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EPIFANY — A smart and fast method for protein inference!!!

This new study in press at JPR is critically important for shotgun proteomics and smarter people than me (which means just about everyone) should really take a good look at this and 1) verify it is as good as it looks and 2) see about integrating the source code or primary logic into all sorts of other tools. (An earlier draft was also made available through biorXIV.) Okay -- so -- shotgun proteomics is really really good at one thing -- making Peptide Spectral Match(es) -- (PSM)s. And if we're working with the best proteins in the whole entire world then each and every one of those PSMs is unique to 1 particular protein and when we identify that PSM and quantify it in a sample we have proven that particular protein is there and we can even get quantification estimates / measurements on that one protein from that one PSM. (I need a word count on sentences). However -- from an evolutionary perspective it doesn't make a ton of sense for each protein to have developed in isolat..

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An Encyclopedia with Quantitative Proteomics of 375 cancer cell lines!?!?!?

Ummm.....whoa....I'm just going to leave this here. This is far too large of a resource for me to tackle on a Sunday morning. Here is an overview and a lot of links to/around/about the study -- including an query-able -- SQL database in case you're not sure where to put 4,000 Fusion RAW files.... And here is a short paper about it....

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Determine if your methionine oxidation is from biology or an artifact!

Okay -- so, despite all appearances, methionine oxidation (Met-Ox)is actually a really important thing. Before I get distracted, you should check out this really smart way of studying whether it is a biological Met-Ox or a sample prep Met-Ox artifact here. This is an aside, but -- holy cow -- the first 11 papers I tried to find to prove this from home were all locked behind paywalls. I had to go back to this 1997 PNAS paper for something that was open access. Are you a US citizen and do you think that if your tax dollars funded some research then those results should have to be openly accessible to you? If so, check out this thing some guy set up.... Here is a direct access link to this petition. With that out of the way -- back to Met-Ox. For real -- this is important. It can be used as a metric for ROS scavenging and for a long time has been thought to be impaired in a lot of diseases and may even be a generic metric of aging. It just turns out that we don't have a great way o..

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BioPlex Update Preprint — 5,500 New Protein Interactomes — in a new cell line!

Ummm....so on a scale of 1 to BioPlex -- how big is your big proteomics data? Holy cow. You know, sometimes when you don't hear about these huge proteomics undertakings its easy to think "maybe they thought the first 10,000 human proteome interactomes was enough..." NOPE. BioPlex is alive and well and providing human protein protein interaction data at a pace that doesn't quite seem possible. Proof? Check out this new preprint! Not familiar with BioPlex? It is a bulldozer type approach to human protein interactions. Instead of doing something complicated and elegant -- why not just synthesize every open reading frame in humans and do an expert level immunoprecipitation -- mass spectrometry experiment on them. Yeah -- every one! BioPlex 3.0 showed about half the theoretical human proteome. For real. It is a project so big and ambitious that is is easy to forget about. How do you take this another step forward? Well -- you throw in some different cell types. And instead of lo..

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CyTOF data on single cells for 281 cancer patients with long term clinical data!

Somewhere around you, possibly within walking distance, depending on the relative funding level and decision making skills of your administrators is probably a big grey and orange box like the thing above. I'd be comfortable betting you $1.14 that it probably isn't doing anything right this second. This box is called a CyTOF and -- I swear -- it has all sorts of promise, but it's a bit of technology that is seeking a real application. And I'm going to jump on every paper I see that suggests we may have finally found it. Imagine that you're doing flow cytometry. You've tagged your cells with a couple of proteins and these proteins have a dye on them. The instrument measures the intensity of these dyes as the cells are sorted and you basically get single cell data on the intensity of these two proteins in each single cell. Now upgrade that idea and replace the dyes with protein tags that you can see with a mass spec. The cells get sorted, go through, get ion..

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Announcing the First Ever News In Proteomics MineAthon (Challenge)!

I have been working on yet another crazy idea off and on for a month or two and it's now almost (like 18%) fully organized. I'll stand by these words all day. Proteomics hardware is about mature. Yeah, we'll get some cooler stuff down the road, but until we figure out how to fix our informatics problem -- who cares if you get 3% more peptide IDs or 10% more spectra? Most of the tools people are using are only converting a tiny percentage of spectra into biological findings. There is much more to be gained with smarter data processing than even applying phase constraint over a wider mass range. In the most popular data processing pipelines people aren't even looking for PTMs, because it's still really hard to do it. SO....Let's see where we are right now! Do you think your data processing pipeline is the best for finding important biological changes and PTMs? Want to prove it, participate in some cool human research, be on a cool paper, a wold-wide webcast ..

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Announcing the First Ever News In Proteomics MineAthon!

I have been working on yet another crazy idea off and on for a month or two and it's now almost (like 18%) fully organized. I'll stand by these words all day. Proteomics hardware is about mature. Yeah, we'll get some cooler stuff down the road, but until we figure out how to fix our informatics problem -- who cares if you get 3% more peptide IDs or 10% more spectra? Most of the tools people are using are only converting a tiny percentage of spectra into biological findings. There is much more to be gained with smarter data processing than even applying phase constraint over a wider mass range. In the most popular data processing pipelines people aren't even looking for PTMs, because it's still really hard to do it. SO....Let's see where we are right now! Do you think your data processing pipeline is the best for finding important biological changes and PTMs? Want to prove it, participate in some cool human research, be on a cool paper, a wold-wide webcast ..

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ShinyGO! A beautiful, simple and powerful online data interpretation tool.

I didn't want to write about this one until I got these stupid manuscript edits out the door, because I needed ShinyGO and I didn't want anyone else slowing it down. "Minor" edits done! Tool sharing time! You can read about ShinyGO here. Don't feel like reading? You can play with ShinyGO online here! Are there lots of tools like this out there hiding on the web? Yup! There sure are, but this honestly might be the easiest way to dig through a bunch of different resources all at once. You will need to get your protein list to universal gene identifiers or something similar (it'll translate several different types) and then you can start doing all sorts of analyses. For the figure above, I let ShinyGO select the closest related organism (ended up being Scumbag Arabidopsis) and I flipped through different databases until I got some visualizations that made my data make some sense (turned out being a nice visualization of KEGG resources with pathway representation scale..

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At long last — A Guidance Document for HLA Peptides!

Twenty somethig years of analyzing HLA Class I/II antigens with mass spectrometry and we need to face facts -- mass spectrometry of these things still sucks. Important? Yes. Super incredibly important. But mobile protons are NOT a fun thing for us to work with as our exclusive charge acceptor. Our technologies work best with doubly charged peptides that end in lysines or arginines. But LCMS is the only thing that has ever worked at all for these molecules, so we're stuck with them. What we need is a set of guidelines to at least reference --- and here is the first one I've seen! Honestly, I expected this to have maybe 50 different authors on it as some sort of an over arching consensus of a big meeting on the topic to sort it out. And, that might make me a little more comfortable, but I tell you what, this document is not bad at all. You know why? This group has actually validated some HLA peptides and successfully utilized them! This isn't a big hypothetical piece. Th..

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