DIA proteomics needs more than powerful search — it needs transparent, reproducible, and scalable software. I’m excited to share that Radiant DIA™ and the Fulcrum Scalable Pipeline™ are now released with publicly available source code.

Translational bottlenecks in blood-based proteomics - Hope there is something inspiring and informative for you in our recent comment at this inflection point. @embomolmed.org @hupo-org.bsky.social @proteinatlas.bsky.social link.springer.com/article/10.1...

Translational bottlenecks in blood-based proteomics - EMBO Molecular Medicine

EMBO Molecular Medicine - The translation of blood-based proteomics into healthcare is no longer constrained primarily by technological limitations, but by unresolved challenges in standardization,...

link.springer.com

www.biorxiv.org/content/10.6... 1/ Proteomics method development often optimizes for IDs. But for cohort biology, IDs only matter if they remain quantitative, precise, and powered. We ask how chromatographic sampling density propagates from peaks → LOQ → discovery. 🧵

I'm sure @leecantrell.bsky.social will do a real tweetorial, but my favorite: "Reduced peak completeness minimally affected detectability (LOD) but substantially degraded quantifiability (LOQ), indicating that identification-centric readouts can remain stable while quantitative utility declines."

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 3mo ago

From Peaks to Power: Systematic Evaluation of Chromatographic Sampling Reveals Determinants of Quantification and Biological Discovery in DIA Proteomics https://www.biorxiv.org/content/10.64898/2026.05.13.724964v1

From Peaks to Power: Systematic Evaluation of Chromatographic Sampling Reveals Determinants of Quantification and Biological Discovery in DIA Proteomics https://www.biorxiv.org/content/10.64898/2026.05.13.724964v1

claude.com/blog/onboard... Wait I know them! (Brendan not on bsky so I'll tag @maccoss.bsky.social ) #TeamMassSpec #proteomics 🧬 🖥️ 🧪

a man in a yellow shirt is sitting in a chair pointing at something

ALT: a man in a yellow shirt is sitting in a chair pointing at something

media.tenor.com

I'm excited to share new results at #HUPO2025! I’ll be presenting our latest work on a next-generation DIA search and FDR pipeline that enables sensitive, accurate and scalable proteomic analysis — in just a fraction of the time required by current algorithms. 📍 Poster PV.01.009 — Monday

I'm excited to see this paper in press! pubs.acs.org/doi/10.1021/...

Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics

The Proteograph Product Suite, a multiplexed nanoparticle (NP) protein corona-based workflow, substantially improves the depth of detection of proteins by mass spectrometry (MS) by compressing the dyn...

pubs.acs.org

Pre-analytical drivers of bias in bead-enriched plasma proteomics | EMBO Molecular Medicine www.embopress.org/do... --- #proteomics #prot-paper

Improving proteomic dynamic range with Multiple Accumulation Precursor Mass Spectrometry (MAP-MS) www.biorxiv.org/cont... --- #proteomics #prot-preprint

🚀 New preprint alert! We've improved IM2Deep for accurate peptide collisional cross-section (CCS) prediction, even for peptides exhibiting multiple conformations in the gas phase! 🎯 Check it out here: www.biorxiv.org/content/10.1...

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

Peptide collisional cross-section (CCS) prediction is complicated by the tendency of peptide ions to exhibit multiple conformations in the gas phase. This adds further complexity to downstream analysi...

biorxiv.org

Out today in Nature Genetics: Using MS-based proteomics, we mapped 1,200+ plasma proteins in 2,100+ children, showing how genetics & development shape blood protein levels during childhood. nature.com/articles/s41588-025-02089-2 #PediatricProteomics #pQTL First author @liliniu.bsky.social explains ⬇️

Plasma proteome variation and its genetic determinants in children and adolescents - Nature Genetics

This mass spectrometry-based proteomic study profiles the plasma proteome in 2,147 children and adolescents and reveals its association with age, sex, puberty, body mass index and genetics.

nature.com

pubs.acs.org/doi/10.1021/... Exciting to get this paper into press! It's a game changer to be able to search thousands of files from Astral on the order of hours.

Cloud-Enabled Scalable Analysis of Large Proteomics Cohorts

Rapid advances in depth and throughput of untargeted mass-spectrometry-based proteomic technologies enable large-scale cohort proteomic and proteogenomic analyses. As such, the data infrastructure and search engines required to process data must also scale. This challenge is amplified in search engines that rely on library-free match between runs (MBR) search, which enable enhanced depth-per-sample and data completeness. However, to date, no MBR-based search could scale to process cohorts of thousands or more individuals. Here, we present a strategy to deploy search engines in a distributed cloud environment without source code modification, thereby enhancing resource scalability and throughput. Additionally, we present an algorithm, Scalable MBR, that replicates the MBR procedure of popular DIA-NN software for scalability to thousands of samples. We demonstrate that Scalable MBR can search thousands of MS raw files in a few hours compared to days required for the original DIA-NN MBR procedure and demonstrate that the results are almost indistinguishable to those of DIA-NN native MBR. We additionally show that empirical spectra generated by Scalable MBR better approximates DIA-NN native MBR compared to semiempirical alternatives such as ID-RT-IM MBR, preserving user choice to use empirical libraries in large cohort analysis. The method has been tested to scale to over 15,000 injections and is available for use in the Proteograph Analysis Suite.

pubs.acs.org

US Government Places Export Controls on LC-MS Instruments for Top-Down Proteomics www.genomeweb.com/po... --- #proteomics #prot-article

The De-Modifier: a tool for screening modification-induced alternate peptide taxonomy in palaeoproteomics www.biorxiv.org/cont... --- #proteomics #prot-preprint

A Technical Evaluation of Plasma Proteomics Technologies www.biorxiv.org/cont... --- #proteomics #prot-preprint

Read our #pQTL study using the SEER #proteomics platform in @naturecomms.bsky.social The full raw MS spectral data is available on PRIDE: ebi.ac.uk/pride/archiv... The paper is here: link.springer.com/article/10.1...

Any #GlycoTime #TeamMassSpec folks who can recommend a good starting point for knowledge background development? Thinking about biology/methods/informatics but also curious if there’s been really cool biology papers in the field worth sharing.

Nice to see #teammassspec critical momentum here. Hoping to never return to the land of Leon. Feed relevance is already much improved. Looking forward to future conversations and learning here!

Here's a new list for early career researchers (=not had your own lab for ages) in proteomics. Feel free to ask to be added or removed, I've tried to make a guess but could've got it wrong. I think it's good to also have an ECR network. #teamMassSpec go.bsky.app/Dp8PHX1

#teamMassSpec here is a starting pack in case you just moved over, or in case you've been absent for a while. This is #proteomics or #massspec related. The pack is not comprehensive but it's a start. go.bsky.app/HH7kqEh