Abstract: This disclosure provides a non-genetic, high-throughput method of introducing and assaying effects of amino acid substitutions at a plurality of positions in a target protein. Mistranslation events are imposed stochastically during the translation of multiple copies of a target protein, resulting in a plurality of variants of the target protein (i.e., protein quasi-species). The analysis can be performed simultaneously for a plurality of different target proteins, including the entire proteome of a cell to produce a statistical proteome. The plurality of quasi-species or statistical proteome can be subjected to functional assays, such as enrichment or profiling assays, to determine the functional effect of the substitutions on the target protein(s).

Abstract: A mass-spectrometry-based method and substrates are provided herein for large scale kinome activity profiling directly from crude lysates using 90 chemically synthesized peptide substrates with amino acid sequences derived from known phosphoproteins. Quantification of peptide phosphorylation rates was achieved via the use of stable isotope labeled synthetic peptides. A method and substrates for obtaining 90 simultaneous activity measurements in a single-reaction format were developed and validated. The kinome activity profiling strategy was successfully applied with lysates of: cells manipulated by combination of mitogen stimulation, pharmacological perturbation and siRNA-directed kinase knockdown; seven different breast cancer cell lines treated with gefitinib; and each of normal and cancerous tissue samples from renal cell carcinoma patients.

Abstract: A mass-spectrometry-based method and substrates are provided herein for large scale kinome activity profiling directly from crude lysates using 90 chemically synthesized peptide substrates with amino acid sequences derived from known phosphoproteins. Quantification of peptide phosphorylation rates was achieved via the use of stable isotope labeled synthetic peptides. Half of these peptides immediately or rapidly showed robust and site-specific phosphorylation after incubation with serum-starved HEK293 cell lysate. A method and substrates for obtaining 90 simultaneous activity measurements in a single-reaction format were developed and validated. Activating kinase pathways through insulin or EGF stimulation reproducibly altered the phosphorylation rates of peptides derived from known pathway protein substrates.

Abstract: The invention discloses 155 novel phosphorylation sites identified in carcinoma and leukemia, peptides (including AQUA peptides) comprising a phosphorylation site of the invention, antibodies specifically bind to a novel phosphorylation site of the invention, and diagnostic and therapeutic uses of the above.

Abstract: The present invention relates to phosphopeptide compositions and anti-phosphopeptide antibody compositions. Also provided are methods of identifying phosphorylation sites in phosphorylated peptides and phosphorylation site motifs.

Abstract: The invention discloses 155 novel phosphorylation sites identified in carcinoma and leukemia, peptides (including AQUA peptides) comprising a phosphorylation site of the invention, antibodies specifically bind to a novel phosphorylation site of the invention, and diagnostic and therapeutic uses of the above.

Abstract: A mass-spectrometry-based method and substrates are provided herein for large scale kinome activity profiling directly from crude lysates using 90 chemically synthesized peptide substrates with amino acid sequences derived from known phosphoproteins. Quantification of peptide phosphorylation rates was achieved via the use of stable isotope labeled synthetic peptides. Half of these peptides immediately or rapidly showed robust and site-specific phosphorylation after incubation with serum-starved HEK293 cell lysate. A method and substrates for obtaining 90 simultaneous activity measurements in a single-reaction format were developed and validated. Activating kinase pathways through insulin or EGF stimulation reproducibly altered the phosphorylation rates of peptides derived from known pathway protein substrates.

Abstract: The present invention relates to phosphopeptide compositions and anti-phosphopeptide antibody compositions. Also provided are methods of identifying phosphorylation sites in phosphorylated peptides and phosphorylation site motifs.