Advanced Proteomics Techniques and Applications

A Comprehensive and Robust Multiplex-DIA Workflow Profiles Protein Turnover Regulations Associated with Cisplatin Resistance

This study introduces a robust multiplex DIA-MS workflow with machine learning and statistical filtering to profile protein turnover in cisplatin-resistant cancer cells, revealing correlations between transcript regulation and protein degradation.

Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines

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.

Unbiased complexome profiling and global proteomics analysis reveals mitochondrial impairment and potential changes at the intercalated disk in presymptomatic R14Delta/+ mice hearts

Paradigm shift in biomarker translation: a pipeline to generate clinical grade biomarker candidates from DIA-MS discovery

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.

Bridging the Gap between Database Search and De Novo Peptide Sequencing with SearchNovo

SearchNovo improves peptide sequencing by combining database search and de novo methods, outperforming existing models on multiple datasets.

FLASHQuant: a fast algorithm for proteoform quantification in top-down proteomics

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

Joint Protein Inference Analysis with PyProteinInference Elucidates Biological Understanding of Tandem Mass Spectrometry Data

PyProteinInference enables joint protein inference analysis of MS/MS data to compute protein-level FDR and support biological interpretation.

An Extensive Atlas of Proteome and Phosphoproteome Turnover Across Mouse Tissues and Brain Regions

The paper presents Turnover-PPT, a resource mapping protein and phosphoprotein turnover across mouse tissues and brain regions, revealing tissue-specific protein lifetimes and phosphorylation's impact on stability.

Phosphoproteomics highlights complex resource management upon inflammatory stimulation of fibroblasts

This study uses phosphoproteomics to show that inflammatory stimulation of fibroblasts primarily drives resource and stress management rather than specific inflammatory effector functions.

Assessment of a high-throughput mass spectrometry method to accelerate biomarker discovery in clinical cancer cohorts using volumetric absorptive microsampling (VAMS) devices.

The paper evaluates high-throughput mass spectrometry methods using VAMS devices to identify differentially expressed proteins in lung cancer patients and healthy controls, finding 36 discriminatory biomarkers with 88.9% AUC.

Mining the Proteome of Human Ovarian Cancer Extracellular Vesicles Using Thermolysin Proteolysis

This study compares Thermolysin and Trypsin/LysC proteolysis for enhancing proteomic analysis of ovarian cancer extracellular vesicles, finding Thermolysin improves peptide complexity and identifies unique proteins like Ly6E and NODAL.

Gender- and Age-Based Characterization and Comparison of the Murine Primary Peritoneal Mesothelial Cell Proteome

This study characterizes gender- and age-related differences in the proteome of murine primary peritoneal mesothelial cells using bottom-up proteomics.

Leveraging HILIC/ERLIC Separations for Online Nanoscale LC- MS/MS Analysis of Phosphopeptide Isoforms from RNA Polymerase II C-terminal Domain

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

Inferring post-transcriptional regulation within and across cell types in human testis

The paper quantifies proteomes and RNA levels in human testis cells to infer post-transcriptional regulation using a Bayesian model called BayesPG.

DigestR an open-source software tool for visualizing LC-MS proteomics data resulting from natural protein catabolism

DigestR is an open-source tool for visualizing LC-MS proteomics data from natural protein catabolism, demonstrating its ability to identify proteolytic cut sites in human and parasite systems.

Ultrafast metaproteomics for quantitative assessment of strain isolates and microbiomes

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

Quantitative proteomic mass spectrometry of protein kinases to determine dynamic heterogeneity of the human kinome

This study quantifies kinase protein abundance in human tissues using proteomic mass spectrometry, revealing heterogeneity in breast cancer subtypes and enabling clinical applications.

Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure

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

A snapshot of the Physcomitrella N-terminome reveals N-terminal methylation of organellar proteins

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.

Capturing the Hierarchically Assorted Protein-protein Interaction Modules of Mammalian Cell

The paper identifies protein-protein interaction modules in mammalian cells using XL-MS data and bioinformatics, revealing hierarchical organization into compartments.

MetaLab Platform Enables Comprehensive DDA and DIA Metaproteomics Analysis

MetaLab enables comprehensive DDA and DIA metaproteomics analysis by supporting both modes without requiring DDA results, improving peptide identification in human gut microbiome studies.

A pilot study for deciphering post-translational modifications and proteoforms of tau protein by capillary electrophoresis-mass spectrometry

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.

Unipept in 2024: Expanding metaproteomics analysis with support for missed cleavages, semi-tryptic and non-tryptic peptides

The paper updates the Unipept software to support analysis of non-tryptic and semi-tryptic peptides, improving performance while maintaining accuracy.

Decoding the Impact of Neighboring Amino Acid on MS Intensity Output through Deep Learning

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

Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity

The paper introduces UFP-MS, a fast proteomics method, and applies it to study drug effects on mouse tissues, revealing tissue-specific metabolic changes.

An expedited qualitative profiling of free amino acids in plant tissues using liquid chromatography-mass spectrometry (LC-MS) in conjunction with MS-DIAL

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 enables deep proteomics of the microbial extracellular environment

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

Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics

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: a comprehensive framework for evaluating the false discovery rate and accuracy of de novo peptide sequencing

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

Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows

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.