Advanced Proteomics Techniques and Applications

An Optimized Stem Cell Secretome Proteomics Platform: Application to Progranulin-Deficient iPSCs

This paper optimizes a secretome proteomics platform for iPSCs and applies it to study progranulin deficiency's effects on extracellular and intracellular proteomes.

Polyploid Achromatium sp. expresses protein variants based on environmental cues

The paper investigates how Achromatium sp. expresses protein variants in response to temperature changes using proteomics and a newly assembled protein atlas.

ProteomeScout v4: An open-source, harmonized, ecosystem for post-translational modifications

ProteomeScout v4 provides an open-source ecosystem for aggregating and harmonizing post-translational modification data with web and code-based access tools.

π-MSNet: A large-scale, AI-ready and continuously reprocessed proteomics data resource

The paper introduces π-MSNet, a large-scale proteomics dataset for AI training and benchmarking, showing performance improvements when models are retrained on it.

Single-cell proteomics workflow for characterizing heterogeneous cell populations in saliva and tear fluid

This study develops a single-cell proteomics workflow to analyze cellular heterogeneity in saliva and tear fluid, identifying biomarkers and therapeutic targets.

Empirical-Bayes and Bayesian Hierarchical Modelling forMissingness and Differential Expression in Proteomics

The paper introduces a hierarchical Bayesian model to handle missing data and improve differential expression analysis in proteomics by accounting for uncertainty in missing values.

MetaUmbra: Statistically Controlled Genome-Level Presence Inference from Metaproteomic Peptides

MetaUmbra infers genome-level presence from metaproteomic peptides using statistical methods, accurately recovering expected genomes in benchmark tests.

In situ polymerized monolith tips for reproducible, format-flexible proteomic sample preparation applied to biofluids

The paper introduces pSPEC, a reproducible proteomic sample preparation method for biofluids that increases protein identification by ~20% compared to in-solution plasma.

Single-cell proteomics resolves major cell populations and protein-defined chondrocyte states in the adult human osteoarthritic joint

This study uses single-cell proteomics to identify protein-defined chondrocyte states and other cell populations in human osteoarthritic joints, complementing single-cell transcriptomics.

Beyond HCD: complementary fragmentation chemistries expand HLA class I immunopeptidome discovery

This paper evaluates CID and IRMPD fragmentation methods for HLA class I immunopeptidomics, finding they identify unique peptides missed by HCD, especially for non-basic anchor alleles and peptides lacking lysine, arginine, or histidine.

Protocol for Single-Cell Patch-Proteomics: identify specific proteins associated with electrophysiological properties from individual neurons

This paper describes a protocol that combines electrophysiological and proteomic analysis to link protein abundance with neuronal excitability in individual neurons.

Global mapping of protein localization in vegetative Dictyostelium discoideum by subcellular spatial proteomics

This study creates the first global subcellular localization map of Dictyostelium discoideum proteins using subcellular fractionation and mass spectrometry, identifying 3,169 high-confidence localizations across 17 compartments.

Proteome-wide quantification of protein turnover in frog and fly embryos reveals divergent strategies of maternal inheritance

The paper quantifies protein turnover in frog and fly embryos using 18O-water labeling and proteomics, revealing divergent strategies of maternal proteome inheritance.

SPEx: Compartment-Resolved Proteomics via Expansion Microscopy-Guided Microdissection

SPEx enables compartment-resolved proteomics by expanding cells, microdissecting regions of interest, and analyzing them with mass spectrometry, revealing novel organelle components.

A subcellular spatial proteome of the non-photosynthetic euglenid Euglena longa

This study maps the subcellular proteome of Euglena longa using SSP to identify 5,909 proteins across 16 compartments, with high-confidence localisations for 2,955 proteins.

ScProteoAgent enables natural-language-driven single-cell proteomics analysis and interpretation

ScProteoAgent translates natural-language requests into single-cell proteomics analyses, preserving analytical state and enabling follow-up queries with high benchmark performance.

A draft atlas of the human plasma proteome at isoform resolution

The paper creates a proteoform-resolved atlas of the human plasma proteome, revealing extensive proteoform diversity and highlighting discrepancies between proteomic platforms.

Affinity Purification: From Interactome Analysis to Targeted Protein Enrichment

This study shows how adjusting purification conditions can direct affinity purification outcomes toward either interactome characterization or selective target enrichment for extracellular chaperones.

Recording proteome dynamics in the late-stage embryo at hour-timescale, spatial, and single-cell resolution with MEMBRYO

The paper introduces MEMBRYO, a method for continuous SILAC proteomics in live embryos, revealing post-transcriptional regulation during neurogenesis.

Conjunctive Targeting Links Drug Synergy to Emergent Proteome Structural States

This paper introduces CoPPRA, a structural proteomics method to analyze drug combinations in AML, revealing peptide-level accessibility changes linked to conjunctive targeting.

PTMExplorer: A Multi-Dimensional Integrative Visualization Platform for Protein Post-Translational Modification Function and Structure

PTMExplorer is a visualization platform that integrates PTM data with 3D structure, functional annotations, and disease associations to identify biologically significant modification sites.

Pulsed-SILAC in single mouse embryos reveals early embryonic protein synthesis dynamics and phosphosite regulation

The paper uses pulsed-SILAC in single mouse embryos to study protein synthesis dynamics and phosphosite regulation during early embryogenesis, revealing active maternal proteome synthesis and post-translational regulation.

ProteoScopeR: A Shiny Workflow for Method Comparison and Reproducible Quantitative Proteomics Analysis

ProteoScopeR provides a reproducible workflow for comparing quantitative proteomics methods and their impact on results.

A Statistical Guideline for Analyzing Repeated-Measures Proteomics Data

This paper evaluates statistical methods for analyzing repeated-measures proteomics data, finding that unstructured covariance models outperform conventional approaches in handling variance heterogeneity and within-subject correlations.

Brain Landscape In Situ Crosslinking Mass Spectrometry (BLIS-XL-MS) Enables Global Analysis of Protein Structural Remodeling in the Brain

BLIS-XL-MS enables proteome-wide analysis of structural remodeling in brain tissue by combining experimental and computational methods to study protein conformational changes in neurodevelopmental disorders.

π-MNovo improves de novo peptide sequencing through microbial-domain adaptation and evidence-guided candidate selection

π-MNovo improves de novo peptide sequencing for metaproteomics by adapting to microbial spectra and selecting candidates based on evidence, achieving higher recall than existing models.

From Discovery Proteomics to Process-Informed Monitoring in Biomanufacturing Chassis Development

The paper evaluates proteomics platforms for metabolic pathway analysis in biomanufacturing chassis organisms, showing varying proteome coverage across different instruments.

Expanding N-terminomics Coverage by Extending N-terminal Peptide Length

This paper introduces two modified CHAMP-N methods to extend N-terminal peptide length, improving N-terminome coverage while maintaining technical reproducibility.

Tracking cellular biomolecular condensate dynamics under proteostatic stress with middle-down phosphoproteomics

This study uses middle-down phosphoproteomics to analyze how protein partitioning into biomolecular condensates changes under proteostatic stress, revealing phosphorylation-dependent and independent mechanisms.

Global proteomic analysis of sea urchin embryos reveals dynamic changes throughout embryogenesis

This study performs a global proteomic analysis of sea urchin embryos across developmental stages, revealing dynamic protein expression patterns and discordant mRNA-protein correlations.