Proteogenomics meets cancer immunology: mass spectrometric discovery and analysis of neoantigens

Targeting cancer-specific mutations by T cell receptor gene therapy

(2015) Thomas Blankenstein et al.   CURRENT OPINION IN IMMUNOLOGY

An overview of bioinformatics tools for epitope prediction: Implications on vaccine development

(2015) Ruth E. Soria-Guerra et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Methionine to isothreonine conversion as a source of false discovery identifications of genetically encoded variants in proteogenomics

(2015) Alexey L. Chernobrovkin et al.   Journal of Proteomics

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

(2015) Tiannan Guo et al.   NATURE MEDICINE

One-hour proteome analysis in yeast

(2015) Alicia L Richards et al.   Nature Protocols

Exploration of peptides bound to MHC class I molecules in melanoma

(2015) Antonia L. Pritchard et al.   Pigment Cell & Melanoma Research

Realizing the Promise

(2015) K. L. Mueller   SCIENCE

Adoptive cell transfer as personalized immunotherapy for human cancer

(2015) S. A. Rosenberg et al.   SCIENCE

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Dendritic Cell-Based Vaccination in Cancer: Therapeutic Implications Emerging from Murine Models

(2015) Soledad Mac Keon et al.   Frontiers in Immunology

Bioinformatics for Clinical Next Generation Sequencing

(2014) G. R. Oliver et al.   CLINICAL CHEMISTRY

Deep and quantitative top-down proteomics in clinical and translational research

(2014) Neil L Kelleher et al.   Expert Review of Proteomics

Profiling proteoforms: promising follow-up of proteomics for biomarker discovery

(2014) Andrey Lisitsa et al.   Expert Review of Proteomics

Evolving role of tumor antigens for future melanoma therapies

(2014) Miles C Andrews et al.   Future Oncology

Profiling the RNA editomes of wild-typeC. elegansand ADAR mutants

(2014) Han-Qing Zhao et al.   GENOME RESEARCH

Identification and Characterization of Proteins Encoded by Chromosome 12 as Part of Chromosome-centric Human Proteome Project

(2014) Srikanth Srinivas Manda et al.   JOURNAL OF PROTEOME RESEARCH

Exome-Driven Characterization of the Cancer Cell Lines at the Proteome Level: The NCI-60 Case Study

(2014) Maria A. Karpova et al.   JOURNAL OF PROTEOME RESEARCH

DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry

(2014) Bo Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Anti-Peptide Monoclonal Antibodies Generated for Immuno-Multiple Reaction Monitoring-Mass Spectrometry Assays Have a High Probability of Supporting Western blot and ELISA

(2014) Regine M. Schoenherr et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics Analysis of Cancer Exosomes Using a Novel Modified Aptamer-based Array (SOMAscanTM) Platform

(2014) Jason Webber et al.   MOLECULAR & CELLULAR PROTEOMICS

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Onco-proteogenomics: cancer proteomics joins forces with genomics

(2014) Javier A Alfaro et al.   NATURE METHODS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

Proteogenomics in microbiology: Taking the right turn at the junction of genomics and proteomics

(2014) Veronika Kucharova et al.   PROTEOMICS

The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology

(2013) O. D. Abaan et al.   CANCER RESEARCH

Antibody and Antigen Contact Residues Define Epitope and Paratope Size and Structure

(2013) J. W. Stave et al.   JOURNAL OF IMMUNOLOGY

Comparison of Protein Immunoprecipitation-Multiple Reaction Monitoring with ELISA for Assay of Biomarker Candidates in Plasma

(2013) De Lin et al.   JOURNAL OF PROTEOME RESEARCH

Distinct Splice Variants and Pathway Enrichment in the Cell-Line Models of Aggressive Human Breast Cancer Subtypes

(2013) Rajasree Menon et al.   JOURNAL OF PROTEOME RESEARCH

Western BlotsversusSelected Reaction Monitoring Assays: Time to Turn the Tables?

(2013) Ruedi Aebersold et al.   MOLECULAR & CELLULAR PROTEOMICS

Impact of deleterious passenger mutations on cancer progression

(2013) C. D. McFarland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Proteome Analysis of the NCI-60 Cell Line Panel

(2013) Amin Moghaddas Gholami et al.   Cell Reports

High Immunogenicity of the Human Leukocyte Antigen Peptidomes of Melanoma Tumor Cells

(2012) Saulius Jarmalavicius et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Detection, Evaluation and Minimization of Nonenzymatic Deamidation in Proteomic Sample Preparation

(2011) Piliang Hao et al.   MOLECULAR & CELLULAR PROTEOMICS

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics

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

Structure and function of major histocompatibility complex class I antigens

(2010) Xian C Li et al.   Current Opinion in Organ Transplantation

HLA and melanoma: multiple alterations in HLA class I and II expression in human melanoma cell lines from ESTDAB cell bank

(2009) Rosa Mendez et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Proteomic identification of an MHC-binding peptidome from pancreas and breast cancer cell lines

(2009) Kwasi Antwi et al.   MOLECULAR IMMUNOLOGY

Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research

(2008) Hong Lin et al.   BMC BIOINFORMATICS

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures

(2008) Alexander Schmidt et al.   MOLECULAR & CELLULAR PROTEOMICS