at Vancouver.

    I would really appreciate if possible keep your blog running.

    Graduate Student
    IOB, India