Journal ArticleDOI
Immunoaffinity profiling of tyrosine phosphorylation in cancer cells
John Rush,Albrecht Moritz,Kimberly Lee,Ailan Guo,Valerie Goss,Erik Spek,Hui Zhang,Hui Zhang,Hui Zhang,Xiang-ming Zha,Xiang-ming Zha,Xiang-ming Zha,Roberto D. Polakiewicz,Michael J. Comb +13 more
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.Abstract:
Tyrosine kinases play a prominent role in human cancer, yet the oncogenic signaling pathways driving cell proliferation and survival have been difficult to identify, in part because of the complexity of the pathways and in part because of low cellular levels of tyrosine phosphorylation. In general, global phosphoproteomic approaches reveal small numbers of peptides containing phosphotyrosine. We have developed a strategy that emphasizes the phosphotyrosine component of the phosphoproteome and identifies large numbers of tyrosine phosphorylation sites. Peptides containing phosphotyrosine are isolated directly from protease-digested cellular protein extracts with a phosphotyrosine-specific antibody and are identified by tandem mass spectrometry. 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.read more
Citations
More filters
Journal ArticleDOI
Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.
Jesper V. Olsen,Blagoy Blagoev,Florian Gnad,Boris Macek,Boris Macek,Chanchal Kumar,Peter Mortensen,Matthias Mann +7 more
TL;DR: A general mass spectrometric technology is developed and applied for identification and quantitation of phosphorylation sites as a function of stimulus, time, and subcellular location to provide a missing link in a global, integrative view of cellular regulation.
Journal ArticleDOI
ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
Shuhei Matsuoka,Bryan A. Ballif,Agata Smogorzewska,Agata Smogorzewska,E. Robert McDonald,Kristen E. Hurov,Ji Luo,Corey E. Bakalarski,Zhenming Zhao,Nicole L. Solimini,Yaniv Lerenthal,Yosef Shiloh,Steven P. Gygi,Stephen J. Elledge +13 more
TL;DR: A large-scale proteomic analysis of proteins phosphorylated in response to DNA damage on consensus sites recognized by ATM and ATR is performed and more than 900 regulated phosphorylation sites encompassing over 700 proteins are identified.
Journal ArticleDOI
Global Survey of Phosphotyrosine Signaling Identifies Oncogenic Kinases in Lung Cancer
Klarisa Rikova,Ailan Guo,Qingfu Zeng,Anthony Possemato,Jian Yu,Herbert Haack,Julie Nardone,Kimberly Lee,Cynthia Reeves,Yu Li,Yerong Hu,Zhi-Ping Tan,Matthew P. Stokes,Laura Sullivan,Jeffrey Mitchell,Randy Wetzel,Joan MacNeill,Jian Min Ren,Jin Yuan,Corey E. Bakalarski,Judit Villén,Jon M. Kornhauser,Bradley L. Smith,Daiqiang Li,Xinmin Zhou,Steven P. Gygi,Ting-Lei Gu,Roberto D. Polakiewicz,John Rush,Michael J. Comb +29 more
TL;DR: 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.
Journal ArticleDOI
A probability-based approach for high-throughput protein phosphorylation analysis and site localization.
TL;DR: 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.
Journal ArticleDOI
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
Peter Hornbeck,Jon M. Kornhauser,Sasha Tkachev,Bin Zhang,Elzbieta Skrzypek,Beth L. Murray,Vaughan Latham,Michael Sullivan +7 more
TL;DR: PhosphoSitePlus as discussed by the authors is an open, comprehensive, manually curated and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins.
References
More filters
Journal ArticleDOI
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
TL;DR: The approach described in this manuscript provides a convenient method to interpret tandem mass spectra with known sequences in a protein database.
Journal ArticleDOI
Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins
TL;DR: A previously unrecognized direct signal transduction pathway to the nucleus has been uncovered: IFN-receptor interaction at the cell surface leads to the activation of kinases of the Jak family that phosphorylate substrate proteins called STATs (signal transducers and activators of transcription).
Journal ArticleDOI
A statistical model for identifying proteins by tandem mass spectrometry.
TL;DR: A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample, and it is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications.
Journal ArticleDOI
Oncogenic kinase signalling
Peter Blume-Jensen,Tony Hunter +1 more
TL;DR: How oncogenic conversion of protein kinases results from perturbation of the normal autoinhibitory constraints on kinase activity is emphasized and an update is provided on the role of deregulated PI(3)K/Akt and mammalian target of rapamycin/p70S6K signalling in human malignancies.
Journal ArticleDOI
Stop and Go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and lc/ms sample pretreatment in proteomics
TL;DR: A novel procedure in which a very small disk of beads embedded in a Teflon meshwork is placed as a microcolumn into pipet tips, finding that the Stage system is well-suited as a universal sample preparation system for proteomics.
Related Papers (5)
Global Survey of Phosphotyrosine Signaling Identifies Oncogenic Kinases in Lung Cancer
Klarisa Rikova,Ailan Guo,Qingfu Zeng,Anthony Possemato,Jian Yu,Herbert Haack,Julie Nardone,Kimberly Lee,Cynthia Reeves,Yu Li,Yerong Hu,Zhi-Ping Tan,Matthew P. Stokes,Laura Sullivan,Jeffrey Mitchell,Randy Wetzel,Joan MacNeill,Jian Min Ren,Jin Yuan,Corey E. Bakalarski,Judit Villén,Jon M. Kornhauser,Bradley L. Smith,Daiqiang Li,Xinmin Zhou,Steven P. Gygi,Ting-Lei Gu,Roberto D. Polakiewicz,John Rush,Michael J. Comb +29 more