Sunday, December 30, 2012


Another example:
pNOVO+ is a new de novo sequencing algorithm that makes use of the complementary fragmentation that we available from HCD and ETD fragmentation.  The authors, Hao Chi  et. al., test their system on peptides derived from a number of different enzymes and demonstrate a staggering level of efficiency.
The paper is available here.
More importantly, as of right now, the link for downloading the program isn't accessible, but it is supposed to be here.  Hopefully it will be up soon!  I can not wait to try it!

This month's JPR is awesome!

You're going to be hearing a lot from me about this month's JPR.  Were they saving up all this great stuff for the New Year?  I'm just kind of floored by how many interesting new studies came out all at once!

Saturday, December 29, 2012

2D isoelectric focusing

This month's JPR includes an article by Maria Pernemalm and Jahnne Lehtio at the Karolinska Institutet.  The subject of the study is a new method for performing 2 dimensional isoelectric focusing.  In the first dimension, proteins are separated by IEF.  The strips are then cut, the proteins digested, and the resulting peptides are separated by IEF.  The  team reports a significant increase in their numbers of resolved proteins.
An advantage of this technique over that of the Offgel 2D system is that you don't have to buy the Offgel.  The disadvantage is that normal IEF strips are a good bit more difficult to work with than the Offgel (IMHO).
A schematic of their technique is shown below.

Friday, December 28, 2012

Convert ppm to mmu to dalton

Just another little tool that I meant to move over from the old blog. It is a simple Excel sheet to convert PPM for a specific m/z to MMU and to Da.  John Dalton approves.

Edit -- 5/15/18 -- moved to Google Team Drive. Direct link here.

Thursday, December 27, 2012

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.

Wednesday, December 26, 2012

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:

Tuesday, December 25, 2012

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!

Monday, December 24, 2012

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.

Sunday, December 23, 2012

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!

Saturday, December 22, 2012


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.

Friday, December 21, 2012

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.

Thursday, December 20, 2012

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!

Wednesday, December 19, 2012

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.

Sunday, December 16, 2012

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.

Friday, December 14, 2012

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.

Thursday, December 13, 2012

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!).

Wednesday, December 12, 2012

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.

Monday, December 10, 2012

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:

Friday, December 7, 2012

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!

Wednesday, December 5, 2012

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.

Monday, December 3, 2012

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:

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

Sunday, December 2, 2012

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  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.

Saturday, December 1, 2012

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.