- by LCMSmethodAdminOfficial site link here! Highlights? 75 Hz in a Tribrid? That's rocket fast. Probably rocking the Excedion Pro's lower resolution Orbitrap scan rates? Unclear, but that would be the safe assumption. It looks like there will be 4 versions of ApeX aimed at different markets? There is a long held tradition for this vendor to take a big 'ol dump on the systems that you currently have…..wow, they rolled out a lot of details on these systems…. but there it is…….a giant jump forward from the venerable Assend….If this is the one that is boring enough to release several days before the conference, […]
- by LCMSmethodAdminI find it more helpful these days to simply point out the failure rate of transcript level measurements (because just about every wet bench scientist out there has ran into it), it is relatively cheap and easy to get those transcript measurements. (However, I've still never been offered a $100 genome. Have you? I hear it's a thing, but it still seems like $100s plural). What if it still had some value (besides finding point mutations in variant call files, of course!)? These authors suggest straight out heresy and suggest implying that you could integrate these data to group those peptide IDs […]
- by LCMSmethodAdminJust leaving this here so I can get back to it later in case we have some drug response data with a lot of variables! Super smart and some of the most honest writing. "Yes, in this dataset this other tool actually proves more sensitive"! I love it. The authors use both simulated and real datasets they generated using DIA and TMT and compared them. Refreshing and clever, even if you can't follow the maths.
- by UnknownI do like it when a new group gets on the the single cell proteomics train and starts optimizing/reoptimizing things. Despite the 300 reviews, 50 method optimization papers and 20 biological studies that have been published, each new one brings a new perspectice and observations.While I don't love every aspect of this paper (some insight on what LC gradients were used when seems to be entirely absent from the main manuscript, which makes me question the title which seems to describe a single workflow) there is some gold in here! In my lab we don't reduce and alkylate the single cell […]
- by UnknownIf you've been on this blog much recently, I am sorry.Also, you have probably seen me in some level of outrage about some recent studies where people have gotten anywhere from 1-4 measurements of the peptides they are looking at. Is it better than Illumina ProteinCrap? Absolutely. But is it good for mass spectrometry data? No. Why is it bad? Because some blogging academic says so? This new preprint looks at the problem in depth and finds that for high abundance proteins in blood, the 1-4 measurements per peak is actually not all that bad. Unfortunately….the cancer biomarker you are looking for […]
- by LCMSmethodAdminThere is some replication is flattery quote, right? I forget what it is.You might need a free account to read this, though. And the stuff from the article that I found most interesting was a link to another GenomeWeb article. Not sure what the rules are for taking screenshots from it…. But the point is that the Oxford people have taken a page out of the ProteomeTools project and have 150,000 peptides multiplexed labeled that they're currently running through nanopores! Smart, right?Which seems similar to what this group recently published on here, except they aren't working from synthetic peptides, rather […]
- by LCMSmethodAdminWhen I first saw this I thought – okay, so someone copied the nanosplits paper but they had an Asstral.And it's almost what this is – …but nanosplits requires a technically tough step where you split the droplet containing your mostly lysed single cells. This protocol gets around that step. They still use the same silly robot to isolate the cells, but you absolutely don't need it here (where you basically do need it for nanosplits, it's tough to print that droplet array in a FACs core), and that's a huge win for anyone who doesn't have the slow silly robot.
- by UnknownI was first going to start with something like this – When I read this title But I realized that 1) That's sorta mean.2) I bet a lot of people thought that all the work that has been done to adjust spectral libraries and deep learning algorithms has been successful3) Not everyone is doing loads of weird cell types by single cell proteomics on TIMSTOFs and probably doesn't run into this every single day that their TIMSTOF happens to be working.4) The giant red light on the whole front of my instrument is bumming me out. Here is the thing. The Orbitraps had a […]
- by UnknownIt might be easier to make a list of things S100 proteins don't appear involved in at this point.This paper is going to be posted here because I'm personally interested in it and I wish my lab had access to these samples. The samples were digested with some amount of trypsin. You'll never find out how much, but I bet it is fine. They were also labeled with some kind of TMT reagents. The TMT labeled (and, presumably, pooled) samples were analyzed with a Q Exactive of some kind, probably, despite the Agilent high flow coupled Fusion system in the diagram […]
- by UnknownAre you an investigator who was assigned a bank heist? Do you suspect a certain goat, recently out of the pen, with an alibi that seems a little too good to be true? If you can find just one hair at the scene of the crime, this is the study and these are the resources you need! Is that goat still baaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaad, or has 20 years on the streets stripped you completely of your idealism about the system and it's ability to reform animals? Find out with proteomics!
- by LCMSmethodAdminWait. Where does thermolysin cut? Does everyone know that and that's why it isn't listed in the methods section of the paper? It's so common knowledge that the Wikipedia page doesn't list them explicitly either? Gemini, which is apparently now installed in my browser without my permission says it's Leu, Phe, Ile, Val, Ala, and Met, so I'll bet you that is NOT where it cuts. However, this is really cool, for real. I love fast cheap enzymes for proteomics! Let's go. However, the reason this paper is great is because they went the extra mile and developed a stable isotope labeled protein […]
- by UnknownI received some questions about my longer term impressions of the amazingly sensitive and somewhat fast TIMSTOF Ultra2. It's been a year already? Yikes. I guess I'll reference my earlier TIMSTOF reviews.Great stuff!1) The sensitivity of this thing is still absolutely unreal. Multiple people are writing up papers on single cells ran on it with DIA label free and the numbers are cell type specific and amazing.Even with a high loss, but very inexpensive and very fast sample prep, most cancer cell check in at well above 2,000 protein groups per cell and human hepatocytes are around 2,500. Throw in a […]
- by UnknownThis new paper maybe isn't for everyone, but I'm excited to look at these scripts. There are a very small number of supported software packages out there in the world (approaching zero) that can make sense out of direct infusion of flow injection analysis quantitative data. We used to have a pile of them. Ion A is 10x higher than ion B in these two matrices, you could extract that a bunch of ways, but that's largely fallen off.I'm also excited to see how many metabolites look real in direct injection in an Exploris 480. The intrascan linear dynamic range of a […]
- by UnknownFor real, I've been telling people about this conversation since we recorded it a while back. Snot is way cooler than you'd guess.
- by UnknownThe fact that some labs have some weird background ions that other labs don't (check my repositories for Pug keratin! There's tons of it!) isn't news. Someone a while back showed they could tell when a study was done in the winter due to the amount of wool peptides ionized in their deposited data. I forget who that was.But this new paper in JASMS shows that it's not just proteomics and peptides. It can even be those nasty adduct things that everyone outside of one group in Madison, Wisconsin ignores is even a thing in proteomics. This is the first time […]
- by UnknownMaybe this was here before? I'm not going to look, but it's definitely out now in JPR.It makes sense in my head, though. The same way that a single population of a million ions ionized at the exact same second might end up being distributed between mostly +2 charged, some +3 and maybe a barely detectable number of +4. Why wouldn't that population of peptides dissolved in acidic buffer also have 2 different possible shapes (or more?) Is that charge linked in some way? Would make sense. The authors suggest a simple calculator for predicting both modes – which would […]
- by UnknownI'm legitimately knocking out a couple of blogposts to get my brain fired up for writing and my hands used to the new (quieter) keyboard I brought to a super intensive 3 day writing camp. R01 resubmit peer pressure time! As you might guess, both R01s I should be writing on are about the human liver and not honey bees, but you probably have a dumb way of doing things as well. Where the f' is the control key? I'd rather look for it here. AND honey bees are super cool! Did you know that worker and drones (which I thought were […]
- by UnknownInteresting! When this group talks about -omics they even include lipids and metabolites. Worth taking a look at for sure. Figure 2 is one of the clearest descriptions I've ever seen of machine learning classifiers. The link to the web portal in the paper appears to need a user name and passcode, but I ain't got time for that.Probably faster to pull the code from this Github anyway.
- by UnknownI had a really weird conversation this week when people were talking about how many "tokens" they were using for making AIs do things poorly for them.Look, I'm also getting AIs to poorly do things for me that I don't know how to do. What I'm not doing is 1) Paying for them…2) Letting some money hoarding corporate weirdos see what I don't know how to do by sending my prompts off to some AI datacenter they knocked down a park to build.And the LLMs on modern hardware can run faster than the cloud based ones because the upload/download speed can […]
- by LCMSmethodAdminI love when a proteomics study makes my newsfeed! Did I know what a gastruloid was before yesterday? Related, do you have gastroids? Here is a link and there are reasons this ultracool study is making the popsci popups!This is one of the earliest stages of mammalian development – studied at ridiculously high depth here by RNA-Seq, proteomics (by TMT SPS RT MS3) and phosphoproteomics by the same.Don't feel like reading? Check out this awesome interactive webpage with protein networks and protein by protein visual analysis. Edit: I thought it had phosphopeptide interactions mapped, but I think I just clicked on a bunch of […]
Mass spectrometry websites, social media, journal feeds, and other links and items of interest to the mass spectrometry community.
