DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

(2020) Chloe Chong et al.   Nature Communications

Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis

(2020) Bo Wen et al.   Nature Communications

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis

(2019) Shivani Tiwary et al.   NATURE METHODS

MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning

(2019) Wen-Feng Zeng et al.   ANALYTICAL CHEMISTRY

Prediction of LC-MS/MS properties of peptides from sequence by deep learning

(2019) Shenheng Guan et al.   MOLECULAR & CELLULAR PROTEOMICS

MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics

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

The Human Immunopeptidome Project: a roadmap to predict and treat immune diseases

(2019) Juan Antonio Vizcaíno 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

Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry

(2018) Lena Katharina Freudenmann et al.   IMMUNOLOGY

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

(2018) Florian Meier et al.   NATURE METHODS

In Immunopeptidomics We Need a Sniper Instead of a Shotgun

(2018) Pouya Faridi et al.   PROTEOMICS

Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes

(2018) Bruno Alvarez et al.   PROTEOMICS

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

(2018) Timothy J. O'Donnell et al.   Cell Systems

PDV: an integrative proteomics data viewer

(2018) Kai Li et al.   BIOINFORMATICS

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

(2018) Brendan Bulik-Sullivan et al.   NATURE BIOTECHNOLOGY

MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments

(2018) Massimo Andreatta et al.   PROTEOMICS

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

GibbsCluster: unsupervised clustering and alignment of peptide sequences

(2017) Massimo Andreatta et al.   NUCLEIC ACIDS RESEARCH

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq

(2016) Bo Wen et al.   BMC BIOINFORMATICS

Mass spectrometry-based antigen discovery for cancer immunotherapy

(2016) Michal Bassani-Sternberg et al.   CURRENT OPINION IN IMMUNOLOGY

Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0

(2016) Matthew The et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

(2016) Juliane Liepe et al.   SCIENCE

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

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

IPeak: An open source tool to combine results from multiple MS/MS search engines

(2015) Bo Wen et al.   PROTEOMICS

An open-source computational and data resource to analyze digital maps of immunopeptidomes

(2015) Etienne Caron et al.   eLife

Conserved Peptide Fragmentation as a Benchmarking Tool for Mass Spectrometers and a Discriminating Feature for Targeted Proteomics

(2014) Umut H. Toprak et al.   MOLECULAR & CELLULAR PROTEOMICS

The OMSSAPercolator: An automated tool to validate OMSSA results

(2014) Bo Wen et al.   PROTEOMICS

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY