iiinova — where your digital self keeps evolving

Luke Gamon @lgamon.bsky.social · 07/10/2026

Ha!! Ok glad we have someone to blame 😂

Luke Gamon @lgamon.bsky.social · 06/10/2026

FWIW - one fell down and almost hit our staff scientist today. Luckily it missed him and also all the equipment. First and only time it’s happened in 10 years…. 🤷‍♂️

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Ben Neely @benneely.com · 06/10/2026

Do you know someone who knows lotsa cool stuff (macro to molecular) about sweat, ear wax, stomach/bowels, or the placenta? Cause we need them for #THEProteomicsShow. I am striking out too hard on these. Person just needs to be excited to chat, expertise is optional. DM or email me.

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Luke Gamon @lgamon.bsky.social · 03/10/2026

Lucky for me I only ever start reviews 1-2 days before the deadline 😇

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Luke Gamon @lgamon.bsky.social · 03/10/2026

Waiting more than a month for a journal to find >2 reviewers for a paper we submitted. In the meantime I accepted invitations to review 2 manuscripts and was told my services were not necessary 1-2 days before the deadline in both cases. How long until this system is turned on its head?

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ypic.bsky.social @ypic.bsky.social · 22/09/2026

🔬 Ready to turn your proteomics idea into reality? The Student Proteomics Fund (SPF) is a student-focused grant designed to support students in bringing their proteomics experiments to life! 📅 Call opens: October 1st, 2026 ⏰ Submission deadline: November 30th, 2026

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Luke Gamon @lgamon.bsky.social · 18/09/2026

I’ve heard of DDM coating vials/plates but never tried it myself. Seems easier to just use it in extraction since it carries through all steps anyway.

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Luke Gamon @lgamon.bsky.social · 18/09/2026

We do 20-200 laser captured ‘cells’ with DDM. Generally 0.05% for the extraction, final 0.02% in the injected sample (20uL full loop injection). We found that it is both the total amount on-column and also number of column volumes for washing that you need to watch out for.

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Luke Gamon @lgamon.bsky.social · 18/09/2026

Just cracked 4k injections. Wild.

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Luke Gamon @lgamon.bsky.social · 10/09/2026

That’s awesome. We always had to rely on our one guy who actually knew how to code for our little QC scripts/visualisation things. Feels very democratising that we can just make our own now.

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Luke Gamon @lgamon.bsky.social · 07/09/2026

Working on a paper about a super niche PTM that quite possibly only a really small number of people on the planet would care about. Incredibly excited to share it with all you nerds 😅

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Luke Gamon @lgamon.bsky.social · 07/09/2026

Also I’m all about refurbs these days. Sooooo happy with my big Thermo centrifuge for 96-well stage tipping.

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Luke Gamon @lgamon.bsky.social · 07/09/2026

Dont remember but I can check. I3x maybe? One is older that’s all I remember….

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Luke Gamon @lgamon.bsky.social · 07/09/2026

Yup! We have two and use them for lots of colorimetric or plate based assays. For UV it’s critical to use UV-plates with low absorbance in the UV range. Less critical for fluorescence. Often need to dial it in for your protocol/application. Eg for some fluoro reads we do multi-point and average.

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Luke Gamon @lgamon.bsky.social · 21/08/2026

Now I’ve started doing more reanalysis of others datasets I am feeling more and more guilty about our lack of sdrf’s…. Can they be added retrospectively by authors? After the datasets are published/manuscripts accepted etc? Or do you mean helping with adding metadata to others existing datasets?

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Luke Gamon @lgamon.bsky.social · 21/08/2026

Pridepy + ChatGPT (for finding and prioritising datasets, and even data files) has been quite fun

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Thanks Hao 😁 I would never have thought of doing it (basically microsurgery on the aorta ✂️). So glad to work with such creative students. P.S. Thanks for the regular flow of CVD literature to follow up on. Keep up the great work!

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Luke Gamon @lgamon.bsky.social · 20/08/2026

1) Not very well at all. Mouse plaques don't rupture like human ones do. Attempts have been made to develop models for stable/unstable plaques in mice but many caveats. The effect of disturbed flow is quite comparable though. 2) Yes! Didn't make it in but we see plenty of matrix processing events.

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Yup definitely. Even TIMS overload causes in-TIMS fragmentation (was published in the TimsTOF + MSfragger paper). This together with the new preprint suggests anyone doing peptide level analysis (peptidomics, terminomics etc) should be filtering out ISF peptides with Rt matched parents.

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Luke Gamon @lgamon.bsky.social · 20/08/2026

I wasn't either!! There is a very nice preprint about it from a few months back. Big issue in semi-specific searches of standard tryptic digests, still an issue in peptidomics. Been looking at some PRIDE datasets and I can tell you that 30% is really not far off. www.biorxiv.org/content/10.6...

biorxiv.org

In-source fragmentation in mass spectrometry-based proteomics: prevalence, impact, and strategies for mitigation

Peptide-level analyses are becoming increasingly popular in mass spectrometry-based proteomics and are being applied, for example, in immunopeptidomics, structural proteomics, and analyses of post-tra...

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Thanks Alison! Took us a long time to work out how best to visualise the data. As one of my students once said “you always have to make things hard, don’t you?” - referring to my love for rather complicated spatial experimental designs 🫣 Control vs treated? WT vs KO? Too easy 😅

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Thanks mate! Glad to be able to share it

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Following from @richard-kay.bsky.social - watch out for in source fragmentation, up to 37% of peptides ID’d <9 AAs are derived from ISF

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Oh yeah for sure, especially with DIA and MBR. We see this for WT vs KO all the time. Typically the hits in the KO are more random when you look at peptide level, highly consistent when you look at WT.

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Oh and BSA peptides are in every single injection now no matter what you do

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Well we know that doing a 200ng load followed by a 20ng load is a very bad idea. Always careful to do proper blocking and blanks between sample types. For differential proteomics we make the assumption that carryover (<5%) will not be statistically siginificantly different (randomise/blocking!)

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Luke Gamon @lgamon.bsky.social · 20/08/2026

@haoyin.bsky.social @eassociety.bsky.social @barteltlab.bsky.social @ucph.bsky.social P.S. Figure captions aren't matched to the correct figures in the autogenerated 'Full text' on BioRxiv. Will upload an updated version ASAP which will hopefully correct it.

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Luke Gamon @lgamon.bsky.social · 20/08/2026

This was an incredibly fun study, my second senior author paper (and Kathrine-Luke dream team publication!) Could not have been done without generous funding from @lundbeckfonden.bsky.social, @novo-nordisk.bsky.social and the expertise of the incredible Christina Christoffersen. 9/9

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Luke Gamon @lgamon.bsky.social · 20/08/2026

So it's a fair to say there is a hell of a lot of biology to be recovered from teeny tiny precious animal samples. Indeed, there may be a higher neutrophil burden in mouse atherosclerosis than previously assumed (very difficult to stain for, very difficult to pick up in RNA analysis). 8/9

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Extracellular matrix proteins were almost a class unto themselves and highly differentially abundant between both plaques and different vascular locations. The 'P4' plaque from the inner curvature of the aortic arch was a clear outlier, likely due to lower shear stress in this location. 7/9

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Again, slightly surprisingly, we show a strong neutrophil component with neutrophil granule proteins being highly abundant in the mouse plaques. While a strong innate immune component is expected, only 10-30% of white blood cells in mice are neutrophils, compared to 50-70% in humans. 6/9

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Luke Gamon @lgamon.bsky.social · 20/08/2026

One of the most interesting findings is evidence of early vascular dysfunction and atherosclerotic burden even in apparently 'healthy' aortic tissue (A1 closest to the heart and first major branch = most affected, A3 furthest from the heart and first part of descending aorta = least affected) 5/9

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Not only could we get a comprehensive proteome out of single plaques from individual mice, we could show there is a clear gradient of atherosclerosis associated proteins moving along the aorta away from the heart. The main drivers were the usual suspects (lipoproteins, immune associated and ECM) 4/9

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Luke Gamon @lgamon.bsky.social · 20/08/2026

We initially started trying to do laser capture microdissection of plaques in the aortic valves (a nightmare at the time) and Kathrine had the brainwave... 'hey, why don't we just cut out the plaques from the aortas with microscissors, I reckon I can do it'. Sure enough, she could! 3/9

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Luke Gamon @lgamon.bsky.social · 20/08/2026

The story actually begins with my first big animal experiment looking at atherosclerosis (build up of fatty plaques) in the aortas of mice. The then MSc student Kathrine and I painstakingly cleaned and imaged all ~60 aortas and quantified the extent of plaque in each one. 2/9

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Luke Gamon @lgamon.bsky.social · 20/08/2026

Get ready for our next spatial proteomics installment. This time - macro scale. Our sparkly new preprint examines protein changes in areas of turbulent flow in the aortic arch. www.biorxiv.org/content/10.6... Time for another science thread! #TeamMassSpec #SpatialProteomics #AtheroSky 🧵 1/9

Workflow figure for location dependent proteomics of the aortic arch. Atheroprone and atheroprotected microenvironments were manually dissected from APOE knockout mice fed a high fat diet.

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Luke Gamon @lgamon.bsky.social · 19/08/2026

Hey proteomics people - is it normal to see chymotrypsin peptides in commercial Pierce HeLa digest? Doing semi-specific searches on some PRIDE data and 40-50% of P1 is F/Y/H, while in other datasets it’s under 20%.

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Luke Gamon @lgamon.bsky.social · 19/08/2026

I call it “The Magic of the Dual Traps”

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Luke Gamon @lgamon.bsky.social · 19/08/2026

Great question! I'll have to go back and check. I think it's 5 aurora elite 15cm x 75µm columns. 5th is at 2.6k injections as we speak.

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Luke Gamon @lgamon.bsky.social · 19/08/2026

Samples types include: Plasma, brain, heart, adipose, liver, atherosclerotic plaques, aorta, skin, synovial fluid, cells of all kinds, lipoprotein particles... From species such as: Human, mouse, rat, pig, turtle... Thats what I can remember off the top of my head at least 😅

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Luke Gamon @lgamon.bsky.social · 19/08/2026

Just cracked 10,000 injections for 2026 on our TimsTOF Pro. Works out to ~40 samples per day including all downtime, idle time, preventative maintenance and also MOVING it from one building to another! (We run 60 or 30 samples per day chromatography - vast majority of those 10k are actual samples)

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Luke Gamon @lgamon.bsky.social · 19/08/2026

I’m all for it (some things are blatantly obvious for abundant isoforms eg plasma vs cellular fibronectin EDA domain) but I haven’t been that impressed so far with bottom-up proteoform analysis in complex samples (ie regular tryptic cell/tissue proteome)

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Luke Gamon @lgamon.bsky.social · 19/08/2026

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Luke Gamon @lgamon.bsky.social · 07/08/2026

Eeep! That’s not a cheap replacement. Been there before. We’ve had a good run the last year or so but I’m sure our luck will run out sooner or later.

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Luke Gamon @lgamon.bsky.social · 07/08/2026

@cashwood.proteaglyco.com I wonder if it’s the column rather than the method which is giving you robustness? We had much much better luck with pepsep vs aurora for peptidomics. I’ve never been involved in our attempts. We have a senior researcher who tried many different preps without success.

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Luke Gamon @lgamon.bsky.social · 06/08/2026

It can be done. With nanoDTSC we routinely get >2000 injections out of Aurora columns. Mixed samples, tissue, cells, isolated proteins, pulldowns, spatial/LCM, FFPE. Only thing we haven’t quite cracked yet is plasma peptidomics. Still bricks columns like crazy.

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Luke Gamon @lgamon.bsky.social · 31/07/2026

First day of holiday - paper accepted Last day of holiday - news that my Erasmus student has completed our first ever DVP experiment Good times!

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