Monday, December 29, 2014

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....

Sunday, December 28, 2014

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)

Saturday, December 27, 2014

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.

Friday, December 26, 2014

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.

Monday, December 22, 2014

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.

Sunday, December 21, 2014

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!!

Saturday, December 20, 2014

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....

Friday, December 19, 2014

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.


Thursday, December 18, 2014

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!

Wednesday, December 17, 2014

Proteomic assessment of wound healing


Whew...finally stopped for lunch and got away from that PC monitor long enough to get on my tablet (sigh...) and read a really cool paper!

I knew this one would be great when I saw how many words in the title of the article that I probably couldn't define if asked right on the spot.  The paper is called "In Vivo Assessment of Protease Dynamics in Cutaneous Wound Healing by Degradomics Analysis of Porcine Wound Exudates" and comes from Fabio Sabino et al.,

The pivotal words here?  Degradomics and exudates.  This study actually uses a pig wound healing model and uses a really interesting (and complex) quantitative technique to determine the level of protease activity in these tissues.  I skipped the methods section regarding how they get the pig wounds.  I'm not that much of biologist.

The sample prep technique is a combination of iTRAQ 4-plex and TAILS (terminal amine isotopically labeling of substrates.  You can read about TAILS at this Wikipedia page here (and I think somewhere on this silly blog as well).  This figure pretty much sums it up, though.


Doing TAILS gives you an idea of the level of proteolysis in your different samples.  But this group stepped it up a level by throwing in iTRAQ 4-plex as well, so we can get quan on this analysis and plex more samples.  Its worth noting that they didn't invent this technique (called iTRAQ-TAILS), these guys did in 2011, but its a new one to me.

All the MS analysis was done with the always awesome (and aging gracefully) workhorse, the Orbitrap XL.  This is a really cool study.  If having a really interesting biological model and impressively complex experimental design wasn't enough, they really do a nice job of their post processing analysis.  The pathways and heatmaps are concise and well-constructed.  All around, this is just a really nice paper.

You can grab it here, where it is currently open access at MCP.


Changing of the guard


On a personal note, about 5 weeks ago I lost my loyal companion, the Reverend Gus the Pug.  Over the last 11+ years, he was one of the very few constants in my life.  He was a used dog when I got him and he lived a very long time, particularly for his noble breed.  After about 10 days I realized I needed to try to fill that hole in my life with something.


And this is Gustoo Orsburn.  He goes by Toro.  He is on a rigorous training schedule right now to become a suitable replacement for the glorious beast he was christened after.  He is showing some real potential, but time will show whether he can live up to his namesake.

Tuesday, December 16, 2014

Proteome Discoverer with Prosight nodes!


Holy cow.  It's almost 3 and I don't think I've left this desk once today....but look what I've got to show for it!  Told you this stuff is real!  I've got a great big solid state hard drive full of RAW files and I'm just trying to break Proteome Discoverer 2.0.  Where are there bugs in this beta copy?  Where does it crash?  Where are the problems?  You know what?  I'm several hours in and I've got nothing to show for it.  This package is looking solid!  If the lawyers wrap up everything, the current plan is to have it out everyone in January.  Stuff happens, but I hope that we can all be running things through this next month!

There are more potential nodes than what I have right now, but this is what I'm focusing on tonight.  I'm just now crunching into the new Prosight nodes for the first time!

High paying postdoc in a cool lab


Postdoc positions suck.  They are supposed to.  But we all (with very very few exceptions) have to do them if we're dumb enough to do a Ph.D.  And if you are dumb enough to try to do phosphoproteomics on a signaling cascade where all of the active serines are surrounded by lysines (like me!) you may get to do a second Postdoc.

We have to do them because they are pretty much essential to prove that we know what we're doing and to get good publications and grant money and that our success (or lack thereof) during our grad school days were the results of us and not our PIs.  They suck because the pay is often bad, you may not get benefits, you might end up with a bad project, and you might end up stuck working for a psycho...or two...

So when a good friend of mine asked me to spread word about a postdoc that doesn't have any of the bad things, I figured I might as well put it up.  I've been busy doing server things all day and haven't read anything anyway.

This position is one where you would work for someone who isn't a psycho, has great toys (Elite, QE Plus, and some nice Q-things) has cool projects, and pays about twice your average postdoc salary. You can check it out here.


Monday, December 15, 2014

Only 4 days left to vote for open ASMS positions

Don't forget to vote for the open positions at ASMS.  The voting closes on December 19th.  If you are an ASMS member you will have the email in your spam filter Inbox!


Something about large molecule quantification


The subtitle of this post is: "How I think I almost learned something on LinkedIn today"

Now, I don't think LinkedIn is useless at all.  I've been involved in a few hiring procedures over the years and the first thing I do is start looking people up on Google to see if I can find anything crazy about them.  Its great when you can find good stuff on people's careers on LinkedIn first before you find that they've been abducted by aliens or prefer Q-TOFs or something equally nutty (just messing with your regarding part of this sentence, of course!)

However, I haven't found LinkedIn to be particularly useful for finding interesting science stuff. I find Twitter far more useful in this regard.  Today, however, was almost an exception.  I clicked on this fascinating looking link.


Which led me to this page (sorry if you can't see it if you aren't a LinkedIn member!) that has a whole lot of acronyms (some of which can't be Googled and aren't ever written out) promising extremely low CVs, LODs, and LOQs regarding quantifying proteins.  So, if you are totally into extremely vague jargon-filled pages obviously written by a person completely overwhelmed by the science or handcuffed by non-disclosure agreements I recommend checking this out!

Sorry, I know this is a violation of my "if you can't blog something nice..." rule, but I really just wanted to complain about a few minutes of my life I'll never get back. 

If you actually want to learn something about how to quantify intact proteins you should check out these two papers:

Label free quantification in top-down proteomics  (I'll have really interesting stuff to talk about this with you guys soon!)


Sunday, December 14, 2014

Wait...are we using ultra long columns and gradients or not?


Okay.  So I was going to start with another Hamlet thing "to use long gradients or not to..." or something else equally stupid.  So, I obviously first Googled "Pug Hamlet" for the 100th time in my life.  This time I got a good image!  And why?  Because some crazy person (not me, I swear) has a KickStarter up where he's trying to put on an entire production of Hamlet just using pugs as actors.  I love when people do stuff that makes me feel more sane.  You can find it here.  And yes, it got funded.

There was a point to this rambling.  Recently, a paper out of the Max Planck institute, who I consider big fans of long columns + ultralong gradients, showed that with a QE HF, moving from a 2 hour to 4 hour gradient did not increase peptide numbers significantly. 

Now, I have a number of friends out there in the field that are using instruments not quite as screamingly fast as the QE HF who are getting huge ID numbers using big columns (btw, I consider big columns 35cm on up) and I'll be visiting a great lab in a few weeks that uses 100cm columns for most experiments and it works really well.

In an interesting analysis in JPR, Hong Wang et al., systematically optimize ultra long columns and gradients on their instrumentation.  Ultra long?  Yeah, they essentially run a 110 cm column before their liquid ESI junction followed by another 50 cm column.  So, 160 cm of total separation power.
I'd almost say we have a controversy here, but we really don't.  If you are sequencing at 20Hz or higher, you are going to get to the bottom of your identifiable/ionizable/detectable/fragmentable peptide list pretty fast and you may not need out of this world chromatography to do it.  If you are running slower than this, you are just going to need to go to extra lengths to get the same or better coverage.

Definitely an interesting paper.  The consensus between the two, interestingly, is that we can get some darned nice coverage these days with new instrumentation and no pre-fractionation!

Friday, December 12, 2014

Preprocessing TMT spectra for better IDs


This is the paper I mentioned earlier that introduced me to TurboRaw2MGF.  This is one of those papers where you think, "this is already published, right?"  Turns out it isn't.

Back up, Ben!  Okay....  When we TMT or iTRAQ tag something and fragment it the reporter ions come off.  Thats how we get quan.  Unfortunately, Sequest looks at those fragments and doesn't know (by itself) that those aren't peptide fragments.

Turns out that if you remove these fragments from consideration, the search engine doesn't have to think about them and everything works better.  In fact, there is a feature in Proteome Discoverer (don't ask me which one, its after 5 on a Friday here and I'm totally jetlagged....) that will take these out.  This paper shows how much better your IDs can be if you deconvolute the MS/MS spectra and take out these reporter ion artifacts.

Worth checking out if you do these kinds of studies.  Maybe it seems kind of obvious, and maybe you've already been doing this, but I doubt it would have published in MCP if you'd submitted it already!  You can find it (currently open access) here.

Thursday, December 11, 2014

Highlights from the Proteome Discoverer User's meeting



What a blast.  I'm so glad I cut my vacation a little short and came by this meeting.  As you can imagine, all we talked about was PD 2.0.  One of the coolest things about PD 2.0 in my mind is that it is much friendlier to developers than previous versions.  Only a few people had the ability to both write new algorithms AND get them to work in PD 1.4.  PD 2.0 changes things around.

My favorite quote from the meeting came from Oliver Kohlbacher's talk about label free proteomics:  "If you have crappy chromatography, you shouldn't try to fix it with bioinformatics."

Here is a more organized breakdown.

Talk 1:  ptmRS and MsAmanda in PD 2.0.  I've mentioned ptmRS and how awesome it is a few times in this blog since Karl let me have it quite a while ago.  I'm a big fan and I'm excited to see everyone using it!  It works even better in PD 2.0.  The highlight of this talk was Viktoria Dorfer describing her implementation of "second search" in MSAmanda.  Chimeric spectra identification in PD?  Its not ready yet due to integration issues, but it works and the results look extremely promising.

Talk 2:  Oliver Kohlbacher describing how great OpenMS is at label free quan AND showing the nodes he is developing for PD.  They won't come in the PD 2.0 install pack, but will be downloadable and installable from the OpenMS website.  Advanced label free quan in PD?!?  Sign me up!

Talk 3: Christopher LoBner (my keyboard doesn't seem to have the funny letter that looks like a super B) from Proteome Sciences described my favorite reagent, the TMT 10plex and its history, development and processing

Talk 4: Jeroen de Keijzer showed his research and the application of PD to solving biological problems in pathogenic bacteria.  I love the bioinformatics, but this was a great reminder that, in the end, we want to use all this cool new stuff to solve a biological problem.

The afternoon was the PD 2.0 team, Michaela and Kai walking us through PD 2.0.  Release is currently slated for January and we're going to work hard to make sure resources are available to help you get going with it out of the box.  Best news of the day?  If you still have PD maintenance (PD full licenses come with 3 years of this), then the upgrade from PD 1.4 to PD 2.0 is free!  If your maintenance has expired you will need to purchase a maintenance deal from your sales rep to upgrade (PD 1.4 and PD 2.0 will exist on the same PC.)

(Day 2) Talk 5:  Lennart Martens took us through a new FDR calculator.  It won't be in the initial PD 2.0 release.  It uses a lot of data reduction steps and is close to as good as percolator, but fast!  Excited to see that one in action.

Talk 6: Richard LeDuc from Northwestern showed us the awesome capabilities of the Prosight nodes for PD 2.0.  Top down in proteome discoverer?  Yup!  And it works.  Release of these nodes should shortly follow the PD 2.0 release.  I just got them myself so I'll be able to check them out and let you guys know how its going soon.

The rest of the time was spent talking about how to do specific experiments in PD 2.0, mostly advanced questions and troubleshooting.

Great meeting with over 65 top-notch scientists in attendance.  My only regret is that I didn't get to meet everyone!  I'm already looking forward to number 5!




Wednesday, December 10, 2014

TurboRaw2MGF, a cool new feature in Proteomic Tools



I was reading a paper this morning that I'll need to tell you about later. The paper is really cool, but the tools that are used are cool enough that they deserve their own post.

The tool package in question is the aptly-named ProteomicTools package that you can download from GitHub here.  There are an absolute ton of cool features in this interface and the above screenshot is just one tab that you can pull down.

One that looks promising is TurboRaw2MGF.  This is a new RAW to mgf or mzml converter with some advanced functionality.  While I recommend this conversion is done with the free Proteome Discoverer Viewer software, this isn't going to be applicable to every single workflow.  For those of you who need an alternative conversion solution, you might want to check this out.


Tuesday, December 9, 2014

The Holy Grail! Complete integration of proteomics and metabolomics data!


Whoa!  Yes, this is a simpler system than a lot of us are using.  But we have to pull off this stuff in simpler systems in order to prepare for more complex systems.

In this awesome paper, iTRAQ quantitative proteomics and quantitative metabolomics to a bacterial system that is stressed with a toxic compound.  Interestingly, they decided to use a bacteria I'm unfamilar with rather than our normal bacterial workhorses of E. coli and Bacillus subtilis.  This paper is a really nice example of using these complementary techniques to build our understanding of a biological event!

Monday, December 8, 2014

Bremen

Turns out this silly blog is popular in some places in Europe.  Some readers approached me and asked for a photo.


Dr. Keijzer (the tallest person in the photo) gave an incredible talk today demonstrating complete proteome coverage of Mycobacterium tuberculosis with an LTQ-FT and some eloquent descriptions of how to validate transport functions in this deadly bacterium!

Note to these brilliant young proteomics experts -- I'd love to have some of the pics from a certain thing that happened when this restaurant closed.  If you'd send a couple to me at: orsburn@vt.edu it would be much appreciated!

A very nice review of label free peptide quan software


I just sat through a great talk by Oliver Kohlbacher detailing the power of OpenMS for label free quantification.  The great algorithms he detailed are old news, apparently, as I was able to find a paper his group published last year where they do a thorough review of label free quantification algorithms.  You can find this paper (open source) here.

What isn't old news, is the work that Oliver's lab has been doing preparing to bring OpenMS functionality to Proteome Discoverer 2.0.  It sounds like they are well developed and I even saw screenshots showing the nodes in Compound Discoverer.  PD nodes may only be a few months away!!

Proteome Discoverer User's meeting


I was already in Europe so I figured I ought to swing by the 4th International Proteome Discoverer meeting!

I've got a camera (don't tell anyone) and I'll share everything here that I'm allowed to.  I'm pretty good at following rules.

Sunday, December 7, 2014

Another great meeting in Austria


What an awesome sounding conference!  Let's see...what in the field should we get together and talk about?  How bout everything on this freaking list?!?!  I've already booked my entire month of January...  Wait, it gets better.  I had to cut this flier so it fits in blog format.  This is what the bottom looks like...


Cause...by the way... it is a January meeting in Austria!!!!  I've never snowboarded in Europe.  It'll happen soon, just not this next month!

If you want to find out more about this awesome conference, click here!

Saturday, December 6, 2014

Proteomic AND phosphoproteomics (seriously?) analysis of preserved tissues!


Have you ever seen a big tissue repository?  I saw one at Hopkins during my postdoc.  It is such an extremely valuable resource to have a chronologically frozen slice of history.  Cancer cell lines are going to change through passages.  We all know it and there just isn't anything we can do about it, cause we know they are still useful and convenient.  Sometimes the genes/proteins of interest don't change through passaging, just other things you don't care about.

Fixed tissues?  Those are forever!  The problem, however, is that most fixation methods crosslink everything.  This makes things tough for us, but there are cool ways around it for us thanks to methods such as FFPE-FASP and about a dozen others.  Formalin fixation is EXTREMELY bad for our friends in the genomics world.  They need their DNA/RNA functional to some extent.

A few years ago, people worried about such things started working with alternative fixation methods. Brian Dunphy patented several that are used extensively in countries where formaldehyde has been banned for years.  Recently, many European hospitals have moved to a reagent called HOPE.  HOPE has been shown to be compatible with many histological assays, recently did great with even RNA-Seq.  In this new paper at JPR, an international team shows that they can take HOPE preserved tissues and get the same number of peptide and, way more impressively, phosphopeptide IDs as they can with flash frozen tissue.

So maybe we've landed on the golden method that will work for everybody!  Doing this stuff?  I'd check this paper out!

Friday, December 5, 2014

Hello from Italy!


I got wifi for a bit and thought I'd say hello!  Anyone in Italy anywhere near Genova or Finale Ligure need a proteomics expert?  I haven't seen the whole world by any stretch, but I'm getting reasonably well- traveled and Capo Noli may be my favorite place I've ever been.  For climbers who might be appalled by the lack of apparent safety involved in taking this picture, I'd like to say my hand was cinched on webbing through a bomber anchor off camera.  If you don't think that is safe, you've obviously never seen my freakishly large hands!

While I've been away this blog turned over 200,000 views!!!!!  Thanks so much for reading guys, this has been, by far, the biggest year for this silly side project of mine, in all categories including: views, posts, and most import (to me!) reader feedback.  200,000 views...holy cow...


Vacation is almost over and I'm heading back to big cities today...sadly...and I've read some great papers I can't wait to tell you about.

Wednesday, December 3, 2014

More glycomics cancer data!


A few months ago some of the big time cancer researchers at Hopkins got pretty excited about this paper in PNAS.  In this study they found an apparent relationship between the length of protein glyco chains and cancer prognosis.  I think its safe to say that a lot of meta-analysis of proteomics data started around the world because of it.  (Okay, I know of at least one big PC that has been chugging through data looking for these relationships...more on this later I'm sure).

We may already have confirmation that this is true thanks to this incredible paper in press at MCP.  Tuomas Kaprio is the lead author but it appears to be a multi-institution study with contributions from researchers in Helsinki and Holland.  In this, they show that they can detect differences in N-glycosylation of proteins between rectal adenomas and carcinomas.

Have you ever done histology?  Years ago, I tried to expand my skill set by getting certified in hematology.  Its amazingly freaking hard.  You look at a small smear of cells and you can tell by their general shape and relationship between different microsopic aspects whether the cells are...I don't know...from an adenoma or a carcinoma (just a growth vs a cancerous growth)?  The people that are good at this: 1) have tons of respect from me 2) deserve to make a lot of money (and I hope they do).  But, as someone who (by the way, didn't get that certification) is an outsider, it seems like there could be a more standardized way to determine the difference between these cells.  There are cancer markers out there, but what if all we need to be doing is looking for differences in our glycosylated proteins in plasma as an indicator of cancer in a system?  How great would that be!?!?

The more I see and hear, the more I think this is just around the corner.  Keep cranking, guys!

Tuesday, December 2, 2014

NPC Progress meeting


I just find this title extremely appealing.  Especially considering how well organized Europe is being with linking proteomics resources to researchers who really need it.  I'm still exceptionally jealous of PRIME-XS and would love to see us implement a similar program in the U.S.  I'm still not joking, we need to emulate this.

There are some big names confirmed for this meeting and if you register before January 7th, there is no fee!  You can find out more about this here.

Sunday, November 30, 2014

On vacation


Just to let you know, I'm going off the grid for a while (rock climbing in France and Italy!!!).  I schedule things on the blog to pop up sometimes at later dates and so there should be new stuff every few days, the only issue is that comments require my approval so none will post until after I return.

Didn't want you to think your insightful additions to this blog were being ignored.  They are, and will always be, sincerely appreciated!

QE HF, first (totally unscientific) impressions!


Last week I finally got my hands on a QE HF for a few hours! (I'd have pictures of me with it, but I signed a thing that said "no photography"...)

Here are my completely unscientific data from those hours!

FAST.  Like, crazy fast.  While running in tune I had to turn on 3 microscans because the accumulation of spectra on the screen was so fast it hurt my head.  At 3 microscans it looked like the rate of spectra accumulation on the QEs I'm used to so I left it like that.

The calibration is more intensive.  Apparently there are additional things to tune and focus because I found calibrating it up with the base cals to be longer than what I am used to.  Mass cal, however, seemed to finish before I was done clicking the button and since that is what you'd most normally be doing, I sure wouldn't worry about it.

Other than that?  Exactly the same QE interface.  If you had the microscans on and set to 2 or three, chances are you wouldn't know it was anything other than my favorite mass spec of all time.  Turn the microscans off and you realize it is that same instrument running 20 pounds of boost with a locked wastegate.  Or, for my less car obsessed friends, I'd just consider it the Q Exactive....

Saturday, November 29, 2014

Using the ENCODE database to hunt down novel proteoforms?


Is this stuff ever going to get simple?  The answer appears to be a resounding "NO!"  We are some crazy complex creatures and the more I learn the more I realize that we are getting just a tiny bit of the biological picture with any technique we use.  Fortunately there are super smart people out there thinking of ways to integrate all of our tools so we can really get to the bottom of stuff!

I'm going to back up a little.  ENCODE is short for the Encyclopedia of DNA Elements and it is an amazing genomics resource at UCSC that has been ongoing since 2002.  ENCODE has been one way of trying to make sense of the wealth of DNA sequencing and expression data that has been rapidly building up out there.  You can learn more about ENCODE at these two pages (the original) (the new ENCODE portal).

Now, when we look at the genomics stuff, one of the big problems is that we know the starting material, either the DNA or the RNA transcripts present.  Like proteomics, or anything where we're making thousands, millions, or billions of observations, False discoveries are a problem.  And we can only score false discoveries based on what we currently know as true.  Man, am I mangling this post or what?

The reason I'm rambling about this is that this sweet paper in press at JPR took a swing at integrating data from ENCODE with proteomics data in an effort to expand more on the CHPP.  While I'm simplifying this completely into the ground, the idea is: how many of these things we can't explain that have been scored as false observations in genomics can be explained by unmatched spectra from the proteomics run?



Turns out?  Unsurprisingly, maybe?  Quite a few!  If unmatched spectra are driving you crazy, you might want to check out cool paper and see if this might help you explain some of them.




Friday, November 28, 2014

...kind of off topic, but an interesting study on data visualization


Sure...this is probably a little off topic, but if I stayed on topic I think this blog would be a whole lot less fun!

This is just a short blog post from a bioinformatician at Michigan State regarding different ways to visualize complex data sets.  In this example he uses the opening moves in a game of chess.  This was totally worth 2 minutes for me.  And I promise I'm not bringing this up as some sort of a statement regarding the quality of the data visualization in some papers I read recently.


A smiling pug!!!!

Monday, November 24, 2014

Cloud computing proteomics!!!


This is really cool.  In fact, if you read a paper today, I think it should be this one.  In it, these researchers detail what is possible if you use the Amazon Cloud to host aspects of the Trans Proteomic Pipeline for processing your data.  End results?  Thousands of files processed in hours, for pennies per file!  They really dig in, too, by showing different ways that this interface can be configured and operated.

The end result, though is the killer.  They load of 1100 files from all sorts of different instruments, from an LCQ Deca through an Orbitrap Velos and process them with 3 different search engines using the TPP-Amazon Cloud.  In the end it ran them about $80 to do so!  As a disclaimer, they start with pre-processed data (mZmL or something) which would lower their overhead.

It would be interesting to see how another super fast processing computer, say a Proteome Destroyer, would compare in a head-to-head, given their sub- 1 minute processing specs.


Sunday, November 23, 2014

FoldIt: Help other researchers by playing puzzles!



I know this is kinda old, but I had a great experience with crowd sourcing research recently and I realized I've never talked about FoldIt.  If you aren't familiar, this is a great (and crazy difficult) puzzle game where you solve protein folding problems.  FoldIt players have contributed to solving a slew of biological problems and were a feature in Nature a few years back as described in this Nature article here.

If you are interested and better at puzzles than me, you should check out FoldIt here.  There is a new version out this month for Apple, Linux, and Windows.

Oh, and here is a great introductory video.


Friday, November 21, 2014

Easy membrane protein prep procedure


I can't describe this one much better than the image I borrowed does.  Membrane protein prep is a pain.  Even if you are using some sort of a subcellular fractionation kit (and the ones I've used have not given me incredible membrane protein yields).  This looks really promising, though and (cheap and) easy!

You can check out this method in JPR's ASAP section here.

Thursday, November 20, 2014

More proteomic automation!


I'm obviously on a big automation kick recently.  But maybe the whole field is.  Last week I was at an incredible lab I don't think I can tell you about, but they had a GIANT robot that did all of their digestion and sample cleanup.  For those of us that can't afford that kind of thing, small time optimization with stuff that is already available may be the best option.

In this paper at JPR, the Jensen lab demonstrates such a process using disposable StageTips and something that looks like an EasyNLC 1000.  Using tons of E.coli preps they demonstrate they can achieve CVs <10% with their technique.  While I'd rather have the giant secret robot (and maybe you would too) this might be a great paper to check out for automated proteomics processing in a more affordable format.

Tuesday, November 18, 2014

Learn Byonic in a half hour!



Have you wanted to try out Byonic, but you were deterred by learning a new software interface?  Never fear, my good friends over at Protein Metric have made their software even more accessible with great videos.

Sit through a half hour of these videos here and be an expert in this great software!

Monday, November 17, 2014

Great slideshow on proteomics data/metadata


I may have posted a version of this previously, but I just went through this and learned more stuff.  This slide deck will lead you through the proteomics pipeline as seen by bioinformaticians -- including some hazards we may not be considering.

You can link to this great resource here.

Sunday, November 16, 2014

Enrich phosphopeptides on your HPLC!



Phosphopeptide enrichment via HPLC?  Sign me up!  While maybe not the most novel idea in the world, this new paper in press at MCP out of Utrecht describes the feasibility of such an approach.  In this analysis, they use an Fe-IMAC column for enrichment.  In comparison to tip based approaches they find massively reduced CVs and overall improved reproducibility.

And the yield does not seem to suffer.  Using an Orbitrap Velos they find ~9,000 unique phosphopeptides when loading directly onto a single dimension LC separation and were able to push it to ~14,000 when adding SAX and performing 2D separation!