Advanced Proteomics Techniques and Applications

ProteoForge: An Imputation-Aware Framework for Differential Proteoform Discovery in Bottom-Up Proteomics

ProteoForge identifies differential proteoforms by imputing missing data in bottom-up proteomics, showing high accuracy in complex datasets and revealing hidden proteoform regulation in lung cancer cells under hypoxia.

Comprehensive evaluation of statistical approaches for differential metaproteomics

The paper evaluates statistical methods for differential metaproteomics, finding that several approaches effectively identify differentially abundant proteins despite data challenges.

HIP-MS: An ultra-high-throughput, sensitive, and versatile affinity enrichment platform for static and dynamic interactome profiling

HIP-MS is an automated platform for high-throughput interactome profiling that improves sensitivity and throughput compared to traditional AE-MS methods.

Development and validation of a streamlined workflow for proteomic analysis of proteins and post-translational modifications from dried blood

The paper develops a streamlined workflow for proteomic analysis of proteins and PTMs from dried blood, demonstrating feasibility and best practices for MS-based quantification.

Proteome-wide quantification of inositol pyrophosphate-protein interactions

The paper develops a mass spectrometry method to quantify inositol pyrophosphate-protein interactions on a proteome-wide scale, identifying new pyrophosphorylated proteins and highlighting Mg2+ effects on binding.

Deep Proteoform Sequencing with Top-Down Direct Mass Technology

This paper introduces a top-down mass spectrometry workflow with DMTm technology and a new software platform to achieve deeper proteoform sequencing and improved sequence coverage.

Revisiting resonance-excitation collision-induced dissociation for data-independent acquisition

This study revisits resonance-excitation collision-induced dissociation (reCID) for DIA proteomics, showing it can achieve performance comparable to HCD with optimized settings and libraries.

A Viral Mutation Profiling and Discovery Strategy for Sensitive Multiplex Detection of Viruses and Variants in Saliva by Proteomics

This paper develops a proteomics strategy for detecting viral mutations and variants in saliva by prioritizing high-prevalence peptides and using G-PTM-D for sensitive variant discovery.

Ground Truth-Based Evaluation of False Discovery Rate and Statistical Power in DIA Proteomics

This study evaluates false discovery rate and statistical power in DIA proteomics using technical replicates and spike-in experiments, revealing discrepancies between nominal and true FDR and showing power dependence on fold change and abundance.

Real-time artificial intelligence prediction of peptide characteristics and MSFragger search improves multiplexed quantification of non-canonical HLA presented peptides in clear cell renal cell carcinoma.

The paper introduces MIRA-MS, a real-time AI-guided acquisition method that improves quantification of non-canonical HLA peptides in clear cell renal cell carcinoma.

SILAC-Site: A streamlined workflow for determining phosphopeptide stoichiometries

SILAC-Site directly measures phosphosite stoichiometries without enrichment, showing low stoichiometry for most phosphopeptides and correlating with direct detection.

Targeted Analysis of >1500 Plasma Proteoforms via Individual Ion Mass Spectrometry

This paper introduces two plasma proteoform panels, PPA 526 and PPA 1514, using Individual Ion Mass Spectrometry to quantify proteoforms in human plasma with high reproducibility and disease discrimination capability.

Expanded Proteome Coverage Powered by Advanced Ion Processing Enables Deep Single-Cell Drug Response Subtyping in Human Stem Cell Derived Cardiomyocytes

This paper introduces an enhanced single-cell proteomics workflow using timsUltra AIP, showing improved proteome coverage and drug response subtyping in human iPSC-CMs.

Mass spectrometry-based proteomics delivers in-depth proteome profiling of FFPE lung cancer biopsies from single glass slides

This study shows that mass spectrometry-based proteomics can profile FFPE lung cancer biopsies from single glass slides, providing actionable protein and biomarker data from limited clinical material.

Single-cell proteomic maps of human induced pluripotent stem cells and their differentiation into motor neurons

The paper reports single-cell proteomic maps of human iPSCs and their differentiation into motor neurons, revealing proteomic and transcriptomic discordance.

Adaptive Focused Acoustics-integrated proteome profiling of macrophages uncovers low abundant proteins associated with immune homeostasis, inflammatory response, and transport

This study evaluates adaptive focused acoustics (AFA) technology for macrophage lysis and proteomics, showing improved proteome coverage, reproducibility, and detection of low-abundance immune proteins.

Confident Identification and Quantification of Mouse Brain Tissues Reveals Sirtuin 5-Dependent Regulation

This paper develops a proteomic workflow to confidently identify and quantify lysine methylmalonylation in mouse brain tissue, revealing its regulation by SIRT5 and its role in myelin stability.

Near-Zero Missed Cleavages with a High-Fidelity Recombinant Arg-C Zero for Mass Spectrometry-Based Proteomics

This paper introduces Arg-C Zero, a high-fidelity protease with near-zero missed cleavages, demonstrating its utility in proteomics, especially for analyzing post-translational modifications.

dia-PASEF Enables Rapid Profiling of the Human Secretome for Deeper Insights into Cellular Dynamics and Inflammatory Mechanisms

The paper introduces dia-PASEF, a mass spectrometry workflow for rapid secretome profiling, revealing novel inflammatory responses and dynamic secretion patterns in macrophages.

Direct Injection NanoHILIC/MS/MS Proteomics from Reversed-Phase StageTip Eluate

The paper introduces DiReCT, a method to improve peptide solubility and recovery for nanoHILIC/MS/MS proteomics by integrating solubilization and elution in a single StageTip workflow.

High-Speed Mass Spectrometers diminish the difference between Data-Dependent and Data-Independent Acquisition Proteomics

This study shows that high-speed mass spectrometers reduce performance differences between DDA and DIA proteomics, but current LC-MS methods still lack comprehensive proteome coverage.

Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler

This paper introduces a method to detect protein conformational changes on a proteome-wide scale using kinase-mediated phosphorylation and phosphoproteomics.

Simultaneous single-cell profiling of the transcriptome and proteome

This paper describes a method to simultaneously profile the transcriptome and proteome from single cells, showing moderate correlation between the two modalities.

PhosSight: a Unified Deep Learning Framework Boosting and Accelerating Phosphoproteome Identification to Enable Biological Discoveries

PhosSight improves phosphoproteome identification by addressing acquisition biases in DDA and DIA, enhancing sensitivity and reducing missing values in cancer research.

A cell type-resolved proteomic atlas of the human body

The paper constructs a cell type-resolved proteomic atlas of the human body using Deep Visual Proteomics, revealing protein abundance patterns and uncovering cancer-testis antigens in oocytes.

Deciphering cytokine-driven ADP-ribosylation signaling networks via Af1521-based mass spectrometry analysis of labile Glu/Asp-linkages

The paper develops an MS-based workflow to detect Glu/Asp-ADPr modifications, identifies over 600 sites in cytokine-stimulated cells, and reveals residue-specific ADPr dynamics in immune signaling.

Unspecific Molecular Adsorption (UMA) sample preparation method for bottom-up and whole protein analysis. The foundation.

This paper introduces a sample preparation method for proteomics that enables both bottom-up and whole protein analysis using unspecific molecular adsorption.

Immunoglobulin sub-class levels define inter-donor plasma variability: a longitudinal dual-lab study

This study identifies immunoglobulin sub-class levels as key factors in inter-donor plasma variability using longitudinal proteomic data from two labs.

Predicting cellular functions of human phosphosites

The paper develops predictors to functionally characterize human phosphosites using integrated data, revealing novel functions and connections to DNA repair and cell survival.

A Unified Framework for Batch Correction and Imputation in Modern Mass Spectrometry Proteomics

NMFBatch reduces technical variation and preserves biological structure in proteomics data through batch correction and imputation.