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The impact of microRNAs on protein output
TLDR
The impact of micro RNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output.
A quantitative atlas of mitotic phosphorylation
TLDR
Analysis of non-proline site-containing phosphopeptides identified two unique motifs that suggest there are at least two undiscovered mitotic kinases, suggesting that many of the proteins identified may be CDK substrates.
Large-scale characterization of HeLa cell nuclear phosphoproteins.
TLDR
Using a strategy based on strong cation exchange chromatography, phosphopeptides were enriched from the nuclear fraction of HeLa cell lysate and determined 2,002 phosphorylation sites, an unprecedented large collection of sites permitted a detailed accounting of known and unknown kinase motifs and substrates.
Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution
TLDR
It is proposed that the regulation of protein function by phosphorylation often depends on simple nonspecific mechanisms that disrupt or enhance protein-protein interactions and the gain or loss of phosphorylated sites in rapidly evolving regions could facilitate the evolution of kinase-signaling circuits.
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.
Large-scale phosphorylation analysis of mouse liver
TLDR
It is demonstrated that a combination of tandem phosphopeptide enrichment methods, high performance MS, and optimized database search/data filtering strategies is a powerful tool for surveying the phosphoproteome.
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