Frequent itemset mining?

What a great way to end the year in the literature!  I found a paper I absolutely love, closed the tab, went looking for it again and found something that might be even cooler.

This paper from Trung Nghia Vu et. al., appears to be a collaboration between labs at several institutions in Belgium and introduces (to me, at least) an interesting way of considering all the stuff in our MS/MS runs that we can't identify.  Basically?  Who cares!  Wait, that's not it.  But it is close.

The idea?  They go through their spectra and mine out the stuff they see all the time, whether they've identified it or not.  It becomes a frequent item.  Maybe it is some contaminant that we see all the time but no one has added it to the cRAP database.  If it is always there and it is always constant, why do we care whether we identify it or not?  Heck, lets go a step further and make sure we don't fragment it anymore.  Someone will one day figure out what it is, and yay for them, but let's get it out of the way.

Like everything I write in these boxes, this is a massive oversimplification.  I recommend this paper to everybody.  It is short, open access, and goes after things in a way I've certainly never thought of.  Now to find that other really cool paper....

Cool blog post on Prosight PWF files and Databases

For those of us that dabble in Top Down proteomics, one of the hard parts about ProsightPC is wrapping our minds around the nomenclature.  In this cool blog post on the Omics Portal, the Prosight team takes a whack at one of the more confusing concepts, the PWF file.  If you're a dabbler, you might want to check it out here. (You might need to be signed in [free to do so] in order to view it)

Touching letters regarding Mike Gross's piloting of JASMS

Its interesting that this cool picture is the first thing that comes up when I Google Image search "JASMS spectrometry"....

Mike Gross recently handed off leadership of JASMS.  Dave Muddiman and many other esteemed members of the mass spec family put together a letter that appears in this month's JASMS.  You can check out this touching tribute here.

Nice review on COPD Proteomics

There is so much literature out there (you guys are crazy productive!) that I really need to bias what I write about according to what I'm thinking about sometimes.  And maybe cutting my holiday at home short cause of some fantastic virus given to me by my disgusting and adorable nieces and nephews treating my like a jungle gym over Xmas made me think about Rhinovirus proteomics.  But my head hurts and I find reviews easier to read than original research articles, and I found this very nice and short review on chronic obstructive pulmonary disorder (COPD) while skimming through Google scholar.

The 3 page review is by Girolamo Pelaia et al., and is open access.  The real highlight of the review is a nice table on the final page that concisely describes original research articles where proteomics was applied to COPD and describes the technology used and the major proteins/peptides identified as linked to this disease. This chart transforms this review from something interesting and useful to a tool.  If I was going after COPD, I'd have this chart taped on the wall beside my monitor.

Install Proteome Discoverer on Windows 8 and Windows Server 2012

Does your Windows on your new PC look all crazy like this thing above?  Is it a pain in the butt to find things like "My Computer" or "My Documents" or anything else that is useful?  If so, then you now have Windows 8 or Windows Server 2012 on your computer.  What does that mean for you Thermo software?

Officially, I'm not 100% sure.  I think you should be running Windows 7 64-bit.  But if you can't then it isn't the end of the world!  I installed Proteome Discoverer 1.4 and 2.0 and Pepfinder all on Windows 8 and Windows Server 2012 Enterprise and they all appear to work just fine.  Installation of Pepfinder on Windows Server 2012 Enterprise required 2 additional steps that I could find by right-clicking on the installation file.  1) "Run as administrator" 2) Run in "Windows compatibility mode" as Windows 7.  Again, I don't know if this installation is officially supported by Thermo and if you run into trouble whether tech support can help you, but if you are in a pinch cause you bought a computer that doesn't have Windows 7 drivers or something, you should be able to make it work.

Social stresses shift metabolic profiles?!?!

Okay...this is one of those papers where you have to do a Google Scholar search to prove that they aren't making this up and/or what the heck they are talking about.  It ends up being a really interesting story, though.

Social defeat stress is the stress that is suffered by the wild (or corporate) baboons at the bottom of the pack. When someone in the pack plays an aggressive alpha and has control over resources and this position is reinforced by the rest of the pack this induces long term stress effects on the bottom monkeys.  (Robert Sapolski did a lot of this research on baboons in Africa, found that the most stressful place to be was the very bottom or the very top, and then another group repeated this study with some corporation somewhere, I forget which).

This is where it gets weird.  Scientists figured out how to reproduce a similar state of social defeat stress in mice.  The first study I can find seems to have been from Golden et al., and made it into Nature protocols.  The way they do it is really complicated.  What I understand of it is that they purposely select hostile aggressive alpha mice and expose those to other mice to impose a strict social hierarchy.  Sound a little hokey?  Sure.  Feel like I would mess it up cause I can't when a mouse (or person...) is being aggressive?  Probably!  But there is a slew of literature to back up these models.

This is where we get over the the paper I want to talk about, called "Plasma and Liver metabolic profiles in mice subjected to subchronic and mild social defeat stress."  This enterprising group developed their own mouse model system to study the effects of mild social defeats.  I'm picturing this as not getting that promotion you really deserve, or being locked in a cage with a passive-aggressive mouse.  I don't know.

Regardless, though, we've all been in situations that we could call mild social defeats. (Heck, if you're reading my ramblings you're either a scientist...or just plain weird... in either case, situations that probably lead to higher-than-average social defeats) and they suck.

Turns out that sucky defeat feeling can cause a measurable shift in your metabolic profile and it can be detected in your urine.  Lots of potential applications of this informations, but I'm tired of typing this morning!!

Looking for a nice 1D SDS-PAGE dataset

Does anyone out there know of a good proteomics dataset generated by cutting 1D SDS-PAGE slices and doing in-gel digestion?  I'm sure I could think of a couple if it hadn't been such a long day, but digging through the databases hasn't yielded me much.  RAW data would be preferable.  I don't particularly care what instrument it was generated with.  HRAM would be slightly better than IT data.

Thanks in advance!  I'm messing around with some cool algorithms...late on a Saturday night... yay for being a grown up....

A great tool to convert protein mass to moles!

I stumbled upon this tool a while back and it was on a post-it in my office to tell you guys about it.

I run into this all the time:  "I have x ug of protein, but I normally inject y picomol.  Sure, the math isn't that hard.  But I'd much rather have it done automatically so I don't misplace a decimal place on a napkin and then end up injection 10x too much protein.

This tool makes it easy.  Its at a site called "Practical molecular biology," and I think it might be a site set up by an institute in Russia a long time ago.

How to analyze oligonucleotides on a Q Exactive

Sorry if I've posted this before, but it keeps coming up.  Can I verify my oligonucleotides on a Q Exactive?  Sure you can!

And the nice people listed above made an awesome step-by-step tutorial on how to do it. You can download the PDF of this method here.  I've messed around with this some here and there, and you really need to get the right column and buffer configuration to pull it off.  Really small nucleotides will adhere to C-18 enough to be okay, but they won't be great.  Using this buffer configuration and column I was able to get masses on darned big oligos on an Orbitrap Fusion on a friend's facility.

Cautions I would throw out there:  1) The oligos I have seen so far have been DIRTY.  Most oligo synthesizing companies will HPLC purify them for a reasonable additional charge.  I'd probably do that if I could.  I'd also consider clean up columns or maybe a quick diversion to waste.

If you just want to verify sequence identity you can use the University of Albany's

nice mass calculator.  You can find this friendly tool here.

Human uniprot FASTA database with the PRTC peptides

A coworker in my day job and I generated a FASTA database today that I think some of you might find useful out there.  It is simply the Uniprot Human database (a few months old) with the PRTC peptides added to the database.  This would be useful, for example, if you wanted to see how low in concentration you could still reliably sequence peptides.

You can download it here (Uniprot_Human_plus_PRTC).

If you were going to search this directly you would need these dynamic modifications K, SILAC labeled + 8 and R, SILAC labeled +10.  You would also need to run your engine with at least 1 allowed missed cleavage, since one of the synthetic peptides has a K in the middle of it.

I'm not guaranteeing there are no typos, but I did try!