Advanced Proteomics Techniques and Applications

Mind Your Spectra: Points to be Aware of when Validating the Identification of Isobaric Histone Peptidoforms

The paper identifies challenges in validating isobaric histone peptidoforms using mass spectrometry and proposes strategies to improve their identification.

Cumulating MS Signal enables polyclonal antibody analysis

This paper introduces a novel MS score framework for analyzing polyclonal antibodies, demonstrating its ability to identify antibody subgroups and predict interactions.

One-Pot Quantitation of Mycobacterial N-terminal Protein Acetylation Peptidoforms and Proteome

The paper introduces OnePotNTA, a one-pot method for quantifying N-terminal acetylation in mycobacteria, achieving high coverage and reducing sample preparation time.

Time-lapse tryptic digestion: a proteomic approach to improve sequence coverage of extracellular matrix proteins

This paper introduces a time-lapse proteomic method to improve ECM protein sequence coverage and identify differential trypsin susceptibility.

dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples

The paper uses laser microdissection and proteomics to compare tumor and stroma in HNSCC tissues, identifying ECM enrichment in stroma and potential targets for disease intervention.

MetaboMiNR: a web application to analyze label free quantitative proteomic experiments with a focus on metabolism and nuclear receptors

MetaboMiNR is a web tool for analyzing label-free proteomic data, focusing on metabolism and nuclear receptors, with features for pathway analysis, gene extraction, and plot generation.

Temporal dynamics of proteome and phosphorproteome during neuronal differentiation in the reference KOLF2.1J iPSC line

The paper profiles proteome and phosphoproteome dynamics during neuronal differentiation of the KOLF2.1J iPSC line, revealing distinct molecular signatures and kinase activity changes.

omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics data.

omicsGMF integrates dimensionality reduction, batch correction, and imputation for bulk and single-cell proteomics data, improving statistical power for differential abundance detection.

Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provides New Insight on Protein Conformational Plasticity within Organelles, Cells, and Tissues

The paper uses quantitative cross-linking and mass spectrometry data to cluster cross-links by their conformational state preferences, providing insights into protein conformational plasticity across different biological contexts.

Chemoproteomic Profiling of PKA Substrates with Kinase-catalyzed Crosslinking and Immunoprecipitation (K-CLIP)

This study modifies K-CLIP to identify PKA substrates, discovering SMC3 as a novel substrate and demonstrating the method's versatility for kinase-substrate profiling.

A Full Window Data Independent Acquisition Method for DeeperTop-down Proteomics

This paper introduces a machine learning-assisted Full Window DIA method for top-down proteomics, enhancing signal intensity and sequence coverage in protein analysis.

Viral fragments in the urine proteome: New clues to the cause of fever

This study identifies virus protein fragments in urine proteomics of febrile patients, revealing potential viral causes of fever and demonstrating high reliability in detection.

DiNovo: high-coverage, high-confidence de novo peptide sequencing using mirror proteases and deep learning

DiNovo improves de novo peptide sequencing by using mirror proteases and deep learning, achieving higher coverage and confidence than single-protease methods.

Illuminating the Dark Cancer Phosphoproteome Through a Machine-Learned Co-Regulation Map of 26,280 Phosphosites

The paper constructs a co-regulation map of phosphosites using machine learning and phosphoproteomic data, revealing kinase-substrate associations and identifying potential therapeutic targets in cancer.

Blood to Biomarker Quantitation in Under One Hour with Rapid Proteomics using a Hyperthermoacidic Protease

This paper develops a rapid proteomics method using HTA protease and LC-MS to quantify blood biomarkers in under an hour.

Visible-Light-Controlled Residue-Selective Cross-Linking for Deciphering Protein Complexes and Dynamic Protein-Protein Interactions in Live Cells

This paper introduces a visible-light-controlled cross-linking method for analyzing protein complexes and dynamic interactions in live cells, showing improved accuracy and temporal control.

Improved determination of protein turnover rate with heavy water labeling by mass isotopomer ratio selection

This paper introduces a method to improve protein turnover rate calculation using heavy water labeling and mass spectrometry, increasing coverage of well-fitted peptides by 25-82% in mouse organ proteomes.

A Novel Algorithm for the Harmonization of Pan-cancer Proteomics

This paper introduces a novel framework for harmonizing pan-cancer proteomics data, demonstrating its effectiveness in improving dataset integration and revealing prognostic markers.

Proteomic Analysis of Endemic Viral Infections in Neuronsoffers Insights into Neurodegenerative Diseases

The paper investigates how endemic viral infections alter the neuronal proteome and links these changes to neurodegenerative disease pathways.

High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells

This study presents a proteomic and phosphoproteomic analysis of the human cell cycle in non-transformed cells, revealing new insights into cell cycle-dependent protein and phosphorylation oscillations.

Candida albicans: a comprehensive view of the proteome

The paper provides an updated Candida albicans PeptideAtlas proteomics resource with detailed PTM data and tools for analysis.

Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

The paper improves bacterial epitope discovery by integrating multiple search engines and rescoring, increasing peptide identification by 27% and detecting 18 new bacterial peptides.

Discovery of RNA-Protein Molecular Clamps Using Proteome-Wide Stability Assays

The paper develops a method to discover RNA-protein-small molecule complexes using proteome-wide stability assays and applies it to identify novel DDX helicase targets of rocaglates.

ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation

ClassiCOL improves species classification from ancient collagen LC-MS/MS data by resolving peptide ambiguity through isoBLAST and taxonomic branching analysis.

Development of a General Purpose Targeted LC-MS Method for Accurate Quantification of the SARS-CoV-2 Spike Protein Expression

The paper develops a targeted LC-MS method to quantify SARS-CoV-2 spike protein expression and enables proteome profiling of infected cells.

Tree-based quantification infers proteoform regulation in bottom-up proteomics data

AlphaQuant improves proteoform regulation detection in bottom-up proteomics by using tree-based quantification and deep learning, revealing new patterns in mouse tissues.

Spatial top-down proteomics for the functional characterization of human kidney

This paper develops a spatial proteomics workflow to identify and map proteoforms in human kidney tissue, revealing spatially distinct proteomic profiles between glomeruli and tubules.

A 96-Well Polyacrylamide Gel for Electrophoresis and Western Blotting

This paper introduces a 96-sample western blot format that improves efficiency and capacity while maintaining compatibility with standard protocols.

Limelight - An open, web-based tool for visualizing, sharing, and analyzing mass spectrometry data from DDA pipelines

diaPASEF analysis for HLA-I peptides enables quantification of common cancer neoantigens

This study evaluates diaPASEF for high-sensitivity identification and quantification of HLA-I peptides, demonstrating improved detection of neoantigens in cancer models.