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Global Survey of Phosphotyrosine Signaling Identifies Oncogenic Kinases in Lung Cancer
TLDR
By focusing on activated cell circuitry, the approach outlined here provides insight into cancer biology not available at the chromosomal and transcriptional levels and can be applied broadly across all human cancers. Expand
Systematic and quantitative assessment of the ubiquitin-modified proteome.
TLDR
The human ubiquitin-modified proteome is characterized using a monoclonal antibody that recognizes diglycine (diGly)-containing isopeptides following trypsin digestion and it is demonstrated that quantitative diGly proteomics can be utilized to identify substrates for cullin-RING ubiquitIn ligases. Expand
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
TLDR
The AQUA strategy was used to quantify low abundance yeast proteins involved in gene silencing, quantitatively determine the cell cycle-dependent phosphorylation of Ser-1126 of human separase protein, and identify kinases capable of phosphorylating Ser-1501 of separase in an in vitro kinase assay. Expand
A probability-based approach for high-throughput protein phosphorylation analysis and site localization
TLDR
A large-scale phosphorylation data set is provided with a measured error rate as determined by the target-decoy approach, an approach to maximize data set sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs) is demonstrated, and a probability-based score is presented, the Ascore, that measures the probability of correct phosphorylated site localization based on the presence and intensity of site-determining ions in MS/MS spectra. Expand
Quantitative Proteomics Reveals the Function of Unconventional Ubiquitin Chains in Proteasomal Degradation
TLDR
It is reported that the unconventional linkages are abundant in vivo and that all non-K63 linkages may target proteins for degradation, and that unconventional polyubiquitin chains are critical for ubiquitin-proteasome system function. Expand
Immunoaffinity profiling of tyrosine phosphorylation in cancer cells
TLDR
Applying this approach to several cell systems, including cancer cell lines, shows it can be used to identify activated protein kinases and their phosphorylated substrates without prior knowledge of the signaling networks that are activated, a first step in profiling normal and oncogenic signaling networks. Expand
Time-resolved Mass Spectrometry of Tyrosine Phosphorylation Sites in the Epidermal Growth Factor Receptor Signaling Network Reveals Dynamic Modules*S
TLDR
A method enabling the simultaneous quantification of tyrosine phosphorylation of specific residues on dozens of key proteins in a time-resolved manner, downstream of epidermal growth factor receptor (EGFR) activation is developed. Expand
Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology
TLDR
A reconstituted system and quantitative mass spectrometry are used to demonstrate that cyclin B1 is modified by ubiquitin chains of complex topology, rather than by homogeneous Lys 48-linked chains, and provide unique insights into the mechanisms of substrate ubiquitination. Expand
The Chlamydomonas reinhardtii BBSome is an IFT cargo required for export of specific signaling proteins from flagella
The Bardet-Biedl syndrome protein complex (BBSome) is a cargo adapter rather than an essential part of the intraflagellar transport (IFT) machinery.
Dynamics of Cullin-RING Ubiquitin Ligase Network Revealed by Systematic Quantitative Proteomics
TLDR
A quantitative proteomics platform centered on multiplex absolute quantification (AQUA) technology is reported to elucidate the architecture of the cullin-RING ubiquitin ligase (CRL) network and to evaluate current models of dynamic CRL remodeling. Expand
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