Aftermarket high resolution FAIMS allows separation of MEGADALTON protein complexes!
News in Proteomics Research
by LCMSmethodAdmin
2d ago
  FAIMS gets a bad wrap because most of the commercial systems have a resolving power of something between 5 and 20. They're great systems if you just don't want to fragment (or see) +1 ions and you want your mass spec to only see +2 or +3 ions. Cleans up your spectra so your mass spec doesn't have to work as hard, and everyone is happy at the end. But....is that a limitation of FAIMS technology itself, or is that what is mass ? produced for the general market? Sure sounds like it's the latter.  In this new study an aftermarket/custom high resolution FAIMS system was coupled to a ..read more
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White House document appears to address sharing of proteomics and metabolomics data?
News in Proteomics Research
by LCMSmethodAdmin
2d ago
  I'm not sure what to make of this, but it is making the rounds on social media. It does appear to be in a fact finding mode. If you're interested in policy and how it might affect how and what data we share internationally, maybe you'd enjoy this quick read.  ..read more
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5-plex your data INdependent analysis methods by modifying dimethyl tags!
News in Proteomics Research
by Unknown
3d ago
This has sat with a bookmark on it for quite a while I hoped that I'd remember to ask someone intelligent questions about it.  Multiplexing DIA sounds like either the best or worst of both worlds. More samples/day but you've increased the complexity of your background so those magical neural network thingies have to think a lot harder.  There is very little chance I'd consider 2-plexing my DIA. That isn't worth it to me in any way at all. 3-plex? That is enough that I bought reagents so I could eventually try it, but I haven't been anywhere near excited enough to actually do the tr ..read more
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Multi-study meta-analysis of dog samples with oral diseases!
News in Proteomics Research
by Unknown
5d ago
  I'm wrapping up a meta-analysis right now that I've bugged just about every proteomic informatics person I know about in one way or another. The insanely beautiful data that I'm working on reanalyzing is from a patient study where they said "you thought CPTAC was thorough? hold my espresso". No joke 33 offline fractions at 2 hrs each on a QE HF on these priceless human samples. The data is perfect for what I'm doing, but during the uploading of data for almost 70 patients, they missed a few here and there. The PI is now retired and the team is dissolved, so I ain't getting patient 36 ..read more
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SEER Proteograph prepped plasma on TIMSTOF Pro2 and HT!
News in Proteomics Research
by LCMSmethodAdmin
5d ago
  There has been lots of excitement (and some scary good data) out of the SEER proteograph system for plasma proteomics. Here is some more!  While the authors clearly intended this to be more of a comparison of two very nice recently released instruments in their lab, as you can probably see from the figure at the top, the proteograph steals the show. Clearly the 14-bit digitizer and higher capacity TIMS improve identifications, but the plasma precursors go up 3x - 4x when moving the prep to a kit that I have absolutely no idea at all how any of you can afford to use.  The pe ..read more
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Deep learning - of glycopeptides!?!?!?
News in Proteomics Research
by Unknown
1w ago
  Okay.....on the surface this was first surprising that the first PTMs we'd see deep learning successfully applied to en masse was going to be glycopeptides. Then I thought....well...the problem is the stupid sugars all have the exact same masses.  Here is an illustration from an unrelated study for fragmenting the fragments of the fragments to figure out what a glycan chain actually is because the fragments of the fragments of these important glycan chains still have the EXACT SAME MASSES.  So maybe this isn't the biggest stretch in the world ever (link to this paper and ..read more
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Asparagine to iso-aspartage conversion in norovirus infection!
News in Proteomics Research
by Unknown
1w ago
                             Holy cow, y'all, this one was definitely not a fun puzzle for these authors to sort out!  The punchline here is that there is a spontaneous post-translational modification - get this one - it is a deamidation of asparagine - which makes it the exact same mass as aspartate - that changes both the protein 3D structure AND alters binding partners. How do you go about even suggesting that is what is happening? It seems like they started with trying to mod ..read more
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Improve intact protein analysis with outlier rejection borrowed from astronomy!
News in Proteomics Research
by Unknown
1w ago
Apparently mass spectrometers aren't the only thing that generate "spectra"! And we aren't the only people who have to worry about averaging lots of measurements because we have limited signal. Would it be worth borrowing some tools from one of these other fields for -- a 45% increase in intact protein identifications?!?!?  Considering how many people in our field will drop $1M for a 20% increase in IDs, I'd say this is worth taking a look at. And - you don't even have to - it looks like you can just upgrade MetaMorpheus and run some topdown proteomics through it (good benchmark dat ..read more
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PRECISE readout of MEK phosphorylation cascades by top down proteomics!
News in Proteomics Research
by LCMSmethodAdmin
1w ago
  .....wow.... I won't lie. I'm stunned. I didn't think we were here yet.... and, to be fair, maybe we arent,but this group is!  Bad background by Ben: A whole lot of the central regulatory pathways controlling tons of things in cells are based on some key central phosphorylation cascades. MAP kinase and MTOR are famous ones. They modify proteins by phosphorylating them because the modification can be fast and it reversible. If you go into any oncology centric place there is probably some really really really skilled pathway scientist (or 4, if they can afford them) who can disse ..read more
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US HUPO 2024 special live episode of THE Proteomics Show is out!
News in Proteomics Research
by Unknown
1w ago
  No joke at all, this is by far, my favorite episode of the podcast so far. RASR has a great radio voice, asks super smart questions and Dr. Olga Vitek has such a cool perspective and story to share! Such great content that Ben couldn't even ruin it. 100% recommended!   ..read more
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