Advanced Proteomics Techniques and Applications

Quantitative profiling of JMJD6-catalysed lysine hydroxylation reveals a graded, residue-dependent readout of oxygen availability

This study quantitatively profiles JMJD6-catalyzed lysine hydroxylation, revealing a graded, residue-dependent response to oxygen availability in lysine-rich regions.

maniFasta and the AllOralsDB: simplifying construction of comprehensive reference databases for metaproteomics

maniFasta and AllOralsDB provide a tool and resource for creating standardized, comprehensive protein reference databases for metaproteomics.

Uncovering the signaling networks of disseminated glioblastoma cells in vivo with INSIGHT

The paper introduces INSIGHT, a platform for phosphoproteomic analysis of rare cell subpopulations, and applies it to study signaling changes in disseminated glioblastoma cells in vivo.

A Robust and Generalizable Low-Input Spatial Proteomics Workflow Enabling Deep Proteome Coverage

The paper develops a low-input spatial proteomics workflow using standard lab equipment, achieving deep proteome coverage of the choroid plexus across age and sex in mice.

ProteoParc: A tool to generate protein reference databases for ancient and non-model organisms

ProteoParc generates custom protein reference databases for ancient and non-model organisms to improve peptide identification and ZooMS marker annotation in proteomics studies.

Mapping the Human Ghost Proteome: Classification and Experimental Detection Biases in the Identification of Alternative Microproteins

The paper develops a workflow to detect and classify alternative microproteins in colorectal cancer cells, identifying biases in extraction methods and validating a subset experimentally.

A targeted mass-spectrometry plasma proteome for simultaneous multi-disease screening

This paper demonstrates that a targeted plasma proteome measurement can detect multiple diseases with high accuracy, though validation remains needed for clinical use.

High-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables Global Structure Profiling and Site-resolved Elucidation of Ligand-Protein Interactions

HOLSER improves proteome coverage and depth for structural analysis of protein-ligand interactions and conformational changes.

Area under the curve quantification outperforms spectral counting in metaproteomics, but matching between runs is detrimental

The paper compares AUC and SpC quantification methods in metaproteomics, finding AUC outperforms SpC in accuracy and dynamic range, but MBR harms AUC results.

Global Profiling of Remodeled Subcellular Structures Due to Drug Treatment and Disease

The paper uses SEC-MS with crosslinking to analyze global changes in subcellular structures in Ewing sarcoma cell lines and after drug treatment, identifying effects on splicing, mitochondria, nucleoli, and peroxisomes.

An organ-resolved rat FFPE phosphoproteome map enables directional kinase activity inference

The paper generates an organ-resolved phosphoproteome map from FFPE rat tissues, showing it preserves signaling biology and enables kinase activity inference.

From Peaks to Power: Systematic Evaluation of Chromatographic Sampling Reveals Determinants of Quantification and Biological Discovery in DIA Proteomics

This study evaluates how chromatographic sampling affects quantification and biological discovery in DIA proteomics, finding that statistical power and LOQ are more critical than identifications.

Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics

The paper develops a pipeline for protein-level cell annotation in human PBMCs using mass spectrometry-based single-cell proteomics and validates it on unsorted samples.

Spectronaut-nf: A Nextflow Pipeline for Parallel Processing of DIA Data with Spectronaut

Spectronaut-nf is a Nextflow pipeline that enables parallel processing of DIA proteomics data on HPC systems, reducing analysis time compared to single workstation execution.

Novel native serum peptidomics workflow enables the discovery of circulating subtype-specific peptide biomarkers in acute ischemic and haemorrhagic stroke

This paper introduces a novel serum peptidomics workflow that improves peptide yield, throughput, and recovery, identifying subtype-specific peptide biomarkers for stroke subtypes.

Toward simple, rapid, and deep plant proteome analysis with an in-cell proteomics strategy

This paper introduces an in-cell proteomics strategy for plant samples, demonstrating improved speed, simplicity, and proteomic sensitivity compared to conventional methods.

SureQuant IS-PRM Enables Cross-Species Targeted Quantification of Retinoid Metabolism and Signaling Proteins in the Heart

The paper develops a targeted proteomics method to quantify retinoid metabolism and signaling proteins across species and tissues, revealing tissue-specific networks and developmental changes in the heart.

STRIDE: Signal Transfer and Aligned Ion-Peak Discrimination for Peptidoform Evidence for Consistent Quantification of Site-Localized Post-Translational Modifications in Large-Scale DIA-MS

STRIDE improves phosphopeptide quantification by reducing false negatives and enhancing consistent peak assignment across DIA-MS runs.

Single-cell proteomics reveals proteome remodeling and cellular heterogeneity during NGF-induced PC12 neuronal differentiation

The paper applies single-cell proteomics to study proteome changes during NGF-induced PC12 differentiation, revealing subpopulations not detected in bulk data.

Improved identification of peptides, modification sites, and cross-link sites by Target-enhanced Accurate Inclusion Mass Screening (TAIMS)

TAIMS improves cross-link and low-abundance peptide identification by enhancing MS2 quality and sensitivity in proteomics.

A targeted plasma-proteomic axis separates autoimmune thyroid disease from growth-hormone deficiency

This study uses targeted plasma proteomics to identify a biomarker axis distinguishing autoimmune thyroid disease from growth-hormone deficiency, but not within-class severity.

Proteogenomic analysis of the differential stability of cardiac protein isoforms

The paper investigates the differential stability of cardiac protein isoforms using proteogenomics and heavy water-based turnover analysis in mouse hearts, revealing widespread stability differences.

Detergent selection as a determinant of lysate melting behavior and drug-target hit-calling in thermal stability proteomics

This study evaluates how detergent selection and timing affect thermal stability proteomics results, finding that DDM improves detection of some drug-target interactions but may obscure others.

FAIMS-GPF XL-MS: crosslinking-mass spectrometry based on gas-phase fractionation

The paper introduces FAIMS-GPF XL-MS, a method for detecting protein-protein interactions using gas-phase fractionation, achieving high sensitivity and coverage without in-solution fractionation.

Miniaturized Lysosome Enrichment through Selective Plasma Membrane Destabilization

This paper demonstrates a method to enrich lysosomes from low cell numbers by combining plasma membrane destabilization with immunoprecipitation, improving proteome characterization from half a million cells.

Plate-based ISD-SPE enables dual proteome-secretome concentration-response profiling of TLR signalling in iPSC-derived macrophages

This paper introduces a plate-based ISD-SPE workflow for integrated proteome and secretome analysis of TLR signaling in macrophages, showing improved reproducibility and scalability for drug discovery.

Age-dependent Structural Reorganization of the Human Plasma Proteome

The paper identifies age-dependent structural changes in the human plasma proteome using Covalent Protein Painting and MRM-LC-MS/MS, revealing patterns that may serve as structural biomarkers.

Deep axonal proteomics of human iPSC-derived neurons by microfluidic separation and DIA-MS

This paper reports the deepest human axonal proteome to date using microfluidic separation and DIA-MS on iPSC-derived neurons, identifying axon-enriched proteins and disease-related pathways.

SoftHybrid: A Hybrid Imputation Algorithm Optimised for Single-Cell Proteomics Data

SoftHybrid improves single-cell proteomics data imputation by jointly modeling missingness and protein abundance, outperforming existing methods at low input and matching them at the mini-bulk level.

High-throughput Single-cell Proteomics Enabled by Integrating nPOP-workflow with Quantitative Hyperplexing

This study develops a high-throughput single-cell proteomics workflow combining nPOP with quantitative hyperplexing, achieving high sensitivity and quantification across multiple cell types.