Is offline fractionation hurting us more than its helping?

This is interesting -- and deserves more time than I can give it on a lunch break.

Its out of something called the Yates lab. Seems familiar, somehow...

The paper is called: "Off-Line Multidimentional LC and Auto Sampling Results in Sample Loss in LC/LS-MS/MS" and you can give it more time (appears open access! here)

Interesting, right?

Single protein matches with Mascot

This is an interesting post from this week on the Matrix Science blog. How to deal with single protein searches is Mascot.

toxoMine -- use all omics to get rid of toxoplasmosis!

Toxoplasmosis is terrifying. Okay, a lot of diseases are....or I'm a coward. Not sure which. But stories of the this disease's subtle but powerful effects have been floating around the pop science scene for years. Malcolm Gladwell even mentions it in one of his great books.

Check out this article, titled: "Parasite makes men dumb, women sexy"

The problem with this disease is how highly evolved it is. Its right up there with Plasmodium in terms of complexity. And beating it...after millions of years of successfully existing in the mammalian population? That's gonna be real tough.

Maybe someone ought to take all the data we have on this thing from every Omics technology and make a great big awesome tool for digging through it!

TAAADAAAA!!!  ToxoMine is exactly this tool. Interested in complicated diseases? This is a nice example of how we can align all the power these big -omics tools can give us!

Proteome Discoverer 2.1 is out!!! Fo real, yo!!!

Officially today all y'all can have all the awesome power that I've had in Proteome Discoverer 2.1

What powers are those?

How 'bout the power to Export your data to Excel format?

What about the ability to filter at any level and apply it to other levels (say, I only want to see peptides with cysteines? I filter at the peptide level and then toggle the tab that says "apply to proteins".  BOOM!! You have only proteins with peptides with cysteines!

What about the ability to generate your own TMT ratios like you could in PD 1.4.  Just want to see the ratio between 126N and 129C, manually generate that ratio!

Have a super computer like the 32 core Proteome Destroyer I hear is coming out, or have PD installed on a server with hundreds of cores?  You can go right into the Administration tab and tell PD how many workflows PD can handle at once. Why run only 2 workflows when your monster PC can handle 8 or 10 or 100 files at once?

The biggest improvements? Advanced TMT quan. Instantly apply corrections to your reporter ion data according to the Signal-to-noise ratio of the individual peptide measurements.  For example, if you have one peptide that had a signal to noise (S/N) of 2000, meaning 99.99% of the signal you're seeing there is from that peptide and not background, this value will have a higher weight in the total protein quan than a peptide that only had 1e3 counts and a S/N of 3.  Better data is weighted to a higher level than lower quality data!

If your Maintenance is current you can download the upgrade from the Thermo Omics Portal and upgrade right now!  Don't have current maintenance? Call your sales rep now!

Everything you ever wanted to know about the Proteomics Standards Initiative

This is an interesting and thorough breakdown of the Proteomics Standards Initiative, one of many groups that is trying to demystify this awesome field of ours to outsiders (Open Access).

Tonight's plan! Learn Compound Discoverer!

Okay, that's a pretty cool icon, right?

What do Proteome Discoverer and Compound Discoverer have in common (besides the obvious overuse of the letter "r") a ton of stuff!

Compound Discoverer looks just like the Proteome Discoverer interface. The goal is to make it easier to move from one data processing workflow to another without having to learn a whole new set of interfaces!

See? It looks just like it. You set up studies the same way, you import data files the same way, and then you just have to figure out what all those funny nodes do!

I'm about to put metabolite ID and metabolism via mass spec on my resume. Even better, when they get around to launching Compound Discoverer 2.0, then this interface can easily do straight up metabolomics.

By the way. If you have used this program (or bought it and would like to learn how to use it) this is the place to find info: WWW.myCompoundDiscoverer.com

Honestly, I wrote this whole post so that the next time I Google: MyCompoundDiscoverer, it'll take me here and then I can direct link to the page. There are instructional videos and overviews!

PRIDE Inspector -- Meta-analyze all the things!

Apparently, I've downloaded several versions of the PRIDE inspector, because I have many .ZIP files in my Downloads folder. For some reason, though, I don't guess I've ever Unblocked the Zip file, unzipped it, and then ran it...or I forgot that I did...

A brand new paper in MCP reminded me of it, and I'm assuming that this means that the newest version I just downloaded is the best one anyway (available here!)

Part of the title of the new paper, btw, is:...moving toward a universal visualization tool for proteomics data standard formats...cool, right?

Some people save their data for archiving in some format or the other like: mzml, mxml, mzxml and xzmlzxmllxmzmlllllllzzMxxmz (just to name a few). These have all been very valiant attempts (except that last one. that guy was just being a jerk) to keep our data in a format that would standardize things, so we have all the important data in one place and we can compare instrument -to - instrument.

Problem is, there have been several of these. And it can be daunting. Say, I'm dosing these cells with a super cool drug and I want to do proteomics on it and I see that another lab previously dosed mice with that drug it might not be easy at all to compare that data.

See where I'm heading?

The PRIDE Inspector reads basically all of these data formats (except that last one. the inventor has been shunned by the field this morning). You get a nice graphical output of the spectra and if the data is processed you can check the results at every level.  Perhaps even as nice, if the study is saved in the PRIDE database you can link directly to the dataset.  Just want to rapidly meta-analyze everything in the PRIDE repository? This might be your window!

Now, notice the fact that the title includes "moving toward a universal". I'm sure that means there is more to be done here. But it looks like a albert heck of a nice start.