Advanced Proteomics Techniques and Applications

Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs)

The paper evaluates protein quantitation in DIA proteomics using controlled experiments on two mass spectrometry platforms, identifying over 10,000 proteins and highlighting the impact of post-processing on accuracy and false quantitative rates.

Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort.

The paper develops and evaluates a multiplexed PRM-MS assay for quantifying plasma proteins in an IBD cohort, demonstrating high quantifiability and consistent data acquisition.

Absolute Quantification of Fluorescent Protein Fusions by Proteomics

The paper develops a mass-spectrometry-based method to absolutely quantify fluorescent protein fusions and estimate their mature chromophore fraction, validated through a case study on expression kinetics.

Patch-Clamp Single-Cell Proteomics in Acute Brain Slices: A Framework for Recording, Retrieval, and Interpretation

This paper introduces a framework for interpreting single-cell proteomics data from patch-clamped neurons in acute brain slices, showing how retrieval quality affects proteomic outcomes.

Pre-Analytical Drivers of Bias in Bead-Enriched Plasma Proteomics

This study evaluates bead-based and conventional plasma proteomics workflows, finding bead methods enhance low-abundance protein detection but are prone to contamination bias, while perchloric acid-based methods resist contamination better.

A procedure for controlling the false discovery rate of de novopeptide sequencing

The paper introduces an FDR control procedure for de novo peptide sequencing and demonstrates its validity and utility.

Accounting for longitudinal peak quality metrics with MSstats+ enhances differential analysis in proteomic experiments with data-independent acquisition

MSstats+ improves differential protein analysis in proteomic experiments by incorporating longitudinal quality metrics to reduce false positives from poor-quality measurements.

Library-Free Multiplexed Targeted Proteomics Enables Quantitative Protein-Level Genotyping

GoDig-LiF enables targeted proteomics without data libraries by using predicted spectra and retention times, applied to quantify mutated proteins in cancer cell lines.

Next-Generation Multiplexed Targeted Proteomics Quantifies Post-Translational Modifications, Compound-Protein Interactions, and Disease Biomarkers with High Throughput

GoDig 2.0 improves targeted proteomics by increasing multiplexing, efficiency, and target coverage, enabling analysis of post-translational modifications and compound-protein interactions.

Development and Validation of a Novel LC-MS/MS Based Proteomics Method for Quantitation of Retinol Binding Protein 4 (RBP4) and Transthyretin (TTR)

This study develops and validates an LC-MS/MS method for absolute quantitation of RBP4 and TTR in serum and plasma, showing good linearity, precision, and correlation with ELISA.

Decoding interaction-induced proteome changes in co-cultures with hybrid quantification and SILAC-directed real-time search

This paper introduces a SILAC-TMT-RTS method to study proteome changes in T cell-cancer cell co-cultures, revealing mechanisms of differential sensitivity to T cell killing.

Peptide-RNA photocrosslinks with tunable RNA chain map RNA interfaces proteome-wide

The paper introduces pepR-MS and SALT to map protein-RNA interfaces at single-amino acid and nucleotide resolution, identifying over 34,000 crosslinks in breast cancer cells.

The Whole Proteome, Phosphoproteome, and Glycoproteome Landscape of Pan-Cancer Cell Lines Profiled by Mass Spectrometry and Reverse Phase Protein Array

The paper profiles proteome, phosphoproteome, and glycoproteome of 54 cancer cell lines using MS and RPPA, revealing tissue-specific patterns and drug targets.

QuickProt: A bioinformatics and visualization tool for DIA and PRM mass spectrometry-based proteomics datasets

QuickProt provides Python-based Colab notebooks for analyzing DIA and PRM proteomics data, enabling quality control, visualization, and interpretation without coding expertise.

SLB-msSIM: a spectral library-based multiplex segmented SIM platform for single-cell proteomic analysis

SLB-msSIM is a single-cell proteomic method that enhances sensitivity and robustness for analyzing cellular heterogeneity and EMT trajectories in pancreatic cancer cells.

Established Sulfopeptide Tandem Mass Spectrometry Behavior and Sulfotransferase Assays Refute Tyrosine Sulfation as a Histone Mark

The paper refutes the claim of histone H3 tyrosine sulfation by showing that published mass spectrometry data do not match known sulfotransferase fragmentation patterns.

Deep Visual Proteomics advances human colon organoid models by revealing a switch to an in vivo-like phenotype upon xenotransplantation

The paper uses Deep Visual Proteomics to show that human colon organoids switch to an in vivo-like phenotype after xenotransplantation.

Transitions in the proteome and phospho-proteome during early embryonic development in Xenopus

The paper analyzes proteome and phospho-proteome changes during Xenopus embryonic development, identifying key transitions in protein expression and phosphorylation patterns.

An Antibody Cocktail-Based Immunoaffinity-LC-MS Method Enabled Ultra-Sensitive and Robust Quantification of Circulating Proinsulin Proteoforms and C-peptide

This paper develops a sensitive LC-MS method to quantify circulating proinsulin proteoforms and C-peptide, showing improved separation of control and T1D groups compared to ELISA.

diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling

This paper introduces an improved chemoproteomics method for mapping kinase PPI networks, showing it identifies more interactions and predicts drug targets in neuroblastoma models.

High-Sensitivity Top-Down Proteomics Reveals Enhanced Maturation of Micropatterned Induced Pluripotent Stem Cell-Derived Cardiomyocytes

The paper develops a high-sensitivity protein extraction method for micropatterned hiPSC-CMs and shows they exhibit more mature molecular signatures compared to traditional cultures.

An Unbiased Proteomic Platform for ATE1-based Arginylation Profiling

The paper introduces an unbiased proteomic platform for ATE1-based arginylation profiling, identifying 235 unique arginylation sites in human proteomes.

End-to-end proteogenomics for discovery of cryptic and non-canonical cancer proteoforms using long-read transcriptomics and multi-dimensional proteomics

The paper introduces ProteomeGenerator3, an end-to-end proteogenomics method that detects non-canonical proteoforms in cancer using long-read transcriptomics and multi-dimensional proteomics.

Stochastic resonance is behind single cell proteomics success

The paper shows that stochastic resonance enhances detection of low-level peptide signals in single-cell proteomics using TMT and a carrier proteome.

Are Solid Particles Ready for Prime-Time Proteomics?

The paper evaluates nonporous C-18 stationary phases in proteomics workflows, finding they provide comparable or superior performance to traditional porous particles in separation and sensitivity.

Limitations of de novo sequencing in resolving sequence ambiguity

This study benchmarks eight de novo peptide sequencing models on proteomics datasets to evaluate their performance and identify limitations in resolving sequence ambiguity.

Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome

Exploring chromatographic dimensions for state-of-the-art proteomics applications

This study evaluates whether chromatographic performance affects proteome coverage under high-speed data acquisition, finding that proteome depth is now more influenced by mass spectrometry than chromatography.

PELSA-Decipher: a software tool for the processing and interpretation of ligand protein interaction dataset acquired by PELSA

PELSA-Decipher processes and interprets PELSA data to extract ligand-protein interaction details like binding proteins, sites, and affinities.

Rapid CE-MS with Real-Time Eco-AI Resolves Proteomic Heterogeneity Among Single Human Neutrophils

The paper introduces a rapid CE-MS platform with AI-based processing to profile single human neutrophils, revealing proteomic heterogeneity across immune functions.