Correlation between iTRAQ reagent sets

A new study in this month's JPR takes a look at the correlation between 2-plex and 6-plex iTRAQ reagent kits. The results are a bit surprising to me, but they two reagent kits show a pretty strong correlation.
You can find this study from Rauniyar et. al., here.
Below is an overview of their experimental design.

Protein Deconvolution Estimator

This is one of those things I posted on the old blog a couple years ago and kept meaning to bring over to this new one.  It is a simple Excel spreadsheet for estimating the deconvoluted mass of an intact protein.  It certainly isn't perfect (+/-1000 Da?), but it is better than what you'll find if you Google "free protein deconvolution," which, last I checked, comes up with nothing.  If you use it, I just ask that you aren't a jerk about it.  ;)
You can download it from my personal bytebuckets account here.

BaseSpace cloud genomics computing

Again, not proteomics.  I may need to re-name this blog soon.  Anyway, BaseSpace cloud genomics is a service from Illumina that is set to kick off in January.  It is an attempt to use brute strength to solve the difficulties of dealing with large amounts of genomics data.  Typical genomics experiment on a dedicated power PC:  design experiment (20 minutes) run experiment (24 hours) find typo in experiment and fix (1 min), rerun (24 hours), etc.,  and this was my experience with around 50 GB of microarrays.  These next gen files can be substantially bigger than even the newest human Affy chips.  By using a cloud computing format, each manipulation will be reasonably quick.  Now we just need dedicated proteomics cloud computers!
Tentative rates are displayed below:

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.