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Proteomics Research 07/15/2020 13:16
I brazenly stole this photo off Twitter this morning from Ryan Julian (JLab @ ). Recognize part of it? Did you throw a couple out? Hold onto it! They came up with a brilliant way of utilizing it for good. On that topic, every year or two I remember to redirect people to the amazing For years, UWPR has kept an awesome part list and directions for how to make your own nanoflow source for Thermo instruments -- both the traditional LTQ interface (that is also on the Q Exactives) and the newer NG source configurations. I hate nanospray, but my plans for single cell for 2020 aren't going to go very far without it, but it doesn't take too much imagination to rig these up for Microflow/microspray, (that fine line before you get <1uL/min when everyt.
Proteomics Research 07/14/2020 07:29
If you are going to catch one random proteomics webinar this week, may I suggest the OCCPR Webinar tomorrow? There are many mysteries here and I think this webinar will make an attempt at answering some of them. On the MSFragger software: How is it so crazy fast? Seriously, what is it doing that other programs aren't doing? What's next for it, and the ? There are other mysteries -- what about the man behind the team behind it? Alexey Nesvizhskii? He's done a lot for proteomics. Is he a ? His dabblings with diverse subjects such as , , and the suggests he I just know that when we really need this mysterious hero, we can put a . Finally, and perhaps, most importantly do you properly say his last name..... I've heard several valiant att.
Proteomics Research 07/13/2020 14:48
What if you could make top down (and NATIVE!) mass spectrometry a whole lot more accessible -- with gel based separation? Would that make you peppy? The P stands for Passive and I'm not sure why, but if more than a few of us are ever (really) going to adopt top-down and native proteomics (I don't mean super pure antibodies, I mean the complex stuff) we need to simplify the front end and this looks like a great new tool for it! ! (Open access!)
Proteomics Research 07/12/2020 07:26
I'm a couple weeks behind...on...well....everything....but I really dig July's special edition cover -- and, in particular, this great summary piece! Want a summary of some new -- or newly improved tools for your workflow? If nothing else, bookmark it, and the next time someone comes by your office with something that you feel like you could probably pull off, but aren't sure how with your typical workflows -- maybe it's here! --. -- and if you see a technique on the list that you've never ever heard of -- it's probably in this special edition! Someone remind me to read up on block's not in my folder, and I think I've retweeted it 4 times so I'll remember....
Proteomics Research 07/11/2020 08:36
"....Google Images, making weird mass spectrometry blogs even weirder, since 2009..". I'm running a lot of MaxQuant right now because I'm running lots of really complex samples with short BoxCar runs and -- if you to quantify BoxCar data, MaxQuant has a little box where you put a checkmark and then it does magic. There are 2 other options for processing BoxCar data. 1) Gibberish quan 2). (Please correct me if something has changed recently, but as long as MaxQuant works, I'm honestly cool with it for these projects) For MaxQuant output, you have loads of options. 1) An persistently hideous spreadsheet format that Excel has even more persistently refused to open 100% successsfully for nearly a decade. 2) The ultra powerful, can do absolutely e.
Proteomics Research 07/10/2020 15:55
MSFragger is FAST. Like really really fast. As features have piled up on MSFragger to make it more useful, it has slowed down, but it is still a program that is darned fast for a desktop CPU program. says something....I'm not sure what....something, for sure....when a 2 hours TIMMYTOF run with PASEF takes 70 minutes, on average, to process with MSFragger and that is massively outstripping the competition. Good news -- there is another tool to process PASEF-TOF data with! Bad news -- you still have to be patient. This data is dense!
Proteomics Research 07/03/2020 12:22
Whoa. This blog has suffered due to the fact that I'm just tired of writing. Or just tired. One of those. My last shift in clinical chemistry was over a dozen years ago and while the instruments have gotten much much much better, the amount of paperwork necessary to prove that your assays are valid when it really counts has....gotten better if you are thinking about thoroughness (the most important part) and...hmmm.... nah...not sure where I was going with that. I'm sleepy even though I'm staying within walking distance of my lab so I can be here ALL THE TIME! WOOOOOHOOOO! What I thought would be interesting to ramble about over lunch is INSTRUMENT QUALIFICATION (sounds the oppositive of interesting, right? However --did you know that when
Proteomics Research 06/23/2020 06:36
WOOOOOOOHHHHOOO!!!! . You do need the Docker Desktop thing, and if you were forced the mandatory Microsoft Edge thing in the last 5 days, Docker may have issues (my 2 PCs that had that update throw an error that my Windows version isn't new enough, my PCs that have updates disabled are just fine). Like most Smith lab software it is really straight-forward. You do need to make sure that you allow Docker access to the hard drive where you have Spritz. You can either download your FASTq files from your "next gen" stuff or you can pull directly from One surprise is that (being a dummy) I thought that Docker was just for GPU based software, so I wanted to make sure to run it on a PC with a decent old GPU, but the software recognizes how many CPU.
Proteomics Research 06/22/2020 13:59
You know what you need right after your 3 weeks of ASMS videos?? Another Proteomics and Metabolomics Symposium!!! Y John Yates is the Keynote and he's a great speaker, and I'm not sure I've ever heard Kathryn Lilley speak (bonus!) and Birgit Schilling always has something cool to talk about how she's working on stopping people (only cool people) from aging. I also get to ramble a little about the #ALSMinePTMs project finally!! But this kind of snuck up on me so the data hasn't all been crunched yet.
Proteomics Research 06/22/2020 13:50
When I read the catchy title of this new paper, I thought of some TV commercial jingle, but if Google images gives you an old Doctor Who image, you use it... . .... Why? I dunno. I just thought it was funny to type. I haven't done tons of plant proteomics. Some cannabis stuff, a few grape vines, or three, maybe a tomato study that I consciously try to forget? seems familiar and besides being a pain to get the proteins out, and seeing anything but ruBisCO, the proteins are typically really short. This group does a stellar job of trying to overcome the two relevant obstacles for them by painstakingly optimizing (in previous studies you'll find in the text) the extraction and digestion methods. They demonstrate here that the use of complementa.
Proteomics Research 06/19/2020 06:20
Rapid highlights? -EvoSep 1 ultra rapid gradients + QE HF-X -Fractionation + DDA for libraries -HF-X DIA for (most of? again, moving fast, busy day ahead) the global proteomics -Interestingly -- DIA for the phosphoproteomics and the # of isolation windows changes for the phosphoproteome, but the collision energy does not. -Some of the prettiest downstream interpretation data you'll see this week. Are y'all keeping artists around for this stuff? My stuff comes out of Perseus looking like this. (I actually Googled "ugliest R plots" and was relieved that most of the things that popped up are even worse than my histograms)
Proteomics Research 06/16/2020 07:24
Okay --- maybe THIS is finally it? Maybe this is the tool that can link all the phosphoproteomics data together into something that saves us from having to look up each and every one, or relying on that one "pathway analysis guru" that you might or might not be lucky enough to have at your work, or occasionally go rock climbing with? (I've been trying to figure out a social distancing rock climbing solution, to no avail....booooo....2020....booo.....). I haven't test driven it yet, but a quick check of the figure above (what I highlighted) MAPK1/3 are definitely linked to the phosphorylations on Q15418. If those are linked to TP53 phosphorylation regulation, UniProt doesn't shout it out in the first page, but it seems very likely that they'd.
Proteomics Research 06/08/2020 07:29
A lot of these tools have been out for a while ().... ...but this is a great compendium of the tools that are available and the super simple command that you can use through the REST interface () to pull up proteomics data from anywhere and basically anything! Proteomic informatics is getting better every day, and we might be leading the way for -omics when it comes to data sharing and transparency (having significantly smaller files might be helpful in this regard, but still)! There is so much power here that you're basically only limited by your own imagination. Need a good example? What if you were really interested in 2 proteins and wanted good experimental spectra from situations where you'd find them? You could make a line like this.
Proteomics Research 06/07/2020 20:00
Hey! Yes, my favorite week of the world is currently happening (#ASMS2020), and the largest acts of civil disobedience in half a century are occurring around the world, buut -- COVID-19 is still happening. Our good friends at the London Proteomics Discussion Group haven't forgotten and they're still trucking away to find the science being done and bring it to everyone's attention. This Friday -- Clinical Classifiers. Huge deal! There are hypotheses being kicked out all over (today I heard that people with certain blood types are faring worse than others? Not sure if that is true, but it's clear some people are doing much worse than others, and viral load (level of exposure) doesn't seem to be answering all the questions.
Proteomics Research 06/06/2020 21:19
I'm woefully behind on ASMS stuff. 2020 (the year itself) has been a little tiring. One takeaway that I've got for this year is that we're finally seeing Graphics Processing Units in Proteomics. I think I've rambled about this here before, but I can't find it. Anyway, in today's computer stuff we basically have 2 kinds of processors Central Processing Units (CPUs) -- these are the stickers on your computer "i7" "XEON" or, more commonly now "Ryzen" and, if you're really lucky, "Threadripper" (I am not this lucky yet) CPUs have a small number of cores but each core has access to tons of resources. Graphics Processing Units (GPUs) have TONS of cores, but each core is capable of doing only very small things, like controlling a few pixels. A lot.
Proteomics Research 06/02/2020 06:19
There is some great -- unfreaking believable -- amazing science streaming as the ASMS reboot and ... just when the world seemed like it couldn't get more chaotic ....protests about excessive use of force by the police were met by even more excessive use of force by police.... during a global pandemic ...and it's hard to pay attention to even the best science in the world. This blog isn't right when it's serious so I'll throw in the true story about the one time that I met Richard Yost. We're all missing our ASMS friends right now. One of mine is about 5 foot tall and hilarious -- and she might be able to lift a small car. One year she'd loaded up on cool vendor swag like cannabis themed light up gear, including a brightly flashing cowboy ha.

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