RUN!!! It's ASMS Abstract deadline!!!

What are the odds that 3 conferences -- 2 months, 4 months and 5 months away would all have their abstract deadlines in the same 10 days?  Wait. What are the odds that we can't present any of the same stuff at any of them...?...how did that happen...? Do we all have super severe ADHD...?

Welcome to January 2019!!!  And this is the big one!!  ASMS ATLANTA!!

Abstracts are due today, Friday February 1st!!!

Uncovering the world of MaxQuant!

 I just stumbled across this really nice breakdown of MaxQuant and Andromeda related terms, and a great new blog.

You can check out ProteomicLandScapes here!

DIA -- An almost perfect tutorial!

Have you finally seen that bit of evidence that said "hey -- DIA would be the way to do this project?" but are not really sure how to get started?

CHECK THIS OUT!

This is a great way to get started. I've gone back and forth on the title of this post. I'm going with "almost perfect" for 2 reasons.

1) This is great if you've got a QE HF/HF-X. There are loads of them out there.
2) It is very focused on the leading (and expensive) software package.

I know. I know. I've got 60+ videos on an expensive software package over there -->. I'm a clumsy insomniac in a glass house full of elderly half-blind rescue dogs who juggle their time between being tripping hazards and barking at invisible things.  That's obviously a metaphor or an analogy for "I don't have room to criticize"...I don't know which.

And this is a 48 year old bichon with orange/purple dreadlocks who showed more energy in this adorable attempted escape from the veterinarian than she has in the last 4 months here combined.

Still -- this is a GREAT guide. If you've got a high field orbitrap you don't have to tinker with anything. If you've got a D30 Orbitrap (QE Classic/Plus) you can start with this and adjust the cycle times and window widths and you are good to go! My dumb calculator might help. It is fair to note, however, that there are several other DIA software packages out there. I have my favorite (Pinnacle, but I'm biased, I used to work with the guy who wrote it and it's got a very government-friendly price tag). I used a VERY early version of SpectroNaut and -- for real -- it was awesome.

So I'm leaving the title as it is.

Raw Beans! Generate loads of graphs from your RAW data!

Sometimes I leave posts written with a goal of checking them the next day for grammar and profanities before posting. Commonly....I appear to forget to go back and hit the big orange "Publish" button...

...now I'm wondering what these 268 things are. A lot of them are me making fun of SWATH and SONAR and the 70ppm mass accuracy of the TIMSTOF Pro, for sure....but not 268 of them....!

Raw Beans is one of these!!  You can stop reading my stupid words and get it here!

Remember RawMeat? If not, don't worry about it. It probably doesn't work with your instrument unless it's older.

You point Raw-Beans at your file full of RAW data and hit the "go" button. And it generates a whole folder full of pretty graphs about your files!

Mass deviation (off your chosen ions in the box above)?

And loads more sophisticated things! 

Twitter Chat on Proteomics February 22nd! Send questions or people with questions!

I'm not entirely sure what we all signed up for.

I'm not entirely sure I understand or like Twitter. It's an amazing tool for rapidly disseminating science but outside of that it's kind of a mess ran by a corporation that obviously puts $$ over ethics at all time. Is that redundant since I typed the word "corporation"? I think so.

Why isn't there a Science Twitter thing? Please start one and if you name it Swatter, I want credit for the idea.

Back on topic:

Some of us Twittering proteomics scientists will be participating in a "Twitter Chat" hosted by the Bioanalysis Zone.

If you've got some proteomics questions or know someone who does, tune in(?) to Twitter on February 22nd. It starts at 3pm GMT (10am EST) and will feature questions answered by:

Matthew Trost (Professor of Proteomics @ NewCastle: www.trostlab.com)

Eduardo Chicano Galvez (Senior Mass Spectrometrist and MS Imaging specialist at IMIBC, Cordoba, Spain)

---I've got questions for both of these guys already....

and on this side of the Atlantic:

John Wilson (Cold Spring Harbor Mass Spec and Proteomics)

and this blogger I know who can't stop just typing and typing and typing.

Please note: Tweets from any of us will be solely our opinions and may not be interpreted as the official statements of the organizations for which we are employed. That sounded fancy enough, right?

Crazy idea allows single protein detection in zeptomole-scale mixtures....

First of all -- big shoutout to Matt Labenski for tipping me off to this crazy new study.

Imagine that Dr. Fenn never invented electrospray ionization, and no one else was smart enough to come up with it either. This whole mass spectrometry revolution never happened, 'cause even if we all devoted all our time to MALDI or FAB or whatever, they'd never have the impact that directly coupling HPLC or CE directly to mass spectrometry has. 

What if you wanted to do proteomics and you had all these fancy genomics/transcriptomics technologies to draw off of for inspiration. In this issue of "what if" Edman degradation is still a thing that is done all the time. 

Maybe this is what you'd come up with....?

Is this kind of brilliant? Absolutely.
Am I scared to try and describe it beyond what is shown here? Yes.
Is it something that will replace our existing technologies? Not yet, obviously, but there is a lot of potential here and loads to think about!

Where can I learn mass spectrometry and proteomics?

A lot of people have noticed already the new page --> over there!

Please keep information coming in. I get this question all the time. There are very very very few mass spectrometry degree programs, despite this explosion in the actual need for actual mass spectrometrists. There are ways to learn this stuff. Ways MUCH better than reading the ramblings of some weird blogger.

If you're setting up a summer school or a workshop or something that is aimed toward educating mass spectrometrists, please shoot me an email. Let's build a list!!

If you've already got a great list that is probably better than I can do in my 4 minutes I get to devote to this blog/day these days I will immediately replace that page with a link to your page, just like the Conference thing I couldn't keep track of!!

My comment thing might be broken again. Probably more efficient to email me directly until I look at it! (orsburn@vt.edu)

Integrative -omics of limb regeneration!

Okay! Now this is a team that isn't afraid to ask the big questions! You can check it out in JPR here.

I don't know what a Cynops is, and -- honestly -- I probably won't like the answer. I'm fine with assuming it's linked to some of the most nostalgic scenes from after-school TV shows of my young life, such as --

-- strange that he'd be the only character to lose limbs multiple times....I guess....or convenient, since I guess he's the only one who could do that.....

Aww...nuts...I had to look up another paper, this is just a salamander....now I'm considering ethical implications that I totally shouldn't.....

To stop you from thinking about these as well --

--you're welcome!

This JPR study is really a re-analysis of this open access study from a few years ago, and this is where we'll find the proteomics details.

Not the details of where the samples came from!!!  Don't read those!

The mysterious samples were labeled with iTRAQ reagent. Whether the labeling was done with  4-plex or 8-plex reagent is a tightly guarded secret....wait...I figured it out! They used channels 118,119 and 121 from an 8-plex kit. The samples are taken at 0, 2 and 6 hours when regeneration is supposed to be happening -- suggesting that Piccolo is much better at this than whatever this organism is.

The labeled peptides were separated into 30 SCX fractions and these fractions were ran on a 10cm column on a Q Exactive using a secret gradient and ultra top secret mass spectrometry parameters. (Meh -- "you just load the autosampler and press the button" -- have I ever told you guys about the guy I interviewed who said that to me during his interview to run an LTQ Orbitrap -- 😰he...umm....didn't get the job....) Data processing was performed in Proteome Discoverer 1.4 using Mascot with 20ppm MS1 tolerance and 0.1Da MS/MS tolerance, which may explain why the instrument method parameters weren't described. The Q Exactive probably didn't survive the fire that caused it to need search tolerances that wide. Proteins were considered significant using the device many proteomics people do that appears to shorten the life span of the statisticians who see our work. 1.5-fold in either direction is considered significant.

I'm joking about most of this of course! I prefer my search tolerances to reflect the maximum capabilities of the instrument that is producing the files, that's me. I'm also tired of the meetings with HR about why the stats guy is crying this time, but if you can get your biology story out of your experiment, that's all that really matters.

This group produced two peer-reviewed manuscripts out of these files and obviously drew some interesting biological implications from them. They integrated a dizzying amount of genetics data with it and validated results with rt-PCR, making it a well-rounded and validated story.

LOPIT-DC: Subcellular proteomics returns -- in a much more accessible form!

LOPIT, HyperLOPIT (excuse capitalization spelling and hyphens that all may be wrong) has appeared on this blog more than once. It's brilliant and provides a way for quantitative proteomics with subcellular fractionation. We're often not doing ourselves any favors by mixing all the organelles from loads of different cells together, but fractionating beyond that seems really really hard.

LOPIT -- as smart as it is -- never cracked my list of "I have to find someone who needs data like this so I can do it" protocols. Primarily because it looked REAAAAALLLLY hard for someone who isn't good at sample prep things. I'm not the only person who was thinking this, I guess....

Let's fix that right now!

The figure at the top that was stolen from this nice open paper shows the old protocol on the left and the new protocol on the right!

Set a timer on your gradient centrifugation and then pull your subcellular fraction? I can do that! End up with single TMTplex experiment for analysis? I can do that as well. I bet you I can even take these files from PRIDE (PXD0112554) and process them in something that doesn't start and end with the letter "R"!

And -- get this --BOOM! -- mass spectrometrist friendly Shiny Web Interface!!

Is LOPIT easy now? No, that's probably a stretch. But these tweaks have made it far easier than it was before -- and what other technique can possibly get you these results? Nothing I've ever seen!

Kudos to these authors. Could they have sat back and established a monopoly on subcellular localization proteomics? Probably. Instead, they took the time and made this amazing technique far more approachable for the rest of us.

Phospho- glyco - proteogenomics of early onset gastric cancer!

I've been waiting for the embargo to be lifted so I could download this data from the CPTAC Portal for what seems like a while now. And the paper is now out, the embargo is lifted and ---

--that's a lot of authors! You definitely need at least this many people to put something like this together!

Now that the RAW data is being very nicely deposited into pre-determined and organized folders by Aspera manager -- wow-- the Q Exactive heavily fractionated N-glycoproteomics files sure look pretty ---

I still have no idea how they did this. I can't just download the data and start pressing buttons, I guess -- it's time to read, I guess....

HOW DO YOU INTEGRATE N-Glycoproteomics and PhosphoProteomics into your ProteoTranscriptomics?

It's got to be in here, because this is what they did.

Want to make it more fun? This is a lot of patient samples. And iTRAQ 4-plex!?!?!

What an ambitious project....and a beautiful output that we can mine for years going forward!

Whoa! Shoutout to @ScientistSaba for providing this awesome video related to this study!