25 Result(s)
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Article
Karl R Clauser
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Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides
We have broadened the utility of the SEQUEST computer algorithms to permit correlation of uninterpreted high-energy collision-induced dissociation spectra of peptides with all sequences in a database. SEQUEST ...
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Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy
Du et al. describe a bead-based method for high-throughput detection of phosphorylated tyrosine kinases and use it to profile 130 human cancer lines. They show that the tyrosine kinase SRC is frequently activated...
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A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease
Rational strategies to prioritize candidate biomarkers should save resources and accelerate progress in diagnostics development. Addona et al. integrate proteomics into a pipeline for biomarker validation and use...
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Integrated proteomic analysis of post-translational modifications by serial enrichment
A mass spectrometry–based method using serial enrichments of different post-translational modifications (SEPTM) enables high-coverage proteomic analysis of multiple PTMs from a single biological sample.
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Open AccessExtracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver
Colorectal cancer is the third most frequently diagnosed cancer and the third cause of cancer deaths in the United States. Despite the fact that tumor cell-intrinsic mechanisms controlling colorectal carcinoge...
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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...
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Addendum: A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages
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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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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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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 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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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 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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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 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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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 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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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 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...
