Lisa Boatner

pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics www.sciencedirect.co...

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#proteomics #prot-paper

📯👨‍🚀 Calling all #bioimage analysis aficionados. #EZInput is out! We wanted to bring #ImageJ’s capacity to record settings to the #Python ecosystem 🐍. It is a declarative library for generating UIs that just work. Done with @guijacquemet.bsky.social lab

arxiv.org/abs/2601.08859 #ScientificComputing

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows https://www.biorxiv.org/content/10.64898/2025.12.09.692895v1

#Chemoproteomics

AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage Abstract. The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL–EBI and Google DeepMind, provides open access to

From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org
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academic.oup.com/nar/advance-...

A framework for AI-ready data Define AI readiness and its underlying principles through our new research.

Data is the foundation of AI. Poor quality data drives up costs and can lead to hidden problems for AI, while biased data negatively affects the performance of AI models. In our research, we seek to define AI readiness and its underlying principles. Read more.

Chemical biology 2026

Registration for THE chemical biology conference of 2026 is now open! EMBO ChemBio 2026 in Heidelberg

DeGrado, Arikin, Picotti (Keynotes). @lmkdassama.bsky.social @brianliau.bsky.social @rhodamine110.bsky.social @benlehner.bsky.social @alitavassoli.bsky.social

www.embl.org/about/info/c...

The ProteomeXchange consortium in 2026: making proteomics data FAIR Abstract. The ProteomeXchange consortium of proteomics resources (http://www.proteomexchange.org) was established to standardize open data practices in the

From the @narjournal.bsky.social #NARDatabaseIssue | ProteomeXchange consortium in 2026: making proteomics data #FAIR | #Bioinformatics #Proteomics #OpenScience 🧪🔓
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academic.oup.com/nar/article/...

This project started 5 years ago. It led us to add isotope-labeling support to #FragPipe/#IonQuant. Since then, the tools have grown so much and are now widely used in #Chemoproteomics.

Huge thanks to everyone, and special thanks to @stephanhacker2.bsky.social and @pzanon.bsky.social

Deep phenotyping of health–disease continuum in the Human Phenotype Project - Nature Medicine Deep phenotyping of an ancestrally diverse group of 13,000 individuals in the Human Phenotype Project highlights diversity and variations in lifestyle factors, clinical features and molecular…

A new Nature Medicine paper introduces the Human Phenotype Project, a large-scale cohort integrating multi-omics, imaging, and lifestyle data. The project reveals molecular signatures of disease and uses AI to create predictive health models.
🧬💻 #MedSky

🚀 We're launching quantms.org — new hub for all #quantms related projects. Explore its components #pmultiqc & #ibaqpy, and check all reanalysis we're sharing with the community: quantms.org/datasets

Meet the Team and Labs behind the project
👉 quantms.org/about

#OpenSource #Proteomics #ASMS2025

Screenshot of the marimo-quarto documentation website showing a browser window with the URL marimo-team.github.io/quarto-marimo/. The page displays "marimo + quarto" as the main heading, with a left sidebar navigation containing tutorial sections including Intro, Dataflow, UI, Markdown, Plots, Layout, and Fileformat. The main content area features explanatory text about integrating Quarto with marimo, followed by a blue-highlighted interactive example box titled "Hello from marimo!" that demonstrates a reactive Python cell. Below this is visible Python code using mo.md() function, and a "What?" section that begins explaining marimo and the qmd format. The page has a clean, documentation-style layout with syntax highlighting for the code examples.

After disrupting the notebook world, #marimo is expanding to markdown with a new #Quarto extension (WIP)!

marimo-team.github.io/quarto-marimo/

What's marimo? Reactive #jupyter -like notebooks that automatically run cells when code changes. marimo islands is making this tech portable everywhere 🏝️

Advances in sulfonyl exchange chemical biology: expanding druggable target space Targeted covalent inhibitors possess advantages over reversible binding drugs, that include higher potency, enhanced selectivity and prolonged pharmacodynamic duration. The standard paradigm for coval...

Jones (Chemical Science 2025) Advances in sulfonyl exchange chemical biology: expanding druggable target space. #ChemBiol #MedChem #DrugDiscovery #OpenAccess #chemsky 🧪
doi.org/10.1039/D5SC...

The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets www.cell.com/cancer-...

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#proteomics #prot-paper

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments | Molecular Systems Biology imageimagehu.MAP3.0 integrates mass spectrometry experiments to identify human protein complexes. Using this resource, this study characterizes covariation of complexes, identifies mutually exclusive ...

Very excited that our work describing hu.MAP3.0 is published in @molsystbiol.org. Here we use machine learning to integrate >25k mass spectrometry experiments to place ~70% of human proteins into 15k protein complexes.

www.embopress.org/doi/full/10....

#ChemBio #Chemoproteomics

Computational Hit Finding: An Industry Perspective Computational hit finding, particularly virtual screening, has been a mainstay of drug discovery campaigns for decades, providing a cost-efficient complement to wet experiments. Innovation in this spa...

Really happy to have contributed to this perspective on computational hit finding approaches! Great team work with Steven Jerome, Fredrik Svensson, Carlos Roca Magadán and Marcel de Groot. #jmedchem #cadd #compchem
pubs.acs.org/doi/10.1021/...

ChemBio in the PUB 2025 Chemical Biology in the PUB

Chembio in the Pub! The tastier, chattier version of the popular Boston conference. Jun 12th is pretty close to the GRC too so whether you're a local or visiting it would be great to hang out www.eventbrite.com/e/chembio-in... #chembio #chemicalbiology #bostonbiotech

The Open Molecules 2025 (OMol25) Dataset, Evaluations, and Models Machine learning (ML) models hold the promise of transforming atomic simulations by delivering quantum chemical accuracy at a fraction of the computational cost. Realization of this potential would en...

It's finally done (enough for a preprint)! Today, in collaboration with so many folks at Meta (shout-out Daniel Levine and Muhammed Shuaibi, who put in superhuman levels of work), Berkeley, Stanford, NYU, and more, I'm proud to announce the Open Molecules 2025 (OMol25) dataset!
#CompChem #ML 🧪 ⚗️

A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes - Nature Biotechnology Protein–protein interactions specific to 11 individual tissues are presented in a comprehensive resource.

A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes - @pedrobeltrao.bsky.social @imsb-eth.bsky.social @opentargets.org go.nature.com/3Z1q0PM

Announcement for the latest version of RStudio (2025.05.0) and Posit Workbench, highlighting new features likely related to console output and package management, as illustrated by the console screenshots showing warnings, informative messages, and package installation details

We’re excited to announce the release of Posit Workbench and RStudio 2025.05.0!

The latest release includes Quarto 1.6 support, genAI integrations, better errors/warnings in the console, and other improvements.

Read more in the blog post: posit.co/blog/rstudio...

#RStats #Python

A thumbnail with a dark background and the VS Code logo that reads “What’s new in Visual Studio Code April Update [1.100] -Performance improvements in chat -Auto-attach instructions to chat -Reuse prompts for common tasks -Smarter chat responses with GitHub, extensions, and notebook tools -Identify staged changes in editor -Improved multi-window support -Quick create for Python Environments -Image and Streamable HTTP support for MCP servers”

💯 v1.100 of VS Code is here! And we’ve got some great updates for you, like:

- Smarter chat responses with new tools
- Improved multi-window support
- Image and Streamable HTTP support for MCP servers

…and so much more. aka.ms/VSCodeRelease

Here are some of the highlights… 🧵

Open-Source and FAIR Research Software for Proteomics Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.

Fantastic review with an unusual history, growing out of a passionate blog post by @willfondrie.com (willfondrie.com/2024/10/the-...), resulting from a storm (in our teacup) on X during @hupo-org.bsky.social 2024. Great teamwork, authors! pubs.acs.org/doi/10.1021/...

GitHub - Graylab/DL4Proteins-notebooks: Colab Notebooks covering deep learning tools for biomolecular structure prediction and design Colab Notebooks covering deep learning tools for biomolecular structure prediction and design - Graylab/DL4Proteins-notebooks

Deep learning for proteins tutorial: github.com/Graylab/DL4P...

TMT-based Multiplexed (Chemo)proteomics on the Orbitrap Astral Mass Spectrometer Ongoing advancements in instrumentation has established mass spectrometry (MS) as an essential tool in proteomics research and drug discovery. The newly released Asymmetric Track Lossless (Astral) ana...

TMT-based Multiplexed (Chemo)proteomics on the Orbitrap Astral Mass Spectrometer #MCP www.mcponline.org/article/S153...

We provide a new checklist for selecting & using chemical probes—valuable for researchers, journal editors, reviewers, and vendors. Ensure best practices in chemical biology! 🧪✅

🔗 Supplementary material: ars.els-cdn.com/content/imag...

#ChemicalProbes #DrugDiscovery #ChemicalBiology

A discord server to discuss proteomics, metabolomics, and lipidomics.. #TeamMassSpec

🚀 Thrilled to share our latest research! With the labs of Yansheng Liu and Junmin Peng we’ve built the largest in vivo protein turnover resource across multiple tissues and brain regions, now published in Cell @cellpress.bsky.social 🔬💡 #Proteomics Check it out! 👇
authors.elsevier.com/c/1koBJL7PXu...

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks Computational tools for structure-based drug design (SBDD) are widely used in drug discovery and can provide valuable insights to advance projects in an efficient and cost-effective manner. However, d...

New Perspective on Community Benchmarking in Structure-Based Drug Design (SBDD)!

#SBDD predictions need reliable benchmarks - diverse targets, high-quality affinity & structural data, and blinded validation. Let’s make it happen!

🔗 Read more: doi.org/10.1021/acs....

#DrugDiscovery #CompChem