Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Neoantigen prediction and the need for validation

(2017) Antonella Vitiello et al.   NATURE BIOTECHNOLOGY

The problem with neoantigen prediction

(2017)   NATURE BIOTECHNOLOGY

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data

(2017) Ying S Ting et al.   NATURE METHODS

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer

(2015) Jan Muntel et al.   JOURNAL OF PROTEOME RESEARCH

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens

(2015) Joshua Tan et al.   NATURE

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Multiplexed peptide analysis using data-independent acquisition and Skyline

(2015) Jarrett D Egertson et al.   Nature Protocols

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

(2015) Etienne Caron et al.   eLife

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

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

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