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Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics*S
Measurements of mass spectral peak intensities and spectral counts are promising methods for quantifying protein abundance changes in shotgun proteomic analyses. We describe Serac, software developedExpand
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Mapping protein post-translational modifications with mass spectrometry
Post-translational modifications of proteins control many biological processes, and examining their diversity is critical for understanding mechanisms of cell regulation. Mass spectrometry is aExpand
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  • Open Access
Mass spectrometry of peptides and proteins.
This tutorial article introduces mass spectrometry (MS) for peptide fragmentation and protein identification. The current approaches being used for protein identification include top-down andExpand
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  • Open Access
Protein analysis by hydrogen exchange mass spectrometry.
Mass spectrometry has provided a powerful method for monitoring hydrogen exchange of protein backbone amides with deuterium from solvent. In comparison to popular NMR approaches, mass spectrometryExpand
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Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry.
Protein interactions between MAP kinases and substrates, activators, and scaffolding proteins are regulated by docking site motifs, one containing basic residues proximal to Leu-X-Leu (DEJL) and aExpand
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Phosphatase Inhibition Leads to Histone Deacetylases 1 and 2 Phosphorylation and Disruption of Corepressor Interactions*
The regulation of histone deacetylases (HDACs) by phosphorylation was examined by elevating intracellular phosphorylation in cultured cells with the protein phosphatase inhibitor okadaic acid. AfterExpand
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The gatekeeper residue controls autoactivation of ERK2 via a pathway of intramolecular connectivity
Studies of protein kinases have identified a “gatekeeper” residue, which confers selectivity for binding nucleotides and small-molecule inhibitors. We report that, in the MAP kinase ERK2, mutationsExpand
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Cdc28/Cdk1 regulates spindle pole body duplication through phosphorylation of Spc42 and Mps1.
Duplication of the Saccharomyces cerevisiae spindle pole body (SPB) once per cell cycle is essential for bipolar spindle formation and accurate chromosome segregation during mitosis. We haveExpand
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Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics.
Identifying proteins in cell extracts by shotgun proteomics involves digesting the proteins, sequencing the resulting peptides by data-dependent mass spectrometry (MS/MS), and searching proteinExpand
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Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma.
Melanoma and other cancers harbor oncogenic mutations in the protein kinase B-Raf, which leads to constitutive activation and dysregulation of MAP kinase signaling. In order to elucidate molecularExpand
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