Sign in

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

PostsRepliesMedia
Alejandro Brenes @ajbrenes.com · 18h
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...
020
Alejandro Brenes @ajbrenes.com · 21h
I've used it to re analyse my neutrophil single cell proteomics data. The representation was excellent and made much biological sense. Mature neutrophils sit close together. Immature branch off. NETing populations are far off. Its great ill keep using Bonsai! Great tool!
182
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...
1124
Alejandro Brenes @ajbrenes.com · 16/07/2026
static.klipy.com
Yolandafister Alan Carr with Lantern
ALT: Yolandafister Alan Carr with Lantern
000
Alejandro Brenes @ajbrenes.com · 16/07/2026
I've left now, was at that campus for the conference, but it was where EMBL EBI is. Yasset should be able to help with that though, but hes doing training today
001
Reposted by Alejandro Brenes
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 Obviously there is a lot of unpublished data here I don'...
031
Alejandro Brenes @ajbrenes.com · 15/07/2026
From the same campus and network as Yasset i also get blocked
100
Alejandro Brenes @ajbrenes.com · 15/07/2026
Great event!
000
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.
152
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…
33423
Reposted by Alejandro Brenes
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...
1227
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.
165
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.
185
Reposted by Alejandro Brenes
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 ?
2124
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.
7383108
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 ...
0123
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
112
Reposted by Alejandro Brenes
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
053
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 ...
011
Alejandro Brenes @ajbrenes.com · 29/05/2026
that is a very poor response!
010
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.
4176
Alejandro Brenes @ajbrenes.com · 27/05/2026
Congratulations Vadim!
010
Reposted by Alejandro Brenes
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.
1122
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.
0105
Alejandro Brenes @ajbrenes.com · 12/05/2026
Thats a ridiculous thing to do ...
110
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
0185
Reposted by Alejandro Brenes
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.
031
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
031
Reposted by Alejandro Brenes
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
1112
Reposted by Alejandro Brenes
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
1105
Reposted by Alejandro Brenes
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...
031
Alejandro Brenes @ajbrenes.com · 23/04/2026
I get a boost for Astral low cell numbers and no change for timsTOF, but still testing more systematically
020
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.
261
Reposted by Alejandro Brenes
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.
1133
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!
062
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 😃
010
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
040
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 ...
074
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...
0114
Alejandro Brenes @ajbrenes.com · 13/04/2026
Nice! Excited to test it out! Congratulations Vadim!
110
Alejandro Brenes @ajbrenes.com · 07/04/2026
Youre assuming Infantino has a shred of decency, and im not sure thats a given
000
Reposted by Alejandro Brenes
ContempraInn 🌹 @contemprainn.bsky.social · 02/04/2026
Cherry Blossoms 🌸 Sakura Season in Japan 🇯🇵
16072281053
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...
000
Reposted by Alejandro Brenes
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.
0411
Reposted by Alejandro Brenes
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
25521
Reposted by Alejandro Brenes
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.
2166
Reposted by Alejandro Brenes
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...
098
Alejandro Brenes @ajbrenes.com · 30/03/2026
Season 1 is from 97, pretty sure its only in terrible version. But quite happy its on anyway
000
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.
041
Alejandro Brenes @ajbrenes.com · 25/03/2026
media.tenor.com
a man in a dark room with the words your journey towards the dark side will be complete below him
ALT: a man in a dark room with the words your journey towards the dark side will be complete below him
031