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.

Parallel Reaction Monitoring -- Do a ton of SRMs at once!

I love SRM.  Hell, everyone loves SRMs.  Nothing beats getting your ion of interest and identifying it with 1) retention time 2) mass, and 3) fragment ion(s).  The problem is that they are sloooooowwww to set up because method optimization is such a drag. You've got to find the right fragment ion and collision energy to make it show up at the highest efficiency (if someone hasn't done it for you -- on your particular instrument, of course). It isn't such an issue in proteomics, but in small molecule work SRM collision energies for particular compounds can be the biggest secrets in the world.

That's why this paper in MCP lab from Amelia Pierson et al., of the  Koon lab is so cool!

 Parallel reaction monitoring uses the targeted multiplex MS2 method on the Q Exactive and essentially lets you get a bunch of SRMs (or MRMs, depending on what you're calling it) all at the same time.  Not only is it faster, but because the Q Exactive has an inclusion list of up to 5,000 ions all selectable by retention time, with the right chromatography system you can validate hundreds of observations in one go. MS based virtual western blots in realistic time may actually be a reality! 

There are some huge advantages here --
1) You are getting high resolution fragments!
2) You are getting a lot of them (all of them?) at once so you can be selective in processing (if you've got a co-eluting compound of striking similarity, you can ignore that fragment ion and focus on ones that are truly unique
3) Less up front setup time!

EDIT: Holy cow. This post was live for 7 years with a really awful typo in it. Thank you to any person who ever saw this and ever talked to me or took me serious about anything in regards to mass spectrometry ever again. Fixed....

Mass Spectrometer on Curiosity Part 3: Conversation with a small molecule expert

Yesterday, I had the chance to run my thoughts on the MS system on Curiosity by a small molecule triple quad expert.  His thoughts really changed my perspective on this.  Apparently +/- 1 Da isn't all that bad for a quadrupole instrument.  Yes, there are better ones out there (such as ones produced by my employer  that can do +/- 0.2 Da without big sensitivity losses), but most +/- 1 Da is pretty much the industry standard.  While most quads can narrow down to smaller mass windows, the sensitivity losses are so severe that we it is completely impractical.
So, while the MS device on Curiosity isn't cutting edge, it isn't as primitive as I originally thought.  Makes you wonder, though, why they just didn't buy one from Thermo...

Mass Spectrometer on Curiosity Part II, more 70s technology?

Curiosity is a historic achievement.  It is the biggest and most complex instrument we have ever landed on another planet.  Virtually every T-shirt I have purchased since it landed has had a NASA logo on it.  I am very very proud of the scientists and engineers who have made this possible.  I am, however, very disappointed in the level of sophistication of the Mass Spectrometer on the Rover.  

This is a schematic of SAM (sample analysis at Mars) lab.  The first thing you'll notice is that SAM uses a quadrupole mass spectrometer.  Sure.  This makes sense.  Quads are robust and can take a jarring without requiring constant recalibration. The mobile mass spectrometers the military uses for detecting chemical warfare agents are almost exclusively quad instruments.

The disappointment comes in when you look at the capabilities of this mass spectrometer. 

The above mass spectrum was taken from this paper detailing the calibration of the quadrupole unit from Curiosity.  I understand, we are taking this instrument and shooting it to another planet, but are we looking at mass accuracy within +/- 1 Da?  That is what I get.  1 Da?  Now the quad has a really interesting mass range, from 2 - 550 m/z.  That is a tough range to work with, but 1 Da?  A guy I've been working with this week has been working with small molecules <100 Da and has been consistently been pulling parts per billion mass accuracy. In my opinion, this is where our technology is today.  I'm sure there are reasons for this drop off, but I can't help but be a little disappointed.