First day of holiday - paper accepted Last day of holiday - news that my Erasmus student has completed our first ever DVP experiment Good times!
Luke Gamon
@lgamon.bsky.social
All things teammassspec/realtimechem. Survives on only the fanciest coffee and beer. Laser capture microdissection | spatial proteomics | protein modification | atherosclerosis | inflammation and oxidation
Paper accepted on my first day of holiday! Taking that as a big win 😅
Tired of AI-generated figures? I asked our talented scientific illustrator Manon Zuurmond to draw some of the instruments and lab equipment we missed in NIH's otherwise fantastic BioArt resource. First batch now available as CC BY. Free for everyone to use in publications: github.com/Center-for-P...
You have missed to submit your Abstract to #EuPA2026? Don't worry! The deadline for the abstract submission was extended to the 10th of July. Submit now your abstract and be part of this years conference program!
In Italy for my first GRC this decade (been a while!). Couldn’t help but squeeze in a couple of hours in the middle of Florence. Feels wrong to not stop by Il Duomo to admire some grandure over an espresso or two. If anyone out there in Bluesky world is going to the Protease GRC - do say hi!
Playing with InfinDIA in DIANN 2.5 for large search space semi-specific searches. Surprisingly competitive with Fragpipe DDA searches, and shockingly fast. DIANN 2.5 still sucks at detecting our singly charged peptides though. Too much chemical background in the +1 peptide cloud for DIA to handle?
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.
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 ...
biorxiv.org
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
Oh life with nanoDTSC. This LC will never be satiated. Can’t imagine what it must be like running 500 SPD like in that new @mannlab.bsky.social preprint
You know it’s gonna be a good Father’s Day when you wake up to this
69 days after national elections the Prime Minister of Denmark Mette Frederiksen has finally managed to negotiate to form a new government. However…. The king isn’t at home in Copenhagen. He’s touring the country on the royal yacht. Could it be more Danish than to formalise a government on a boat?
Taught our new Erasmus student and staff scientist how to do laser capture microdissection spatial proteomics yesterday. Got the workflow down to <5hrs from tissue on a slide, to first peptides eluting into the mass spec. Gotta love a sub-one day protocol. #TeamMassSpec
What is it with people writing (IF 6.8) on LinkedIn posts about their new research papers? Grumble grumble old man noises
Obsessed with agentic coding for making handy little tools and quick data QC etc. Absolutely DESPISE the dearth of LLM written “look at our awesome paper” LinkedIn posts. At least on BlueSky you can still hear peoples ‘voice’.
Today’s Codex adventure - peptide charge-state prediction based on non-tryptic enzymatic in-silico digest. Literally one prompt for the pipeline, one more prompt for a clean html/pdf report. Validated later in the day with real samples and fragpipe search results.
(BioRxiv All) Spatial Single-Cell Proteomics Reveals Molecular Trajectories Of Tangle-Bearing Neurons In Alzheimer's Disease: Neurofibrillary tangles composed of hyperphosphorylated tau are a defining pathological hallmark of Alzheimer's disease (AD); however, the pathways and… #BioRxiv #MassSpecRSS
Spatial Single-Cell Proteomics Reveals Molecular Trajectories Of Tangle-Bearing Neurons In Alzheimer's Disease
Neurofibrillary tangles composed of hyperphosphorylated tau are a defining pathological hallmark of Alzheimer's disease (AD); however, the pathways and mechanisms associated with the transition from physiological tau to tangle pathology remain unclear. Here, we integrate laser microdissection of post-mortem, fixed human AD brain tissue labelled with an antibody recognizing tangle-associated phospho-tau (AT8) with mass spectrometry-based proteomics, applied to individual neurons and to small neuronal pools. This approach identified ~2,000 and ~5,000 proteins, respectively, and enabled direct detection of disease-associated tau phosphorylation sites without prior enrichment. A layered analysis of the proteome of tangle-positive and tangle-negative neurons revealed heterogeneous disease-associated states. Pseudotime analysis, combined with an AI-driven analytical framework, indicates that neurons do not segregate into discrete classes but instead organize along a continuum of proteomic changes that correlate with tau abundance. This organization enabled the construction of a trajectory of pathological neuronal responses that can be resolved within an individual brain. Early stages of this trajectory are characterized by coordinated remodeling of proteostasis networks, including reduced proteasome component abundance and increased lysosomal acidification machinery, followed by disruption of synaptic pathways. Notably, despite extensive proteomic remodeling, neurons bearing tangles show little evidence of activated cell-death programs, suggesting prolonged molecular adaptation rather than acute degeneration. Together, these findings establish a framework for single-cell-resolved proteome analysis of human brain disease in situ and define a continuum of neuronal states underlying tau pathogenesis, revealing early vulnerabilities and adaptive responses during AD progression.
dlvr.it
Officially 0/6 for grants in the last 12mths. Tough out there but also the name of the game. I actually got feedback for 3 of them (1 was very detailed) so I can see the consistent complaints and work on them for the next round 🤞 To all the ECRs out there - may the odds be ever in your favour!
Damn this is cool. Neutrophils are the best. (Also not the best in all the diseases we study but hey that’s life)
Evelyn Strickland@strickland-evelyn.bsky.social · 4mo agoWhat if you got to work with some of your best friends on a science project? I can't publish how fun this was, but I can show you the data (🧵)! Last week, we posted our second neutrophil swarming paper to bioRxiv and I wanted to post my favorite videos here~ www.biorxiv.org/content/10.6...
ANZSMS is proud to support The Bieske-O’Hair Symposium held at the University of Melbourne, School of Chemistry in July. Registration is essential and covers catering across the symposium in addition to an evening social event. #TeamMasSpec (1/3)
Just found an absolutely epic email from a shared MS facility ca. 2015 😂 True words of wisdom. #TeamMassSpec
On the 15th of April we will host a seminar as part of our ProteoBench hackathon in Copenhagen. Swing by and hear more about Protebench, EuBIC and other interesting projects! Find details here: eubic-ms.org/events/lates... See you there! 😄
Latest developments and tools for data analysis
EuBIC Seminar 2026 Event Schedule for Wednesday the 15th April 2026 Location is in the Mærsk tower at Panum on the 15th floor in the seminar room 7.15.92 (Foredragssalen): Take the elevator to the 15 ...
eubic-ms.org
1) Proteomics has a severe problem. We keep pretending database search is “good enough”, while systematically missing everything that isn’t already known. No genome/proteome → no ID Variant peptide → invisible Novel biology → filtered out
Nice work but please if you’re going to try LCM with the PalmRobo just capture + process directly in a PCR cap either open in a humid chamber or with them placed on top of a 96-well PCR plate. Then acidify + spin into evotips or homemade stagetips. pubs.acs.org/doi/10.1021/...
MR-SP2: A Microreactor-Based Workflow for Few-Cell Spatial Proteomics on the Legacy Zeiss PALM MicroBeam
Laser capture microdissection (LCM) combined with liquid chromatography–tandem mass spectrometry (LC-MS/MS) enables spatial proteomics at the few-cell level but is constrained by cumulative losses during specimen capture, surface adsorption during processing, and sample transfer prior to LC-MS/MS analysis. The capture-associated losses are particularly relevant for pressure catapulting systems such as the legacy Zeiss PALM MicroBeam, which, despite discontinuation, remains in active use and therefore requires compatible low-loss workflows. We present MR-SP2 (microreactor-based sample preparation for spatial proteomics), a one-pot workflow integrating reproducible Zeiss LCM-cut specimen capture, processing with minimized adsorptive losses, and pipetting-free transfer with Evotip disposable precolumns. The workflow was evaluated using a formalin-fixed paraffin-embedded (FFPE) murine kidney tissue analyzed by timsTOF flex LC-MS/MS analysis. Across 50,000 μm3 regions (22 cells), MR-SP2 modestly improved proteome depth (3381 ± 80 versus 3174 ± 59 proteins). Decreasing sample input further accentuated the advantage of MR-SP2 in maintaining higher identification rates, highlighting the successful reduction of the adsorptive losses. At 12,500 μm3 (5–6 cells), identifications increased to 1145 ± 188 versus 302 ± 126. At 3125 μm3 (1–2 cells), identifications reached 695 ± 112 versus 206 ± 51. MR-SP2 improves identification depth for few-cell FFPE samples by nearly 3-fold compared to conventional tube-based workflows.
pubs.acs.org
Latest agentic coding adventure: Lightweight rust based contaminant QC tool to process directly from bruker .d files (with inspo from HowDirty and RawTools). 5s per file runtime on my Mac with SSD. Janky but does the job.
Pretty hilarious to use the fact that collagen is missing an essential amino acid as a selling point “Look how great this is, we have 8 out of 9 essential amino acids!”
So the EU and Australia have finally reached an agreement on free trade. Let the Vegemite flow!!! Seriously though… our supplies are at critical levels. Send help.
TimsTOF people / people who understand ion mobility devices - is it normal that +2/+3 ions overload the trap before +1 ions? We are observing that both +1 IDs and intensities keep going up with increasing loads but +2/+3 saturate quickly.
