prot_papers
@protpapers.bsky.social
🤖 Feed for papers about HLA/MHC neoantigens, immunopeptidomes and HDX-MS from PubMed and bioRxiv. Run by @ab604.uk inspired by @phypapers.bsky.social and https://bsky.app/profile/r-bloggers.bsky.social. Code: https://github.com/ab604/prot-paper-bot
Spatially Resolved Determination of Small Molecule Protein Affinities by Hydrogen Deuterium Exchange Mass Spectrometry
https://www.biorxiv.org/content/10.1101/2025.11.13.688232v1
November 14, 2025 at 5:39 AM
Spatially Resolved Determination of Small Molecule Protein Affinities by Hydrogen Deuterium Exchange Mass Spectrometry
https://www.biorxiv.org/content/10.1101/2025.11.13.688232v1
Antigenic Dark Matter: Unexplored Post-Translational Modifications of Tumor-Associated and Tumor-Specific Antigens in Pancreatic Cancer https://pubmed.ncbi.nlm.nih.gov/41228299/
November 13, 2025 at 5:40 PM
Antigenic Dark Matter: Unexplored Post-Translational Modifications of Tumor-Associated and Tumor-Specific Antigens in Pancreatic Cancer https://pubmed.ncbi.nlm.nih.gov/41228299/
NeoAtlas-Tumor and NeoBert: A Database and A Predictive Model for Canonical and Noncanonical Tumor Neoantigens https://pubmed.ncbi.nlm.nih.gov/41224698/
November 13, 2025 at 5:42 AM
NeoAtlas-Tumor and NeoBert: A Database and A Predictive Model for Canonical and Noncanonical Tumor Neoantigens https://pubmed.ncbi.nlm.nih.gov/41224698/
Inferring residue level hydrogen deuterium exchange with ReX https://pubmed.ncbi.nlm.nih.gov/41214241/
November 11, 2025 at 5:39 AM
Inferring residue level hydrogen deuterium exchange with ReX https://pubmed.ncbi.nlm.nih.gov/41214241/
Immunolyser 2.0: An advanced computational pipeline for comprehensive analysis of immunopeptidomic data https://pubmed.ncbi.nlm.nih.gov/41209766/
November 10, 2025 at 5:38 PM
Immunolyser 2.0: An advanced computational pipeline for comprehensive analysis of immunopeptidomic data https://pubmed.ncbi.nlm.nih.gov/41209766/
Non-Enzymatic Structural Modifications Reshape Peptide Presentation and Antigen Recognition
https://www.biorxiv.org/content/10.1101/2025.11.06.687013v1
November 8, 2025 at 5:38 AM
Non-Enzymatic Structural Modifications Reshape Peptide Presentation and Antigen Recognition
https://www.biorxiv.org/content/10.1101/2025.11.06.687013v1
Immunopeptidomics can inform the design of mRNA vaccines for the delivery of Mycobacterium tuberculosis MHC class II antigens https://pubmed.ncbi.nlm.nih.gov/41191777/
November 6, 2025 at 5:39 AM
Immunopeptidomics can inform the design of mRNA vaccines for the delivery of Mycobacterium tuberculosis MHC class II antigens https://pubmed.ncbi.nlm.nih.gov/41191777/
Investigating the conformational landscape of human histidine-rich glycoprotein using amide HDX-MS https://pubmed.ncbi.nlm.nih.gov/41190777/
November 5, 2025 at 5:38 PM
Investigating the conformational landscape of human histidine-rich glycoprotein using amide HDX-MS https://pubmed.ncbi.nlm.nih.gov/41190777/
Epitope mapping of diagnostic antibodies targeting SARS-CoV-2 nucleocapsid protein using hydrogen-deuterium exchange mass spectrometry https://pubmed.ncbi.nlm.nih.gov/41126529/
November 5, 2025 at 5:40 AM
Epitope mapping of diagnostic antibodies targeting SARS-CoV-2 nucleocapsid protein using hydrogen-deuterium exchange mass spectrometry https://pubmed.ncbi.nlm.nih.gov/41126529/
In vitro Characterization of Peptidomimetic Proteolysis Targeting Chimera (PROTAC) as a Degrader of 3-Chymotrypsin-Like Protease (Mpro/3CLpro) against SARS-CoV-2
https://www.biorxiv.org/content/10.1101/2025.10.30.685646v1
November 3, 2025 at 5:37 PM
In vitro Characterization of Peptidomimetic Proteolysis Targeting Chimera (PROTAC) as a Degrader of 3-Chymotrypsin-Like Protease (Mpro/3CLpro) against SARS-CoV-2
https://www.biorxiv.org/content/10.1101/2025.10.30.685646v1
Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes https://pubmed.ncbi.nlm.nih.gov/41166551/
October 31, 2025 at 5:39 AM
Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes https://pubmed.ncbi.nlm.nih.gov/41166551/
A Unified Protein Embedding Model with Local and Global Structural Sensitivity
https://www.biorxiv.org/content/10.1101/2025.10.27.684815v1
October 28, 2025 at 5:41 AM
A Unified Protein Embedding Model with Local and Global Structural Sensitivity
https://www.biorxiv.org/content/10.1101/2025.10.27.684815v1
Comprehensive Internal Standards for Hydrogen-Deuterium Exchange Mass Spectrometry https://pubmed.ncbi.nlm.nih.gov/41140027/
October 27, 2025 at 5:37 PM
Comprehensive Internal Standards for Hydrogen-Deuterium Exchange Mass Spectrometry https://pubmed.ncbi.nlm.nih.gov/41140027/
PeptiLine: an interactive platform for customizable functional peptidomic analysis
https://www.biorxiv.org/content/10.1101/2025.10.23.684139v1
October 26, 2025 at 5:35 PM
PeptiLine: an interactive platform for customizable functional peptidomic analysis
https://www.biorxiv.org/content/10.1101/2025.10.23.684139v1
Pan-cancer analysis reveals that tumor microbiomes generate specific epitopes through transcriptional reprogramming
https://www.biorxiv.org/content/10.1101/2025.10.22.683275v1
October 25, 2025 at 5:37 AM
Pan-cancer analysis reveals that tumor microbiomes generate specific epitopes through transcriptional reprogramming
https://www.biorxiv.org/content/10.1101/2025.10.22.683275v1
ERAP1 Allotypes 2 and 10 Differentially Regulate the Immunopeptidome of Melanocytes https://pubmed.ncbi.nlm.nih.gov/41130749/
October 24, 2025 at 5:38 PM
ERAP1 Allotypes 2 and 10 Differentially Regulate the Immunopeptidome of Melanocytes https://pubmed.ncbi.nlm.nih.gov/41130749/
Mapping the structural dynamics of red- and blue-emitting beetle luciferases revealed by HDX-MS https://pubmed.ncbi.nlm.nih.gov/41130797/
October 24, 2025 at 5:38 AM
Mapping the structural dynamics of red- and blue-emitting beetle luciferases revealed by HDX-MS https://pubmed.ncbi.nlm.nih.gov/41130797/
Epitope Mapping of Diagnostic Antibodies Targeting SARS-CoV-2 Nucleocapsid Protein Using Hydrogen-Deuterium Exchange Mass Spectrometry https://pubmed.ncbi.nlm.nih.gov/41126529/
October 23, 2025 at 5:38 PM
Epitope Mapping of Diagnostic Antibodies Targeting SARS-CoV-2 Nucleocapsid Protein Using Hydrogen-Deuterium Exchange Mass Spectrometry https://pubmed.ncbi.nlm.nih.gov/41126529/
Immunopeptidome analysis reveals SERPINB3 as an autoantigen driving eczematized psoriasis https://pubmed.ncbi.nlm.nih.gov/41124250/
October 23, 2025 at 5:38 AM
Immunopeptidome analysis reveals SERPINB3 as an autoantigen driving eczematized psoriasis https://pubmed.ncbi.nlm.nih.gov/41124250/
Methionine Oxidation Footprinting in Intact Proteins (MOFIP) Using Top-Down Proteomics https://pubmed.ncbi.nlm.nih.gov/41116609/
October 22, 2025 at 5:34 PM
Methionine Oxidation Footprinting in Intact Proteins (MOFIP) Using Top-Down Proteomics https://pubmed.ncbi.nlm.nih.gov/41116609/
Utilizing Protein Bioinformatics to Delve Deeper into Immunopeptidomic Datasets with AIMS: An Automated Immune Molecule Separator https://pubmed.ncbi.nlm.nih.gov/41085626/
October 21, 2025 at 5:40 AM
Utilizing Protein Bioinformatics to Delve Deeper into Immunopeptidomic Datasets with AIMS: An Automated Immune Molecule Separator https://pubmed.ncbi.nlm.nih.gov/41085626/
A Novel Machine Learning Post-processing Filter for Mass Spectrometry-Based Proteogenomics Leveraging Retention Time Deviation and Peptide Physicochemical Properties https://pubmed.ncbi.nlm.nih.gov/41085625/
October 20, 2025 at 5:40 PM
A Novel Machine Learning Post-processing Filter for Mass Spectrometry-Based Proteogenomics Leveraging Retention Time Deviation and Peptide Physicochemical Properties https://pubmed.ncbi.nlm.nih.gov/41085625/
Characterization of Human Leukocyte Antigen (HLA) Proteins with Integrated Immunopeptidomics and Proteomics Approach https://pubmed.ncbi.nlm.nih.gov/41085623/
October 20, 2025 at 5:39 AM
Characterization of Human Leukocyte Antigen (HLA) Proteins with Integrated Immunopeptidomics and Proteomics Approach https://pubmed.ncbi.nlm.nih.gov/41085623/
High-Coverage Immunopeptidomics Using timsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MS(2)Rescore https://pubmed.ncbi.nlm.nih.gov/41085619/
October 19, 2025 at 5:35 PM
High-Coverage Immunopeptidomics Using timsTOF Mass Spectrometers with Thunder-DDA-PASEF Boosted by MS(2)Rescore https://pubmed.ncbi.nlm.nih.gov/41085619/
Targeted Analyses of MHC-I Peptides Using TOMAHAQ https://pubmed.ncbi.nlm.nih.gov/41085618/
October 19, 2025 at 5:39 AM
Targeted Analyses of MHC-I Peptides Using TOMAHAQ https://pubmed.ncbi.nlm.nih.gov/41085618/