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Open AccessWorkflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and...
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Cancer proteogenomics: current impact and future prospects
Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the functions of the vast majority of somatic mutations a...
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Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
Tumor-associated epitopes presented on MHC-I that can activate the immune system against cancer cells are typically identified from annotated protein-coding regions of the genome, but whether peptides originat...
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Article
Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma
Interactions between T cell receptors (TCRs) and their cognate tumour antigens are central to antitumour immune responses1–3; however, the relationship between phenotypic characteristics and TCR properties is not...
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Open AccessAuthor Correction: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics
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Open AccessDeep learning boosts sensitivity of mass spectrometry-based immunopeptidomics
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for develo** vaccines and drugs for immune-oncology. Still, the identification of non-tryptic pe...
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PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis
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Noncanonical open reading frames encode functional proteins essential for cancer cell survival
Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candi...
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Open AccessSuppression of pancreatic ductal adenocarcinoma growth and metastasis by fibrillar collagens produced selectively by tumor cells
Pancreatic ductal adenocarcinoma (PDAC) has a collagen-rich dense extracellular matrix (ECM) that promotes malignancy of cancer cells and presents a barrier for drug delivery. Data analysis of our published ma...
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A large peptidome dataset improves HLA class I epitope prediction across most of the human population
Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained o...
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Open AccessMicroscaled proteogenomic methods for precision oncology
Cancer proteogenomics promises new insights into cancer biology and treatment efficacy by integrating genomics, transcriptomics and protein profiling including modifications by mass spectrometry (MS). A critic...
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Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry
Here we present an optimized workflow for global proteome and phosphoproteome analysis of tissues or cell lines that uses isobaric tags (TMT (tandem mass tags)-10) for multiplexed analysis and relative quantif...
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Open AccessSite-specific identification and quantitation of endogenous SUMO modifications under native conditions
Small ubiquitin-like modifier (SUMO) modification regulates numerous cellular processes. Unlike ubiquitin, detection of endogenous SUMOylated proteins is limited by the lack of naturally occurring protease sit...
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Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry
This protocol describes the deep-scale analysis of the blood plasma proteome. By combining abundant protein depletion, sample multiplexing with isobaric labeling and fractionation, this enables rapid quantific...
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Open AccessCorrection: Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts
Nature Communications 8: Article number: 14864 (2017)); Published: 28 March 2017; Updated: 25 April 2017 The original version of this Article contained a typographical error in the spelling of the author Beifa...
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Open AccessProteogenomic integration reveals therapeutic targets in breast cancer xenografts
Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xe...
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Open AccessQuantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression
The angiogenic switch, the time at which a tumor becomes vascularized, is a critical step in tumor progression. Indeed, without blood supply, tumors will fail to grow beyond 1 mm3 and are unlikely to disseminate....
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Proteogenomics connects somatic mutations to signalling in breast cancer
Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. Here we describe quantitative mass-spec...
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Addendum: A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages
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A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages
The cell-biological program termed the epithelial–mesenchymal transition (EMT) confers on cancer cells mesenchymal traits and an ability to enter the cancer stem cell (CSC) state. However, the interactions bet...
