Advanced Proteomics Techniques and Applications

The paper introduces a new MS platform with enhanced acquisition rates and real-time chromatogram alignment, enabling high multiplex targeted proteomics with improved sensitivity and throughput.

This paper uses chemoproteogenomics to identify gain-of-cysteine variants in cancer and healthy genomes, revealing their prevalence and potential for drug targeting.

This study combines quantitative proteomics and interactomics to analyze molecular differences between three human cell lines, revealing cell-type-specific changes in protein interactions and conformations.

This paper introduces TEAQ, a software tool that selects clinical-grade biomarker candidates from DIA-MS data by evaluating protein quantification metrics in a discovery cohort.

FLASHQuant is a fast, accurate, and open-source algorithm for label-free quantification of proteoforms in top-down proteomics, resolving co-eluting signals efficiently.

The paper identifies 2884 calcium-regulated proteins across human, mouse, and yeast proteomes using thermostability assays and reveals novel calcium engagement in metabolic enzymes and the spliceosome.

The paper develops a proteomics method to identify drug targets across the proteome, revealing organ-specific interactions and global drug effects.

This paper evaluates HILIC and ERLIC chromatography for resolving CTD phosphopeptide isoforms, finding ERLIC improves separation of phosphorylated peptides for LC-MS/MS analysis.

This paper introduces an ultrafast metaproteomics method using Orbitrap MS to rapidly and accurately assess microbial identity and functional activity without peptide fragmentation.

This study introduces a formaldehyde-based fixation method that improves in situ XL-MS performance while preserving cellular ultrastructure in human A549 cells.

The paper analyzes the N-terminome of Physcomitrella to reveal N-terminal methylation of mitochondrial proteins and identifies a methyltransferase involved in plastid, mitochondrial, and cytosolic methylation.

The paper develops a mass spectrometry-based PRM assay to quantify histone H1 subtypes and shows differences in H1 complement between CML responders and non-responders.

This paper presents a pilot study using CE-MS techniques to analyze PTMs and proteoforms of tau protein, identifying more phosphorylation sites and detecting dimers.

The paper uses deep learning to analyze how neighboring amino acid pairs affect MS1 intensity, identifying key motifs and their impact on peptide response.

This paper presents an LC-MS method using MS-DIAL to qualitatively profile free amino acids in plant tissues, simplifying data analysis for plant biologists.

EXCRETE improves exoproteome identification in cyanobacteria, revealing 85% of predicted secreted proteins and highlighting key functions in cell envelope maintenance and nutrient acquisition.

This study uses engineered nanoparticles to enrich low-abundant proteins in human plasma, enabling top-down proteomics to detect proteoforms at lower concentrations and expand proteome depth.

NovoBoard evaluates de novo peptide sequencing methods using benchmark datasets and FDR estimation to assess accuracy and significance of peptide-spectrum matches.

This study benchmarks label-free and TMT-MS2 methods for spatial proteome mapping, showing label-free provides deeper coverage and higher dynamic range, while TMT-MS2 offers faster throughput.

This study introduces a top-down proteomics method to precisely identify proteoforms in nanoparticle protein coronas, revealing biomarkers not detectable by bottom-up approaches.

metaExpertPro constructs metaproteomics spectral libraries and analyzes DIA-MS data, achieving high peptide quantification and low FDR in human fecal samples.

This paper introduces DIA-SiS, a method combining DIA with spike-in SILAC to improve proteome coverage and quantification, showing better performance than label-free approaches.

FragPipe-Analyst provides an R shiny web server and R package for downstream analysis and visualization of quantitative proteomics data from FragPipe.

The paper introduces a framework for quality control in quantitative proteomics, combining internal and external QC measures with tools for data analysis and deposition.

The paper develops a dual-species proteomics approach to study host-pathogen protein interactions and demonstrates targeted intervention using a novel inhibitor.

The paper modifies the Casanovo model to account for digestion enzyme bias but finds no significant improvement in sequencing accuracy.

This paper introduces a new native proteomics technique using nCZE-MS to measure proteoforms and protein complexes in complex samples, achieving high sensitivity and resolution.

The paper develops an assay to quantify adsorption effects of surfaces on analytes during sample preparation, using LC-MS/MS-based proteomics to identify and measure peptide adsorption to different vial materials.

The paper extends antibody databases for mass spectrometry by mining millions of sequences from the OAS database to improve antibody peptide identification in SARS-CoV-2 plasma samples.