11 Result(s)

Article

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...

**yan Du, Paula Bernasconi, Karl R Clauser, D R Mani… in Nature Biotechnology (2009)

Article

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...

Terri A Addona, Xu Shi, Hasmik Keshishian, D R Mani… in Nature Biotechnology (2011)

Article

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.

Philipp Mertins, Jana W Qiao, **al Patel, Namrata D Udeshi… in Nature Methods (2013)

Article

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...

Haihui Lu, Karl R. Clauser, Wai Leong Tam, Julia Fröse, **n Ye… in Nature Cell Biology (2014)

Article

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...

Hasmik Keshishian, Michael W Burgess, Harrison Specht, Luke Wallace… in Nature Protocols (2017)

Article

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...

Philipp Mertins, Lauren C. Tang, Karsten Krug, David J. Clark… in Nature Protocols (2018)

Article

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...

Siranush Sarkizova, Susan Klaeger, Phuong M. Le, Letitia W. Li… in Nature Biotechnology (2020)

Article

PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis

D. R. Mani, Myranda Maynard, Ramani Kothadia, Karsten Krug… in Nature Methods (2021)

Article

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...

John R. Prensner, Oana M. Enache, Victor Luria, Karsten Krug… in Nature Biotechnology (2021)

Article

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...

Tamara Ouspenskaia, Travis Law, Karl R. Clauser, Susan Klaeger… in Nature Biotechnology (2022)