Tranche! Download proteomic data 1 out of 10 tries.

This is me being overly critical of a service that costs me nothing, right?  The Tranche Proteomics repository at the Proteome Commons is a great idea.  A completely essential idea.  It is awesome that we have it.  But why doesn't it ever seem to work?  I can go to a cloud service like ByteBuckets and set up a 1 TB data access port and put 1 TB of data on it and then download it from anywhere in the world.  As long as you don't password protect it, it works pretty much seamlessly.  Why, then, can't I ever seem to successfully access the data at Tranche?  I tried 4 times today to pull down a small stack of files and once got as far as 20% into it before it failed.  My record up to this point is 1 successful download out of >10 tries.
Sorry, this is more of a rant than useful information, but that's how I roll sometimes.
Anyway, I'm not the only one with this opinion.  This same problem was a topic of a review that appeared in Nature Methods in April of this year.

Improved chromatography and lower back pressure?

I'm no chromatography expert.  I'm a biologist.  My graduate advisor, however, made chromatograms that would make people at conferences stop in their tracks.  He is just that good (also a biologist...).  I absorbed just enough to get by.
So anything that makes my life (and separations) easier, I'm all for.  And I just learned about a recent revolution in LC packing material that promises to do just that.  Apparently it works by using solid core beads with small permeable channels...or something.  The result is that you get much better separations at significantly lower back pressure.  Sounds like a win to me.  I had the luck to see one in action at the Mayo Clinic and I'm impressed.
 It looks like these new chromatography materials are available from just about everyone.  Below is a video that describes how these new materials work.  Definitely check this out.  The Thermo offering is called Accucore.

Mass Spectrometry Geekery

I recently stumbled across this page (Mass Spectrometry Geekery) and have revisited a couple of times.  You should definitely check it out. Alex does a great job (definitely better than I'm doing!) of keeping up with the new literature and commenting on it (she also has a great sense of humor!).

Venny Venn Diagram

A while back I wrote about my favorite Venn Diagram tool.  The Venny Venn Diagram Plotter may actually be better.  It is a freely available, web accessible Venn plotter that will plot your redundancy for you.  For example, if you have an output list of upregulated proteins by gene name from Proteome Discoverer and a list of upregulated genes from a microarray list, you simply copy the column from your Excel file and place it into Venny.  It is plotted automatically, saving you tons of time and perhaps even DigDB analysis (necessary if you are comparing lists of 3 or more).
You can use Venny for comparing up to 4 lists at the author's site here.

If you need to compare a 5th list, a modified version of Venny is available at the Genotoul Bioinfo page here.

iORBI talks for download

Did you miss the 2012 iORBI?
Don't despair!  All of the talks presented at all of the iORBI meetings are available for download on Planet Orbitrap.  There are talks on: Tuning and Calibrating your Orbitrap, how best to set up bottom-up and top-down experiments, ETD and PTM analysis, metabolomics, lipidomics, Proteome Discoverer, and the abilities of the Q Exactive
To download, go to Planet Orbitrap and look in the libraries section.

You can also access the talks here:  iorbi.na-mast.com

Tabb lab proteomics software

There is a lot of proteomics software out there.  Some good and some...not so good.  But there is just so much now that sometimes really comprehensive and long standing developments will slip right around your notice.  The work of the Tabb lab at Vanderbilt is one of these for me. This lab has been developing and improving their proteomics workflow for quite a while and has a well polished open source package available.  This week we ran some phosphopeptide standards though both this package and Proteome Discoverer and this package came up with nearly 75% of the IDs that PD did.  If you are interested in an alternative for processing your shotgun proteomics data, this is definitely worth an investigation!

Zwittergent -- another MS compatible detergent

This week I learend about Zwittergent, another MS compatible detergent (like Rapigest and that other thing one I wrote about a while ago).  Zwittergent, however is unique in that it maintains its zwitterionic behavior in solution across a wide pH range.  A group I am currently working with uses it quite a lot and it is obviously not hurting their results because their data is amazing.

Measuring Hormones with LC-MS/MS

This week, Dr. Rien Blankenstein will be giving a free talk via webinar on the potential of LC-MS/MS for the measurement of hormone levels.
If you are interested in the clinical applications of LC-MS, this talk is probably for you.  For more information, follow this link:  http://view6.workcast.net/register?pak=1820817017334891&referrer=ei2

The talk is provided by Science Direct and sponsored by Thermo.

MS Amanda -- another cool new PD node

Thanks to Santosh for letting me know about this!  MS Amanda is a new high speed scoring node for Proteome Discoverer that is available through pd-nodes.org.  It promises a new and rapid metric and full compatibility with both PD 1.3 and 1.4.  The instructions for download and install appear easy to follow.  I'll post when I get a chance to run a good data set through it.

Wine Proteomics

I recently wrote about a paper on beer proteomics.  A recent review by Righetti et. al., is a concise and comprehensive overview of the field of wine proteomics.  The review summarizes many of the recent reports on the protein content of wine and digs into many of the recent controversies of the field, including the well publicized report on allergens in wine.  The real center of this review is the results of 3 publications from the review's authors using a peptide library enrichment technique that has broad implications on wine technology.  In the studies in question, the authors demonstrated the ability to detect trace quantities of wine impurities including, but not limited, to fining agents and fungal proteins.  This paper is both and extremely interesting and entertaining read due to the authors' brassy tone and obvious sense of humor.