Bulk transcriptome and proteome correlate only modestly, but this has not been investigated in the same cell or across cell-state changes. Here we introduce a scalable technology that quantifies thous...

Vascular smooth muscle cells (VSMCs) drive atherosclerosis through phenotypic switching, yet their spatial organization and protein signatures within plaques remain poorly characterized. Here, we appl...

The functional complexity inherent in microbiomes complicates analytical approaches aimed at defining phenotype. As proteins are the functional effectors of microbiome phenotypes, improving the performance of mass spectrometry-based metaproteomics is critical to achieving the functional characterization of these systems. Data-independent acquisition (DIA) improves protein coverage and reduces data missingness when compared to data-dependent acquisition (DDA) in metaproteomics. However, the application of DIA to complex microbial systems remains constrained by analytical throughput and computational scalability. Here, we optimized LCMS/MS acquisition parameters for both DDA and DIA using a model microbiome, demonstrating how DIA enables increased sample throughput without compromising quantitative performance. In addition, we demonstrated a computationally efficient, library-free DIA workflow that overcomes reliance on empirical spectral libraries. Our analytical and computational innovations establish a scalable and cost-effective pipeline for metaproteomics of complex microbial communities.

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...

Atherosclerotic plaque rupture underlies many cerebrovascular events, yet the molecular determinants of vulnerable plaque morphology remain poorly defined. Using histomorphology-guided spatial proteom...

Protein biogenesis is a stress- and error-sensitive process that can lead to nascent protein misfolding and aggregation, challenging cellular proteostasis. Co-translational ubiquitination (CTU) is a c...

Using the single-cell Deep Visual Proteomics technique, the authors develop a resource providing spatially resolved proteomic analysis of individual cells in human liver tissue.

Mass spectrometry-based label-free proteomics data often suffer from missing values, especially for low-abundance proteins or when a protein is completely absent in one condition. This makes it challe...

What's Changed Increase dev version by @ypriverol in #579 fixing of bug in msstats_tmt.R (Issue: Error in the msstats_tmt.R function parse_contrasts #577) by @kai-lawsonmcdowall in #578 Pass corre...

User description Pull Request Description Brief description of the changes made in this PR. Type of Change Bug fix (non-breaking change which fixes an issue) New feature (non-breaking change whi...

A focused analysis of the histone proteins and post-translational modifications in single cell proteomics provides insight into the heterogeneity of histone deacetylase inhibition.

Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...

Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and...

Is your awesome new instrument generating so much data that you can't process it fast anymore? My data density has jumped about 5x from my...

You will contribute to the development of core database applications, web services, data ingestion workflows, and the PRIDE Web platform as part of the PRIDE ecosystem. Working closely with the team, ...

Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...

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...

Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...

Transformer models are great? For several years, there has been this idea that one can pre-train advanced deep learning models, e.g.

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