Karl Makepeace

Proteomics 🩸 Mass Spectrometry ✨ Structural & Network Biology 🧬🕸️ Bioinformatics 💻 Canada 🍁 @Columbia 🗽 🦋

[Karl Makepeace @ionsbyfriday]

🍁

[Karl Makepeace @ionsbyfriday]

Looking closer at "de novo only" peptides + sequence variants not mapped to your proteogenomic database just got a lot more interesting.
#proteomics #proteoforms #RNA #centraldogma

[Prof. Nikolai Slavov @slavov_n]

Our article is in today's issue of Nature.

It shows that our proteome is more diverse than we thought, remarkably so !

This has been a long and exhilarating journey beginning in 2019. It has opened perspectives that we are very eager to explore. https://t.co/6bWeQY987Z

[Karl Makepeace @ionsbyfriday]

@okazz_ 👌

[Karl Makepeace @ionsbyfriday]

Homer, Herodotus, Sophocles... Bonhomme de Neige ☃️
#Columbia #NYC #Snow

[Karl Makepeace @ionsbyfriday]

Feature-engineered rescoring is a big help.

We saw a similar big jump in IDs when we applied this logic to XL-MS:
https://t.co/k1A7UWfnau

#proteomics

[bioRxiv Bioinfo @biorxiv_bioinfo]

quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational ... https://t.co/XE8NUgOpSn #biorxiv_bioinfo

[Karl Makepeace @ionsbyfriday]

Proteome-wide Monitoring of Drug Action in Living Cells using a Novel Label-free Solvent-based Shift Assay - Molecular & Cellular Proteomics https://t.co/oQHu1a9GFa

SPICE (Solvent Proteome Profiling In Cells)🧪💡

#MCP #Proteomics #DrugDiscovery

[Prof. Nikolai Slavov @slavov_n]

Proteoforms encoded by the same gene have different interactomes.

This challenges:
1⃣ The interpretation of data from reagents directed towards shared epitopes.

2⃣ The assignment of functions to genes.

When will biological research focus on such functional differences?

[Karl Makepeace @ionsbyfriday]

Multiplexed LFQ. 👀

SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics | Journal of the American Society for Mass Spectrometry https://t.co/RxATYZeHCO

[Karl Makepeace @ionsbyfriday]

Another Manhattan quake? 🤔
#earthquake #nyc

[Karl Makepeace @ionsbyfriday]

Robot metabolism: Toward machines that can grow by consuming other machines | Science Advances https://t.co/nIZAxDP4Oq

[Karl Makepeace @ionsbyfriday]

👀
https://t.co/HAXsN7nhWR
#MCP #proteogenomics

[Ian Maurer 🧬 @imaurer]

Announcing BioMCP, a biomedical research MCP server that wraps public APIs for clinical trials, pubmed articles and genomic variants.

MIT license, more info below.

[Karl Makepeace @ionsbyfriday]

430 ppm 😮‍💨 #heatwave #nyc
https://t.co/oT5eeupBTl

[Brian Searle @briansearle]

People have asked about how MAP-MS works so here's a tweetorial on @teerap16's new preprint: https://t.co/s3palUNQbE. MAP-MS takes advantage of parallelization in a trapping MS, collecting Orbitrap MS1s with 2x the dynamic range by differentially amplifying parts of the ion beam.

[Cinder Biological (@cinderbio.bsky.social) @CinderBio]

Want better #denovosequencing of #antibodies? See what we see using our Krakatoa protease to achieve superior breadth and depth of coverage. If you’re interested in getting ahead, click here https://t.co/k2XglM0USe

#proteomics #TeamMassSpec

[Karl Makepeace @ionsbyfriday]

@bayraktar_lab Incredible figures 🤩

[Karl Makepeace @ionsbyfriday]

🗳️👀☑️🍁
#Canada #Vote

[Elections Canada @ElectionsCan_E]

Attention Canadian citizens living abroad! Did you know that you can vote by mail regardless of how long you’ve lived abroad? Apply early to vote by mail by April 22, 2025, 6 p.m., Eastern time. Exercise your right to vote! https://t.co/Uku6Ho4F8e

[Karl Makepeace @ionsbyfriday]

👀 Wow.
https://t.co/GA5W6JbwYB
#Canada #USA #Travel

[Karl Makepeace @ionsbyfriday]

👀 #proteogenomics

[Klebanoff_Lab @KlebanoffLab]

🚨Today in @Nature, we show that mRNA mis-splicing creates clonal public neoantigens in solid cancers. An amazing collaboration between @UCSFCancer and @MSKCancerCenter driven by @DarwinKwok1 and co-led by Hideho Okada, @josephcostell14 and @KlebanoffLab. https://t.co/lDEGbQr7cT

[Karl Makepeace @ionsbyfriday]

@BlackBerry @skyworksinc Can we *please* get some 📱 mobile hardware for Canadians by Canadians? 🍁 Now's the time.
#TeamCanada

[Karl Makepeace @ionsbyfriday]

😧

[Science Vs @sciencevs]

🚨NEW EPISODE OUT🚨 The Trump administration has thrown the science world into chaos — we talk to @maxdkozlov and @jocelynkaiser about what's going on

@spotifypodcasts

https://t.co/QUauVZkkEq