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Precision FDA — Free super computing power preloaded with applications!

Okay -- I now have a PrecisionFDA account and I've just uploaded data to it, and I'm trying to reduce some spectra with RIDAR with it -- and I have no idea why this is here, but I like it. Disclaimer: Since this is an HHS US government thing it might be for US people only? But...I'm in Japan right now and I logged right in, even with the 2-factor identification thing. You can go to PrecisionFDA here. What do I know about it? Well...they are the ones responsible for the CPTAC challenge to identify mislabled samples -- so they're clearly the good guys. That was cool, even if the start and end of the challenge deadline made it clear they didn't expect anyone interested in participating had a job. Scientists tend to be busy people, yo. If you want them to volunteer for stuff and they see they have to start and complete in like 3 weeks, no one is going to take you up on it. What else do I know about them? I just got a free account and uploaded data to their cluster...

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Wanna go fast?!? SPEED Acid digestion!

I'm going to start off by admitting I mostly moved this paper up the blogging queue so I would have excuses to put more Ricky Bobby quotes on this blog. However, there are clearly some jewels in here. It might seem off topic, but -- THERE ARE MICROBIOME STANDARDS FROM ATCC!!! -- and they use one for the gut microbiome in this study. I've written a lot of commercial groups that do genetics microbiome standards to see if they had anything for proteomics and I've been ignored. Probably because everyone in the world but me knows that ATCC has already locked up that market? Great. I hear they make good standards and it looks to me like they'll be perfect for metaproteomics and metabolomics. The paper I'm going to ramble about is this brand new one. With the dozens (hundreds?) of sample prep methodologies out there, why would you use this one? Cause... ...that was a joke... SPEED isn't a crazy fast digestion method like FLASH or sTRAP (which can be killer fas..

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Static Percolator allows application to smaller datasets!!

Okay -- if we've talked at a meeting about data processing -- we've talked about this. I'm at an amazing meeting right now and I was in 2 great conversations about this concept already. Percolator is fantastic. It is the gold standard for false discovery rate calculations, but it was designed for global applications. If you've looked at your data you've seen this phenomena where all the sudden you can't seem to trust what it is giving you by default. Some of those videos over there on Proteome Discoverer are like 7 years old now? And I ramble incoherently about it there. But what is the solution? Could it be this!?!? I have a finite number of stored Obama Boom GIFs left, but this deserves one. Static modeling percolator!! What's the difference? Normal percolator is dynamic. It learns from that big 'ol dataset you just gave it and that's what it uses to set your parameters. Static modeling flips the switch. What if it learns from a big ..

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FragPipe — MSFragger made a bit more mortal, and a lot more powerful!

I've been meaning to do some tests with the new iterations of MSFragger and finally had a few minutes to do some extremely limited tests. More coming. Let's clarify what we have here: MSFragger is the search engine. It is impossibly ridiculously fast in command line format. If you had to remember one thing about MSFragger it's that it's the open search engine. Let it search for any delta mass shifts within 500 Da of your target. It'll find those masses, and it will find them in seconds or minutes not hours, days, months, or millenia (some engines might honestly take more than a human lifespan to do a delta search, I don't have the patience to verify). I also only used 500Da as an example. MSFragger nodes work directly in Proteome Discoverer and the newest ones even work with all the quan nodes! From what I wrote in that post, I'm trying to guess which computer I used for it...and I'm going to guess it was a 7th gen i7 laptop that I don't ..

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The Okinawa Analytical Instrument Network Meeting 2019!

Have you ever heard of OIST? I'll be honest, neither had I. I am, however, 100% confident that you will hear lots about it soon. OIST stands for the Okinawa Institute of Science and Technology and it might be the most beautiful campus on earth. No picture I've taken has done it justice at all. The facility is built on mountaintops to responsibly protect the ecosystems around it. And it is growing! I was inexplicably invited to talk at the Analytical Instrument Network Meeting this year along with some serious mass spectrometry experts. I'm going to ramble through an overview of this meeting here: Day 1: Meet people, see the amazing facility and Q/A session. This facility has an amazing array of instrumentation and hardware. From robotics through NMR and various arrays of GCMS and LCMS to support the needs of a facility dedicated to primary scientific discovery. The work they are doing is on a lot of organisms I've never even heard of. The best part of day #1, howe..

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PDV — An integrated proteomics data viewer!

Do you mess around with all sorts of different search engines? Would it be awesome if someone spent a ton of time making sure that you could look at all your data in the same downstream interface? Paper link here. Are there other ways to visualize data from a bunch of different engines and tools? Sure. But PDV is probably the easiest and most widely compatible -- and has some features that are ridiculously handy. This little Java file does the perfect job of looking simple but pulling off crazy powerful. You can get it at this Github where you'll see the ridiculous number of tools it supports. I can't take a screenshot that is big enough to capture them all. Basically if you can think of a search engine, PDV can upload the results and it all comes out looking like this! Did you, for example, reprocess a bunch of MaxQuant files from PRIDE with MetaMorpheus and MSFragger to see if the original analysis missed anything? Have 4 little Java windows open at once and look at the..

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Finally! An Exploris 480 paper!

What took so long? Geez. It's like this thing just came out! The results are....impressive....and....ummm..... ....ummmm......well. I still love the HF-X and the data I've got from the two I was lucky enough to get to use is still some of the most dense and awesome I've ever searched through. Somehow in the haze of ASMS and all the cool stuff I missed something SUPER CRITICAL. Phase constraint is activated -- in a limited sense -- on the Exploris!! TMT11-plex can be resolved -- just like in the paper above -- in 32 milliseconds!! WTFourier? I'll be reading this cover to cover repeatedly cause this got powered up while I was in Okinawa -- (Finally an Orbitrap small enough that you can hug in a photo! Who knew we needed that?) ...and in the one day I was around to mess with it I found a lot of stuff to try -- like NATIVE BOXCAR and BOXCAR DIA!! Guess what can set variable TSIM windows?

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Awesome review of Python in Proteomics!

Google is very nice about telling me when I log in about whether people care about what I've posted. It says some really interesting stuff about my audience. One thing that is very clear is that y'all don't care for R and Python and Linux. However, my increasing sense of horror about being force fed the habanero and turd sandwich that is Windows 10 is going to keep showing up here. As such, I'm going to need to keep checking out new tools (good-bye Visual Studio...wow...I paid way too much for you over the years....) hello free Python IDEs that all about 90% work! I love this new Python unreviewed review and I might just be leaving it here so I can find it. I only have the direct PDF download and this is the link to it. As an aside, I've been tricking myself into getting more comfortable with Python by making it a game. I've got a pretty much 100% functional Tetris that insults the player and a side scroller that I'm even making all the ultra-professi..

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Auto STOMP Shows Protein Structure in Subcellular Structures!

I'm unclear on why the word STOMP in Google images provides tons of pictures as awesome as whatever is going on above. However, if you're going to go jumping through the air with trashcan lid shields, I'm going to find a way to circulate it. I think this may contribute to the short halflife of my friends on the Fakebook thing. What was I talking about? How about a way to look at things under a microscope and then BOOM crosslink them while you're looking at them? Cooler than trashcan lid dance fighting? Yo, I'm not even done. What if your microscope was smart enough that it went around and found the things you wanted to look at and then crosslinked them itself and then emailed you when it was done? Science fiction? Nope. You can read about it here! First off -- STOMP isn't new. If you had 48 straight hours to spend behind the lenses of a microscope in a dark room and you could code patches in multiple languages -- oh -- and could synthesize your own specia..

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