MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates

Most non-canonical proteins uniquely populate the proteome or immunopeptidome

(2021) Maria Virginia Ruiz Cuevas et al.   Cell Reports

Universal Spectrum Identifier for mass spectra

(2021) Eric W. Deutsch et al.   NATURE METHODS

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

(2021) Mathias Wilhelm et al.   Nature Communications

Immunopeptidomics for next-generation bacterial vaccine development

(2021) Rupert L. Mayer et al.   TRENDS IN MICROBIOLOGY

Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling

(2020) Sibylle Pfammatter et al.   ANALYTICAL CHEMISTRY

Biogenesis of HLA Ligand Presentation in Immune Cells Upon Activation Reveals Changes in Peptide Length Preference

(2020) Fabio Marino et al.   Frontiers in Immunology

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions

(2019) Ana S C Silva et al.   BIOINFORMATICS

Mass spectrometry–based identification of MHC-bound peptides for immunopeptidomics

(2019) Anthony W. Purcell et al.   Nature Protocols

Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques

(2019) Ralf Gabriels et al.   NUCLEIC ACIDS RESEARCH

Epitope Prediction by Novel Immunoinformatics Approach: A State-of-the-art Review

(2019) Ehsan Raoufi et al.   International Journal of Peptide Research and Therapeutics

MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics

(2019) Leon Bichmann et al.   JOURNAL OF PROTEOME RESEARCH

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes

(2019) Julien Racle et al.   NATURE BIOTECHNOLOGY

spectrum_utils: A Python Package for Mass Spectrometry Data Processing and Visualization

(2019) Wout Bittremieux   ANALYTICAL CHEMISTRY

ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion

(2019) Niels Hulstaert et al.   JOURNAL OF PROTEOME RESEARCH

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands

(2019) Marthe Solleder et al.   MOLECULAR & CELLULAR PROTEOMICS

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction

(2018) Viktoria Dorfer et al.   JOURNAL OF PROTEOME RESEARCH

Proteome analysis of an Escherichia coli ptsN -null strain under different nitrogen regimes

(2018) Fernanda Gravina et al.   Journal of Proteomics

In Immunopeptidomics We Need a Sniper Instead of a Shotgun

(2018) Pouya Faridi et al.   PROTEOMICS

Chemical Derivatization Strategy for Extending the Identification of MHC Class I Immunopeptides

(2018) Rui Chen et al.   ANALYTICAL CHEMISTRY

The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands

(2018) David Gfeller et al.   JOURNAL OF IMMUNOLOGY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows

(2017) Kenneth Verheggen et al.   MASS SPECTROMETRY REVIEWS

High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome

(2017) Chloe Chong et al.   MOLECULAR & CELLULAR PROTEOMICS

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity

(2017) Michal Bassani-Sternberg et al.   PLoS Computational Biology

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

MS2PIP prediction server: compute and visualize MS2peak intensity predictions for CID and HCD fragmentation

(2015) Sven Degroeve et al.   NUCLEIC ACIDS RESEARCH

MS2PIP: a tool for MS/MS peak intensity prediction

(2013) Sven Degroeve et al.   BIOINFORMATICS

Fast and Accurate Database Searches with MS-GF+Percolator

(2013) Viktor Granholm et al.   JOURNAL OF PROTEOME RESEARCH

Analysis of the Resolution Limitations of Peptide Identification Algorithms

(2011) Niklaas Colaert et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods

(2008) Hao Zhang et al.   BIOINFORMATICS