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.

Metabolic Fate of Tea Polyphenols in Humans

This new paper in JPR isn't really a proteomics paper, its more of a metabolomics (metabonomics) study, but it is definitely interesting enough to warrant a quick mention.
In the study, 20 healthy men and 20 healthy women were put on a specific polyphenol-free diet (no caffeine or chocolate for 6 weeks).  The exception to this diet was the daily administration of a concentrated tea that was the equivalent of ~5 cups of commercially available tea.  The participants then submitted urine samples over a rigorous schedule, with some participants submitting samples 6 times daily.
The urine samples were analyzed with LC-MS using a Waters ACQUITY UPLC system coupled to a Micromass Q-TOF.  The samples were also analyzed by GC-MS using an Agilent 6890N GC and a Pegasus HT TOF system.
The study determined the rate of clearance of the polyphenols present in these teas as well as the appearance of compounds that resulted from metabolism of these molecules.  One interesting fact the study found was that although caffeine appearance in the urine peaked 1 hour after the tea was ingested, it didn't completely clear the body until 9 hours post ingestion.
The most interesting part of this study, in my opinion, was the use of multivariate statistics for results analysis.  I am encouraged when I see the science of statistics infiltrating the analysis of MS data.  Its interesting to me how rare this has been so far, especially considering how essential statistics is to genomics.

MCP frontpage down

If you've tried to access the new issue of MCP through the Highlights page, I'm sure you noticed that all of the links are down.  I alerted Andrew Harmon at MCP of the problem this morning, and they are working to resolve it.  Hopefully they'll get it fixed soon, they have some great stuff in this issue!