Alejandro Brenes

Excited to share our work at @natcomms.nature.com We used single cell proteomics to define the functional heterogeneity of human neutrophils in glioblastoma, finding pro and anti-tumorigenic effector states invisible to scRNAseq. SCP will revolutionise immunology, this is just the start

How we’re approaching AI at bioRxiv and medRxiv Large language models and other AI tools are reshaping how research is done and shared. We’ve been listening to our community, and our new blog post shares our current thinking. Read it here → lnkd.in/gg_-JMhN

Mike MacCoss will be the Next Editor-in-Chief of Journal of Proteome Research. axial.acs.org/analytical-c...

The IonOpticks HUPO T shirts did not survive contact with the outside world. Walking with the protein junkie T-shirt and i get asked at work: "So are you really into whey?" 😂

Proteomics analysis has always lived in its own universe. AlphaPeptTools puts it in #scverse instead, so that proteome, transcriptome and spatial data live in one ecosystem. 11 search engines (DDA+DIA) read in, proteomics-specific statistics, #scverse native. doi.org/10.64898/202...

Missed SCP2026 - here are the published and preprinted highlights - day 1 - proteomicsnews.blogspot.com/2026/07/prep... and day 2 proteomicsnews.blogspot.com/2026/07/prep...

Great to be at #BSPR2026 in Hinxton this week, supporting the UK's key proteomics gathering. On Monday, conference conversations continued at our Peaks & Pints event - it's been a pleasure connecting with so many of you. If you're still here today, stop by - we'd love to hear what you're working on.

A drop in the number of international students coming to the UK cost the country nearly £3 billion, according to new estimates https://www.timeshighereducation.com/news/fall-international-student-numbers-cost-uk-ps29-billion

New preprint: Cell-type-resolved spatial proteogenomics, matched genome AND proteome of the same cells. The trick: the flowthrough we normally discard after loading peptides onto an Evotip contains genomic DNA at 85–95% yield. One tip, two molecular layers. www.biorxiv.org/content/10.6...

As usually, the Single-Cell Proteomics Conference aims to maximize accessibility. Thus, #SCP2026 will enable virtual attendance via Zoom. It's free but requires registration at single-cell.net Only presentations by speakers who consent to Zoom broadcast will be included in the virtual program.

Switzerland and the UK making the most of their participation in the EU research funding initiatives with Switzerland tied with Germany for the largest number of grants in life science.

A decade ago, the money wasted on poor antibodies was estimated to be US $800 million / year. Global research antibody spending is ~$4-6B/year now vs $1.6B in 2015. What is your estimate for money wasted on poor antibodies in 2026 ?

What an amazing story.❤️

New preprint out! We benchmarked SCP workflows across instruments, software and library strategies. We compare DIA-software, search parameters, quantification precision and quant reliability across 3 cell types: large A549, medium RKO, and the very challenging ex-vivo peripheral blood neutrophils.

Celebrating IRR research, innovation and impact. Our 2026 symposium showcased our fantastic research talent. Congratulations to Flash Talk Prize winner Ellen McGregor, poster prize winner Jenny Riches and poster prize runners-up, AJ Boyland, Kellie Horan and Skye Jolly. 🎉 🔬 🏆https://edin.ac/4fBVzsP

Luke Gamon, Asst Prof at @ucph.bsky.social, built a spatial proteomics workflow from standard lab equipment: PCR tubes, centrifuges, basic plastics. When a single Aurora column can handle 2,500 injections and still perform, that kind of longevity changes what's feasible. Learn more: bit.ly/4ulX2XL

I’m delighted to announce that my first paper has been published in eLIFE! In this paper, we explore how B cells alter their metabolism to fuel changes in cell growth and proliferation following stimulation with the toll-like receptor 4 (TLR4) ligand lipopolysaccharide.

This is REALLY bad of Thermo. They've got caught, and their statement (in thread) smacks of a complete misunderstanding of of what they've done and disregard for their customers. What would happen if I submitted a paper with an image that had been "adjusted for presentaton purposes". Quite.

QuantUMS is the default method in our DIA-NN software. www.nature.com/articles/s41...

Companies selling faulty products by accident recall them and reimburse the customers. Some cost, some (temporary) loss in prestige perhaps. No one goes to jail. This is not the case here. This is more akin to the Theranos or VW emission scandals. And people did go to jail for these.

Congratulations to Nikolai Slavov, recipient of the 2026 ASMS Biemann Medal! This award recognizes significant early-career achievement and highlights emerging leaders shaping the future of #massspectrometry. #TeamMassSpec

BSPR 2026 is on 13th-15th July. Early bird discount til 15th May, register here: www.bspr.org/annual-meeti... We have exciting sessions covering: Comput. Proteomics/AI Native/Structural proteomics Clinical proteomics Population proteomics/non-MS proteomics single-cell/low input/spatial proteomics.

Matrix Science will be attending BSPR2026 in Cambridge, UK, on 13-15 July. Come chat with us about the latest developments with Mascot. Abstract and early bird registration deadline is 15 May, so it's best to book your place soon! #proteomics #massspec #BSPR2026

If you are annotating SDRFs from public proteomics data or your own submission, and you have access to #Claude; #gemini #OpenAI #Codex or ClaudeCode, you can use #SDRF-skills; really simple github.com/bigbio/sdrf-...

🚀 SDRF Validator is LIVE! Check it out 👉 www.ebi.ac.uk/pride/servic... With #SDRF v1.1.0, we’ve rolled out tailored templates for different experiment types - from Single Cell proteomics #SCP to Crosslinking, & more. The new validator + web interface makes it easy to catch issues before submission.

New Publication: Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma @edinuni-irr.bsky.social @cruk-si.bsky.social @edinunineuro.bsky.social @pranvera.bsky.social @ajbrenes.com www.nature.com/articles/s41...

for keen DIA-NN users, be aware that DIA-NN 2.5 has 5% FDR on by default!! not 1% like all previous versions. You have to change it manually every time.

MAJOR update for SCP Viz! github.com/OrsburnLab-P... - all the smart SCP code everyone hid on line 7,000 of their R package in a GUI with push buttons, lassos, and primary colors. Plus a special tab for peer reviewers who don't want to download 3TB of instrument .raw data. Live on the Pitt HPC now!

Hey #UKimmunomet26 attendees 👋 Come and say hello at the BSI stand! Chat with Laura Franklin (our Journals Manager) and Ellie Pearson (intern at the BSI) about our journals, how to submit your work, and the other opportunities we offer. We’d love to see you there!

I have to say the train ride down to #UKimmunomet26 is a beauty. Now looking forward to the next two days hearing about immunometabolism. Excited that there are even multiple neutrophil talks 😃

For those of you who, like me, were eagerly waiting for it, the cherry blossoms on the meadows are finally out #sakura #hanami

Excited to share our new @natcomms.nature.com study with the @garyrlewin.bsky.social lab and @amapruns.bsky.social. Using deep visual proteomics, we created the first neuronal subset-resolved proteomic map of sensory neurons with potential implications for pain treatment. go.nature.com/481nr4R

Assessing error control is fundamental in mass spectrometry-based proteomics. @bo-wen.bsky.social @maccoss.bsky.social @urikeich.bsky.social et al introduce a theoretical foundation for entrapment along with a method for more accurate evaluation of FDR control. www.nature.com/articles/s41...

Cherry Blossoms 🌸 Sakura Season in Japan 🇯🇵

Senescence applied to neutrophils is just silly. None of them are dividing ... and thats how its meant to be...

I want AI to do my email and admin so that I can do science and writing, not for AI to do my science and writing so I that I can do email and admin.

Congratulations to John R. Yates III, Ruedi Aebersold and Matthias Mann, recipients of the 2026 Canada Gairdner International Award. Prof. Yates: www.gairdner.org/winner/john-... Prof. Aebersold: www.gairdner.org/winner/ruedi... Prof. Mann: www.gairdner.org/winner/matth... #2026GairdnerAwards

Getting the ol' grad school gang back together with Carafe2 -- Bo Wen (@maccoss.bsky.social and Bill Noble) and @jspaezp.bsky.social (@willfondrie.com at @talusbio.bsky.social) teamed up for essentially some late night hackathons to build out Carafe for @brukercorporation.bsky.social timsTOF data.

Job opportunity for a #FlowCytometry technician, School of Biology, University of Edinburgh, UK. We do cool flow with fungi, bacteria, diatoms, space particles, as well as mammalian cells. Spectral, conventional and sorts. Join us! Details here: elxw.fa.em3.oraclecloud.com/hcmUI/Candid...

Post Docs are junior doctors/resident doctors of the scientific world. Current funding cuts combined with their traditionally poor treatment is turning off a generation of PhD students. Long term effects will be devastating. This 'correction' will be effectively permanent.

FragPipe users: I've updated PSManalyst shiny app. Check it out and enjoy the easiest way to evaluate the quality of your runs. Now you can map peptides to protein coverage counting PSMs. github.com/41ison/PSMan...

"bioRxiv is exactly the type of living experiment we all should be striving for, to achieve our shared goals of optimizing how research evidence is shared and used.” via @chrisnsimms.bsky.social www.nature.com/articles/d41...

Measles is one of the most highly infectious diseases, and it can make children seriously unwell. But it is preventable. Protect yourself and others by ensuring you’re up to date with your and your children’s MMRV vaccines.

"All major LLMs can be used to either commit academic fraud or facilitate junk science...guard rails are easily circumvented" Is anyone surprised? www.nature.com/articles/d41...

Single-cell proteomics revealed neutrophil populations in glioblastoma that transcriptomics missed. Some may be blocking blood vessels & worsening outcomes. @ajbrenes.com on the hidden complexity of "soldier cells" & his journey from accidental researcher to Wellcome Trust fellow: bit.ly/46HuIGu

As journalists working today many of us are taught to recognise disinformation when we see it and fight back against it. Unfortunately there are some who willingly seek it out and put it on their front pages. A disgrace to the profession.

ICYMI: Intermittent fasting evicts long-lived plasma cells from survival niche

Yikes, you know performance is bad when the figures of merit for the Astral Zoom MS2/Orbitrap MS3 comparison are # of IDs and a PCA. Please wait until they release a new Tribrid before buying a Thermo TMT instrument (or buy an Eclipse). The Astral Zoom doesn't look suitable for that application.

Make no mistake this is a concerted and organised attempt to completely undermine science and expert opinion. This is Covid denialism on steroids and it’s on all of academia to see this for what it is and push back as strongly as possible

Veins in the skull can rearrange their borders to accommodate patrolling immune cells go.nature.com/4tLrKul