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MOTIVATION Mass spectrometry yields complex functional data for which the features of scientific interest are peaks. A common two-step approach to analyzing these data involves first extracting and quantifying the peaks, then analyzing the resulting matrix of peak quantifications. Feature extraction and quantification involves a number of interrelated(More)
We describe a strategy for comprehending signaling pathways that are active in lung cancer cells and that are targeted by dasatinib using chemical proteomics to identify direct interacting proteins combined with immunoaffinity purification of tyrosine-phosphorylated peptides corresponding to activated tyrosine kinases. We identified nearly 40 different(More)
The AKT/PKB kinase is a key signaling component of one of the most frequently activated pathways in cancer and is a major target of cancer drug development. Most studies have focused on its activation by Receptor Tyrosine Kinase (RTK) mediated Phosphatidylinositol-3-OH kinase (PI3K) activation or loss of Phosphatase and Tensin homolog (PTEN). We have(More)
BACKGROUND Tyrosine kinases drive the proliferation and survival of many human cancers. Thus profiling the global state of tyrosine phosphorylation of a tumor is likely to provide a wealth of information that can be used to classify tumors for prognosis and prediction. However, the comprehensive analysis of tyrosine phosphorylation of large numbers of human(More)
We hypothesized that elucidating the interactome of epidermal growth factor receptor (EGFR) forms that are mutated in lung cancer, via global analysis of protein-protein interactions, phosphorylation, and systematically perturbing the ensuing network nodes, should offer a new, more systems-level perspective of the molecular etiology. Here, we describe an(More)
UNLABELLED Peptide-based proteomics supports identification and quantification as well as localization of post-translational modifications (PTMs) within proteins extracted from biological samples. The 'bottom-up' approach involves the digestion of proteins into peptide fragments that can be detected and sequenced with liquid chromatography coupled with(More)
Noise reduction is a critical step in proteomic profiling by mass spectrometry for identification of disease biomarkers. We propose a new method for characterizing chemical noise in MALDI TOF mass spectrometry using wavelet analysis of multiple noise realizations. The use of multiple measurements of the noise process enables a more reliable characterization(More)
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