Ready to get HYPE(d) and AMP(ed)?

At first you might think I was initially a fan of this paper because looking up the protein and nucleotide in the title is a gold mine on Google images. I'm not saying you're wrong, but there is more to this cool paper even than the JPGs I'm probably going to insert while I'm writing this.

A few years ago people were pretty hyped about AMP. Remember this?

It looked like AMP was going to be a great big important PTM.  Turns out, however, that its an absolute pain in the foot(?) to study with LC-MS. A couple labs gave it a good hard try and got some nice results, but their techniques maybe looked a little too painful for us to want to replicate.

In this new study in MCP from Malgorzata Broncel et al., we get to see a high throughput, high sensitivity, high resolution way of studying this modification!

How'd they do it? Without radiation!  They used inert chemical probes that are attached to analogues of AMP. This technology was developed by other groups for doing visualization or protein arrays. Turns out, though, that they make a nice target for selectively pulling down proteins that had picked up the labeled AMP, and are conducive to ionizing and fragmenting in a Q Exactive.

If you are interested in this PTM, you've got a protocol now!  And along the way they studied some super important protein named HYPE that has a lot to do with bacterial infections and may lead to nice drug targets for us to use in the post-antibiotic era!

Single protein equilibrium in a cell

Wow. This is just fascinating!  Thanks PastelBio for sharing.

This link will take you to what I'm talking about. Its a press release of sorts about a new study in Nature Physics. Interestingly, from the time of the press release until now, it appears that they decided to change the name of the paper and it is available here (paywalled, sorry!)

The press release explains it better than I can, honestly, but they took that crazy super computer down in Tennessee, the Titan (19,000 CPUs AND 19,000 GPUs)

What they did was single cell protein modeling with all that processing power.

What did they conclude? That considering protein production speed and turnover via degradation, proteins may never actually achieve equilibrium within a cell. That you'd constantly be looking at a moving and changing population of even one single gene product. So if you were able to pull out just two proteoforms of a given gene product at any point in time, they probably wouldn't be the same.  One might be just formed and the other might be partially degraded...or reacted, or modified.

Is it real? Who knows? Its fascinating, though!  I guess it probably doesn't affect what we do much. I mean, we're looking at the averages of signals from thousands of copies of proteins from thousands or millions of cells at once, so maybe all of this averages out into just noise, but I always love things that highlight how little we still know about biology.

Can you run Proteome Discoverer on Windows 10?

I've been asked this question a couple of times. And maybe now I know the answer.

At first run, it certainly looks like PD 2.1 installs just fine with nothing special whatsoever on Windows 10.

Now...that being said, this isn't officially supported by the vendor. And just because the couple HeLa runs I just did seem to go just fine doesn't mean that every feature will be ready...but, again, I haven't had a problem yet!

Nice and short review on proteogenomics in Springer

Like an awful lot of people right now, I'm kind of obsessed with the magical thing called "proteogenomics". Which...honestly...seems a little bit like magic. Getting good quality transcriptional data and filtering it so that you can see new mutations....that you can trust...AND THEN using this information to find new matches to your MS/MS data....that you can trust....

A few people have totally pulled it off....and I have the papers stacked up in front of my PC all marked up and highlighted and...well...maybe I'm dumb...but I still don't know how they did it.

For a good starting point, check out this nice review from Sam Faulkner et al.,. While I'm on the topic of magic, you might be surprised to see this is an article from Springer that isn't behind a paywall!

Oh yeah! And here is the link!

2SC --- another important PTM to look for?

Great...another protein post-translational modification...cause my search space isn't nutso enough already....

Oh! Hi, there!  Ever looked at this one? Its called 2SC...and it turns out that it has a role in human diseases. Its even detectable by other molecular techniques and has been implicated in diabetes. A brand new paper from Gianluca Miglia et al., takes a computational approach and analyzes a ton of proteins. Turns out that it mostly sticks to Cysteines. Which makes me wonder if our typical techniques of cysteine reduction/alkylation/assumption of 100% cysteine alkylation means that we probably don't see it in our RAW data and can't see it in our processed data if it was there.

The abstract suggests that this modification is prevalent enough that they have seen multiple 2SC modifications per individual protein. I can't get much further because I'm stuck behind a paywall at this Panera this morning. An Open Access paper on this modification in people is available here, though its worth noting that they appear to have done all their work with Western blots. As a side note, it appears there are a lot of journals out there, and it appears that people are running out of names for them.

Ever wanted a great label free proteomics dataset?

"Hey guys, here's this awesome new algorithm for label free analysis!!!!"

Want a GREAT dataset to test it out on?

EDIT 8/22/16: Since I've been sending this paper link and/or the PXD number to everyone I know we found two things: 1) I miscopied the PRIDE number (fixed) and 2) I overlooked the fact that 3 author contributed equally to this.  This incredibly useful resource should correctly be called:

Claire Ramus, Agnes Hovasse, Marlene Marcellin, Anne-Marie Hesse, et al., 

{End EDIT}

Check out this cool new paper from Claire Ramus et al.,!  In this, they developed a great standard that all of us can download and use for free. They also use it to test a bunch of the current algorithms people are using.

The sample is the Sigma UPS1 48 protein mix (all equimolar proteins) spiked into a Yeast digest background at different concentrations. The spike-ins range from 50amol to 12,500 amol (yeah...there is a more efficient way of writing this, but I'm not great at metrics...thanks American public schools! I love sounding like an idiot to everyone else in the world...)

You can download the dataset...wow...my internet is slow right now...well, I guess you can download the dataset...from PRIDE. It will be PXD001819 after it is published. The authors were kind enough to provide a way to download the dataset prior to publication (wow, right!??!) that you can find in the abstract.

Got a couple files. This study was on an Orbitrap Velos running High-Low (FT for MS1 and CID ion trap MS/MS scans). It looks like 60k resolution at the MS1 (around 400m/z)

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!