حب وحياة

Proteomics Mineathon Challenge update — we’re almost there!

This might possibly be one of my very favorite idea I've had in my life. Current status, we have: 1) A ridiculously cool and important 2) Some impressive impartial judges 3) An almost ready launch page! 4) Like 30+ awesome (and patient) participants!!!! We're reviewing the rules and some final details and we should be good to go. Had no one signed up, it would have launched right on time (probably) but with so many people volunteering their time I owe it to everyone to try and come as close as possible to doing it right.

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Is a peptide quantitatively measurable? Here’s how you find out!

Okay....are you guys ready for this one? I wish I could say I was, but it's too important for us as a field to not think about.... Matrix matching? "Analytical figures of merit"?? Hey! This is the proteomics party, don't you come in here with all your boring analytical chemistry validation stuff....oh.....ugh...okay.... (Yes. I had to make that. You're welcome.) Why is this (study) important? In part because it addresses 2 separate concepts that need to be separated -- and they're right in the abstract: "....Our results demonstrate that increasing the number of detected peptides in a proteomics experiment does not necessarily result in increased numbers of peptides that can be measured quantitatively....." What? First of all, this study is like 4 pages or something and it represents an absurd amount of work. SRMs and DIA experiments (QE HF, I think) and a bunch of different HPLCs and the matrices are all sorts of fun -- CSF and FFPE and yeast digest and maybe I mi..

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The single cell proteomics revolution!

There are seriously 10 papers open on my desktop that I want to blog about -- and will! -- but I'm busy, so time for another super lazy post. Last year some cool people asked me if I'd be interested in doing some articles about things happening in proteomics that I absolutely thought the outside world should know about. My first thought?!?? Single cell proteomics (by SCoPE-MS). This is the best I could come up with. (Of course, I love to type, so I also talked about the study I credit with making proteomics a reality for the rest of us.) On this topic, I recently was so sleepy that I went through all the "comments" on my blog. There was around 2,000 spam messages suggesting all sorts of terribleness, but there were also some legit comments. And -- I tell you what -- SCoPE-MS gets some comments. Particularly regarding aspects of the RAW data in the public repositories, and I think that is something we will really need to talk about at some point. My opinion is that we've ..

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Purple — Pick unique peptides for viral (and other?) experiments from FASTA!

Hey you! Are you looking for a tool to help you select viral peptides for targeted assays? Unrelated --- what is the best color of dinosaur? I got you, yo. Check this out. Before you panic, when they wrote the paper "Purple" was just a Python script that you can get here. I assure you this is no longer the case. There is a very straight-forward (to install) executable that will set you up with a GUI that looks just like this -- -- that you can get here. What does it do? Well, it helps you select peptides that are ideal for targeted assays from the databases you feed it. Imagine Picky, but you can load stuff that isn't human into it. (If you are doing human proteomics -- you should be using Picky, btw. It's amazing). Purple: Feed it your peptide sequences you're interested in: Feed it your contaminating background. Choose your rules. Get your peptides!

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Remember that Prosit thing everyone was talking about? It is super easy to use!

It's about time that we talked about how to add.... ...well...deep learning...(but...come on, I HAD to use that when I found it, right?!?) to your proteomics workflow! Don't want to read my rambling about why Prosit is awesome and just want to do it? Skip to Part 2 below! I almost guarantee that there is someone at your facility who drops all sorts of words like this around -- and maybe that same person has given you reason to question their intelligence in other matters, but as long as they keep saying things about "neural networks" and "semi-supervised" whatevers it seems like everyone wants to talk to them, and maybe give them lots of money. Follow this easy walkthough and THAT COULD BE YOU. I jest, because Prosit is the real deal and has real world advantages, including more and higher confidence identifications right now. For a biomolecule, the peptide bond is a joy to work with -- energetically -- crudely optimize the collision energy and you'll break most of the..

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Covalent Protein Painting to measure in vivo protein misfolding!

If there is an easier looking experimental method to measure protein misfolding in vivo, I've never seen it. If you are interested in structural proteomics stuff at all, I highly recommend this preprint. Formaldehyde is pretty efficient at binding to proteins! Turns out that: 1) you can get heavy stable isotopically labeled formaldehyde 2) in your cells the formaldehyde can only get access to the outside of your protein 3D structures, effectively "painting" the surface of them. 3) You can compare different biological conditions by using "heavy" and "light" formaldehyde. Digest your proteins with chymotrypsin and 'voila -- you can quantitatively compare the outside of your proteins and protein-protein complexes! The downside here is that you have to think hard about the peptide identifications as -- CDH2 : 13CH3 , 13CH3 : CDH2 , 13CHD2 : CD3 , CD3 : 13CHD2 -- could correspond to Disaster Level: "deuterated deamidation" study. To fully eliminate this an issue, these authors ac..

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22 Phosphoproteomics Data Analysis solutions go head to head!

Sometimes I take a dataset and compare 2 different data processing pipelines. One time, maybe I compared 3? 22? What? Wow! Why do we even have 22 pipelines? The abstract suggest that there are very good reasons, actually -- the results aren't the same....and they propose a solution for this. Only a paywall and a biological requirement for sleep stand in my way of reading this right now! As a reminder -- there is a super epic community proteomics PTM challenge coming up in less than 2 weeks and I think maybe 10 labs have signed up for it so far. I think that this is probably a great resource to help set the stage.

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Peptide biomarkers for bacterial pathogens!

I've only got a few minutes, but -- wow -- is this ever worth reading! Microbial ID by shotgun proteomics is NOT new. But promising study after promising study seems to end up with -- no new clinical assays. MALDI-TOF with a BioTyper is easier in the clinic, I guess, but maybe we just need the right technologies to get us over the hump. Clearly, the insistence of researchers to continue utilizing NanoLC is a big hurdle, but maybe innovative sample prep methods would also help bridge the gap? They use some crazy technology in this one. A flow cell digestion method that allows a tryptic digest of bacterial proteins in one hour? And a depletion technology that removes "host" (human!) biomass?? I have to mention that this study is a big collaboration between groups in Stockholm (where HUPO 2020 is!) and Gothenburg, a city blessed by some dark metal gods or something to be the birthplace of the greatest bands that have ever walked this earth. Yup, I definitely had to mention that.

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صور حب وكلام حب عظيم كلام للمشاعر النبيلة

المصدر : صور رومانسية pexexls قلبي ينبض بأسمك كل دقيقة ممتنة لكل شئ جعلك لي أحبك فوق طاقتي فوق المسافات التي تفل بيننا فوق كل الاشياء التي تقف امامنا فوق هذا الحنين والشوق والأنين بداخلي أحبك كلام حب رومانسي وكل نبضات قلبي تنطق لكِ حباً ولأنك حبيبي فأنا اجمل الناس …

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