Category Archives: Uncategorized

What great timing. I was just whining about how I can’t make Perseus do something that seems really simple in my head — BOOM! 4 new Perseus videos! You can access the MaxQuant Summer School videos on the YouTube page here. I’m personally going to start with video T4. Because I suspect I’m missing somethingContinue reading “MaxQuant Summer School 2019 videos are up!”

Do you have 4-5 weeks? Do you need to get an absolute understanding of the rates of protein turn-over IN A LIVING ANIMAL SYSTEM? This isn’t the first technique for protein turnover measurements. This may be, however, the most complete picture that we’ve been able to get. If your strengths aren’t exactly centered in theContinue reading “Precise protein turnover — IN LIVE ANIMALS — the ultimate protocol!”

Recently there has been an explosion of new evidence that proteomics has value in forensics analysis. While it’s obvious that this is a great thing — I’d also argue that it might be kind of a scary thing as well. Could you, for example, determine every sample I’ve ever prepared in my life from theContinue reading “Forensic proteomics is coming fast — Genetic variation detection in hair keratins!”

Talk about a surprise! I am cranking on this cool dataset for a talented young biologist and I thought — what the heck — I haven’t put anything into STRING in so long I’m not even sure if it is still supported and —  The output is just stunning — and reeeeeeeaaaaaaaaly helpful for hisContinue reading “STRING 11.0 — You should take time to revisit this resource!”

I’ve mentioned Picky on this blog before, but I don’t think it’s possible to bring enough exposure to some tools and Picky is definitely one of them. You can read about it at Nature methods here.  But that’s probably not what you actually want to do. What you actually want to do is go here: Continue reading “Picky — Shiny magic to build the ultimate targeted assay online!”

At 3 meetings I spoke at this year, I ran into an enthusiastic person after my talk who wanted to give me Ribo-Seq data so we could compare our proteomes and “translatomes”.  I get a lot of offers to take hard drives full of other people’s data and spend all my free time on it.Continue reading “RiboSeq is better than RNASeq for correlating with protein abundance but still not the same thing!”

I’m as close to without words as I may be able to get. As awesome as this new study is, it sets a scary new bar for what biologists and clinicians can expect from the interpretation of -omics datasets. You should just go check it out here: http://www.ProteomeHD.net This study goes to a depth ofContinue reading “ProteomeHD.net — A coregulation map of 12.5MILLION human protein measurements”

I haven’t done a subcellular fractionation in a while, but I’ve got a project coming my way probably since global didn’t do a good job of grabbing the nuclear protein(s) of interest. Most (all?) of the subcellular fractionation techniques were designed for something else. Maybe they were for getting nuclear DNA or for electron microscopyContinue reading “Easy & Fast Subcellular Fractionation — All MS-compatible reagents!”

There is a lot of basic physiology to learn from in this great new study study in “Histology.” It’s so cool to pick up study that you can already follow most of (in my case, the proteomics, most of the time) and then use that framework to fill in all sorts of things you’d neverContinue reading “Proteomics of Single Muscle Fibers!”

In the “how on earth did they get enough material to pull this study off?!?!” department, I present this new paper at JPR!  Have you ever dealt with people with human brains? My gosh, you’d think it all comes directly from the investigator’s skull the way every microgram of material you ask for causes groansContinue reading “Quantitative Subcellular Proteomics of Cortex of Schizophrenia Patients!”