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Alejandro Brenes

@ajbrenes.com
1.4K followers 1.1K following 687 posts

Wellcome Early Career Fellow @edinuni-irr.bsky.social @edinburgh-uni.bsky.social | neutrophils single cell proteomics | road cyclist and aero bike enthusiast 🇨🇷🏴󠁧󠁢󠁳󠁣󠁴󠁿 Creator of the Immunological Proteome Resource @immpres.bsky.social

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Reposted by Alejandro Brenes
Mann Lab @mannlab.bsky.social · 15/09/2026
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...
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ProteomicsNews (Ben Orsburn) @proteomicsnews.bsky.social · 16/07/2026
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...
proteomicsnews.blogspot.com
Preprinted data featured in Day 1 at SCP2026!
I've got to start a new page of notes for day 2 or OneNote will definitely crash. Obviously there is a lot of unpublished data here I don'...
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Reposted by Alejandro Brenes
IonOpticks @ionopticks.com · 15/07/2026
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.
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Reposted by Alejandro Brenes
Times Higher Education (THE) @timeshighered.bsky.social · 09/07/2026
A drop in the number of international students coming to the UK cost the country nearly £3 billion, according to new estimates www.timeshighereducation.com/news/f…
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Mann Lab @mannlab.bsky.social · 10/07/2026
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...
biorxiv.org
Cell-type-resolved spatial proteogenomics from matched genome and proteome of the same cells
The genome and proteome of the same cells are rarely measured together, which is especially consequential in cancer, where somatic mutations vary across clones and drive disease. We show that a single...
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Reposted by Alejandro Brenes
Nikolai Slavov @slavov-n.bsky.social · 25/06/2026
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.
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Reposted by Alejandro Brenes
Pedro Beltrao @pedrobeltrao.bsky.social · 23/06/2026
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.
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Nikolai Slavov @slavov-n.bsky.social · 23/06/2026
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 ?
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Reposted by Alejandro Brenes
Kit Yates @kityates.bsky.social · 18/06/2026
What an amazing story.❤️
bbc.co.uk
Cervical cancer deaths fall to zero in young women given HPV vaccine
A new study finds that hundreds of lives have been saved since school-age girls were offered the HPV jab in 2008.
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Alejandro Brenes @ajbrenes.com · 16/06/2026
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.
biorxiv.org
The Single Cell Proteomic blueprint, navigating instrumentation platforms, software tools and high-load libraries in neutrophils, RKO and A549 cells
Mass spectrometry-based single cell proteomics (SCP) is rapidly emerging as a powerful approach for biological research, with applications extending beyond in-vitro cancer cell lines. Recent advances ...
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Reposted by Alejandro Brenes
Institute for Regeneration and Repair @edinuni-irr.bsky.social · 10/06/2026
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
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IonOpticks @ionopticks.com · 10/06/2026
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
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Reposted by Alejandro Brenes
dcheung26.bsky.social @dcheung26.bsky.social · 29/05/2026
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.
elifesciences.org
Lipopolysaccharide stimulates dynamic changes in B cell metabolism to promote proliferation
B cell activation and antibody class switching requires coordinated metabolic rewiring, with essential roles for amino acid transport, cholesterol metabolism, and prenylation in driving proliferation ...
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Reposted by Alejandro Brenes
Richard Unwin @rdunwin.bsky.social · 29/05/2026
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.
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Vadim Demichev @vadim-demichev.bsky.social · 27/05/2026
QuantUMS is the default method in our DIA-NN software. www.nature.com/articles/s41...
nature.com
Accurate quantification in proteomics with QuantUMS - Nature Biotechnology
QuantUMS implements uncertainty estimation for protein quantification in mass spectrometry.
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Reposted by Alejandro Brenes
Magnus Palmblad @magnuspalmblad.bsky.social · 22/05/2026
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.
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Reposted by Alejandro Brenes
ASMS @asms.org · 08/05/2026
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
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British Society for Proteome Research @ukbspr.bsky.social · 05/05/2026
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.
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Reposted by Alejandro Brenes
Matrix Science @matrixscience.bsky.social · 05/05/2026
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
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Yasset Perez-Riverol @ypriverol.bsky.social · 04/05/2026
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-...
github.com
GitHub - bigbio/sdrf-skills: Agentic plugins to annotate SDRF using Claude; Codex; Cursor; Gemini
Agentic plugins to annotate SDRF using Claude; Codex; Cursor; Gemini - bigbio/sdrf-skills
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Yasset Perez-Riverol @ypriverol.bsky.social · 30/04/2026
🚀 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.
ebi.ac.uk
SDRF Validator
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One Health Genomics Edinburgh @onehealthgenomics.bsky.social · 24/04/2026
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...
nature.com
Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma - Nature Communications
Neutrophils infiltrate glioblastomas with the capacity to engage pro/anti tumoural responses. Here the authors developed proteomic workflows to stratify neutrophil heterogeneity by function. This work...
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Alejandro Brenes @ajbrenes.com · 23/04/2026
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.
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ProteomicsNews (Ben Orsburn) @proteomicsnews.bsky.social · 17/04/2026
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!
github.com
GitHub - OrsburnLab-Pitt/SCPViz: The new home of the SCP Viz program
The new home of the SCP Viz program. Contribute to OrsburnLab-Pitt/SCPViz development by creating an account on GitHub.
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Reposted by Alejandro Brenes
British Society for Immunology @britsocimm.bsky.social · 16/04/2026
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!
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Alejandro Brenes @ajbrenes.com · 16/04/2026
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 😃
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Alejandro Brenes @ajbrenes.com · 15/04/2026
For those of you who, like me, were eagerly waiting for it, the cherry blossoms on the meadows are finally out #sakura #hanami
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Reposted by Alejandro Brenes
Coscia Lab @coscialab.bsky.social · 13/04/2026
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
go.nature.com
Deep visual proteomics uncovers nociceptor diversity and pain targets - Nature Communications
Sensory neuron subtypes are defined by transcriptomics, but their proteomic identities remain unclear. Here, authors show distinct protein signatures of electrophysiologically defined nociceptors and ...
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Reposted by Alejandro Brenes
Nature Methods @natmethods.nature.com · 16/06/2025
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...
nature.com
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature Methods
A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass spectrometry analysis p...
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Reposted by Alejandro Brenes
ContempraInn 🌹 @contemprainn.bsky.social · 02/04/2026
Cherry Blossoms 🌸 Sakura Season in Japan 🇯🇵
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Alejandro Brenes @ajbrenes.com · 03/04/2026
Senescence applied to neutrophils is just silly. None of them are dividing ... and thats how its meant to be...
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Wolfgang Huber @wkhuber.bsky.social · 01/04/2026
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.
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The Gairdner Foundation @gairdnerawards.bsky.social · 31/03/2026
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
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Lindsay K Pino @lindsaykpino.com · 31/03/2026
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.
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Perona Lab, Edinburgh, UK @peronalab.bsky.social · 30/03/2026
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...
elxw.fa.em3.oraclecloud.com
Flow Cytometry Technician
We are looking for an enthusiastic person to join the flow cytometry facility in the King’s Buildings campus at the School of Biological Sciences in the University of Edinburgh. This role involves pro...
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Reposted by Alejandro Brenes
Shabaz Lab @shabazlab.bsky.social · 27/03/2026
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.
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Alison Chaves @alisonchaves.bsky.social · 13/03/2026
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...
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Richard Sever @richardsever.bsky.social · 12/03/2026
"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...
nature.com
How bioRxiv changed the way biologists share ideas – in numbers
Four million articles are now downloaded from bioRxiv every month, according to an analysis of the life-science preprint server’s first 13 years of existence.
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Mayor of London, Sadiq Khan @london.gov.uk · 07/03/2026
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.
nhs.uk
MMR (measles, mumps and rubella) vaccine
Find out about the MMR vaccine for measles, mumps and rubella, including who should have it, when it's given and possible side effects.
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Richard Sever @richardsever.bsky.social · 05/03/2026
"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...
nature.com
Hey ChatGPT, write me a fictional paper: these LLMs are willing to commit academic fraud
Mainstream chatbots presented varying levels of resistance to deliberate requests for fabrication, study finds.
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IonOpticks @ionopticks.com · 04/03/2026
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
bit.ly
Armed and ready: How Alejandro Brenes is uncovering the hidden lives of neutrophils in brain cancer
Dr. Alejandro Brenes, a Wellcome Trust Early Career Fellow at the University of Edinburgh’s Institute for Regeneration and Repair, is uncovering hidden neutrophil populations in glioblastoma that coul...
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Liam Thorp @liamthorp.bsky.social · 01/03/2026
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.
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Nature Reviews Immunology @natrevimmunol.nature.com · 28/02/2026
ICYMI: Intermittent fasting evicts long-lived plasma cells from survival niche
dlvr.it
Intermittent fasting evicts long-lived plasma cells from survival niche
Nature Reviews Immunology, Published online: 27 February 2026; doi:10.1038/s41577-026-01286-2Zhu et al. report in Immunity that ketogenesis resulting from intermittent fasting causes the downregulation of CXCR4 expression on plasma cells, triggering their egress from the bone marrow and impaired humoral immunity.
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Chris Ashwood @cashwood.proteaglyco.com · 26/02/2026
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.
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Alan McNally @alanmcn1.bsky.social · 23/02/2026
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
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Nature @nature.com · 22/02/2026
Veins in the skull can rearrange their borders to accommodate patrolling immune cells go.nature.com/4tLrKul
go.nature.com
How ‘skull drains’ keep the brain safe from damage and pathogens
Nature - Veins in the skull can rearrange their borders to accommodate patrolling immune cells, a strange behaviour called ruffling.
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Michael MacCoss @maccoss.bsky.social · 21/02/2026
Excited we renewed our long-term relationship with Sciex to ensure our software tools Skyline, MSConvert, Panorama, AutoQC, etc... work seamlessly with Sciex hardware. We have big plans for Skyline in the upcoming year.
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Damian Shields @damianshields.bsky.social · 20/02/2026
Talisker tides, Isle of Skye #Scotland #IsleofSkye #Talisker www.damianshields.com
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Wolfgang Huber @wkhuber.bsky.social · 19/02/2026
We're live-watching the 21st century version of authoritarian propaganda. Facebook, of course, was the pioneer. doi.org/10.1038/s415... 20th century totalitarians had to do with newspapers, radio, TV.
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Chris Ashwood @cashwood.proteaglyco.com · 16/02/2026
We’ve all had samples where BCA/qubit quant correlates poorly with LC-MS TIC. Looks like those assays aren’t always needed: “protein quantification and physical normalization steps can be omitted…without incurring an unacceptable increase in measurement variability after computational normalization”
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