Immunoproteomics

Introduction to the Immune System.- Immunoproteomics: The Evolution from Classical Methods to Emerging Techniques.- Serological Proteome Analysis for Antigen Identification.- Targeted Analyses of MHC-I Peptides using TOMAHAQ.- High-Coverage Immunopeptidomics Using timsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MS²Rescore.- Identification of Antibody-Cognate Antigens via a High-Throughput, Affinity-Chromatography-Based, Shotgun Immunoproteomics Pipeline.- Identification of Disease Characteristic Immune Complex Antigens.- Enrichment of Phosphorylated and Glycosylated MHC Peptides for Mass Spectrometry-Based Neoantigen Analysis.- Characterization of Human Leukocyte Antigen (HLA) Proteins with Integrated Immunopeptidomics and Proteomics Approach.- Artemis: Mass Spectrometry-Based Identification of MHC Presented Peptides Across Alleles, Classes, and Species using Soluble Single-Chain MHC Constructs.- A Novel Machine Learning Post-Processing Filter for Mass Spectrometry-Based Proteogenomics Leveraging Retention Time Deviation and Peptide Physiochemical Properties.- Utilizing Protein Bioinformatics to Delve Deeper into Immunopeptidomic Datasets with AIMS: An Automated Immune Molecule Separator.- Ribosome Profiling for Novel Antigen Discovery.- Multiplexed Detection of Autoantibodies to Glycopeptides Using Microarray.- Preparation of the Low Molecular Weight Serum Proteome for Mass Spectrometry Analysis.- MHCII MAPPS for High-Confident Immunogenicity Risk Assessment of Biotherapeutics.- FLEXMAP 3D Immunoproteomics: A Protocol to Characterize General Human Antibody Profiles Against Pathogens.- Profiling Norovirus Antibody Specificity and Function Using Luciferase Immunoprecipitation System (LIPS) Assays.- Nucleic Acid Programmable Protein Arrays for Autoantibodies Discovery, A Step-by-Step Guide.- Epitope Screening by Hydrogen-Deuterium Exchange Mass Spectrometry for Improved Immunotherapeutic Outcomes.- Intact Mass Spectrometry Analysis of Immuno-Isolated Human Therapeutic Antibodies from Serum.- Prioritization of Therapeutic Targets of Inflammation Using Proteomics, Bioinformatics, and In Silico Cell-Cell Interactomics.