Happy Xmas!!! Better top down analysis with ETD

Happy Xmas to my readers who celebrate this holiday.  To my readers who don't, I hope you at least get the day off from work.
Short blerb today on an article in this month's issue of MCP.  The study from Fornelli et al., evaluate a new way of calculating intact mass by using a different strategy for averaging the transients in the Orbitrap.  This method results in a massive increase in sequence coverage of a protein as big as IgG.  It is also a heavy hitter article, the authors include Dr. Makarov and Neil Kelleher.  If you are doing top down, get on this article now!

Papers. A viable alternative to EndNote?

Papers is a program to help us keep track of our citations.  While it is primarily useful for keeping track of literature you have downloaded, it also has handy functions for creating citations in your papers.  At first glance, the $80 price tag for PC puts it right in the range of several other citation programs, but the $15 price for the program for iPAD makes puts it in a really nice price range for those of us who do most of our writing/reading literature on these devices. Another plus is that it auto-updates between the devices you have installed it on, a minus is that you would have to own both the PC and iPAD version for it to work.

Targeted quan on a Q Exactive

A new paper in MCP from Gallien et. al., explores the power of the Q Exactive instrument for targeted analysis of proteins and peptides.  The end result:  770 tryptic yeast peptides monitored successfully in a 60 minute gradient!

PathCase

PathCase is an NSF funding project at CWRU focusing mapping out biological pathways.  The most unique aspect of this project is the metabolomics analysis workbench.  This project is focusing on sorting out the findings of the rapidly growing field of metabolomics and making sense of it all.  Perhaps best of all, this tool is available for free at the App store.  The app runs smoothly and appears to me to be a nice way to quickly sort through a ton of elucidated pathways.  The app also appears to be available through the Android marketplace and for the Amazon devices.

Delayed fragmentation for improving reporter ions

This article is from 2011, but it had slipped past me until my friend Santosh brought it to my attention recently.  In the study, Savitski, et. al., study the effect of various settings of the chromatography function on an Orbitrap Velos on their number of quantifiable reporter ions.

Their results demonstrate that delaying the fragmentation of peptides bearing reporter ions, using optimal settings, can result in an increase in both identification and quantifiable peptides.  A surprise (to me) side effect is that they show a marked decrease in coisolation.  This is an extremely interesting proposal since other methods for reducing the coisolation of peptides in iTRAQ experiments cause a large increase in cycle time, where this one does not.

MaxQuant summer school videos

This week, the good people at the Max Planck Institute who gave us MaxQuant released all of their lectures from their summer school series on YouTube.  They are broken into individual lectures of between 40 and 80 minutes each.  You can visit the MaxQuant YouTube channel here and have access to all 10 lectures, including lectures on Perseus!

Catching up!

I've been having some technical problems lately, primarily relating to my ability to access the internet while on the road.  This hasn't stopped me from typing, however, and I'll be backdating a number of entries that have built up over the last couple of weeks.  I apologize if this causes confusion.  Hopefully I'll be all sorted out soon.

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!).