Mapping protein post-translational modifications with mass spectrometry

[1]  R. Wait,et al.  Protein Sulfenation as a Redox Sensor , 2007, Molecular & Cellular Proteomics.

[2]  Zee-Yong Park,et al.  A proteomics approach to identify the ubiquitinated proteins in mouse heart. , 2007, Biochemical and biophysical research communications.

[3]  H. Ball,et al.  Enhancement of ionization efficiency and selective enrichment of phosphorylated peptides from complex protein mixtures using a reversible poly-histidine tag , 2007, Journal of the American Society for Mass Spectrometry.

[4]  Yi Tang,et al.  Lysine Propionylation and Butyrylation Are Novel Post-translational Modifications in Histones*S , 2007, Molecular & Cellular Proteomics.

[5]  K. Orth,et al.  A newly discovered post-translational modification--the acetylation of serine and threonine residues. , 2007, Trends in biochemical sciences.

[6]  Blagoy Blagoev,et al.  Quantitative proteomic assessment of very early cellular signaling events , 2007, Nature Biotechnology.

[7]  D. Lauffenburger,et al.  Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks , 2007, Proceedings of the National Academy of Sciences.

[8]  W. Lehmann,et al.  Analysis of protein phosphorylation in the regions of consecutive serine/threonine residues by negative ion electrospray collision-induced dissociation. Approach to pinpointing of phosphorylation sites. , 2007, Analytical chemistry.

[9]  Ruedi Aebersold,et al.  An Integrated Chemical, Mass Spectrometric and Computational Strategy for (quantitative) Phosphoproteomics: Application to Drosophila Melanogaster Kc167 Cells{ , 2022 .

[10]  D. Taillandier,et al.  A New Method of Purification of Proteasome Substrates Reveals Polyubiquitination of 20 S Proteasome Subunits* , 2007, Journal of Biological Chemistry.

[11]  Lewis Y. Geer,et al.  Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry , 2007, Proceedings of the National Academy of Sciences.

[12]  Ruedi Aebersold,et al.  Reproducible isolation of distinct, overlapping segments of the phosphoproteome , 2007, Nature Methods.

[13]  Benjamin A Garcia,et al.  Characterization of histones and their post-translational modifications by mass spectrometry. , 2007, Current opinion in chemical biology.

[14]  Steven P. Gygi,et al.  Large-scale phosphorylation analysis of mouse liver , 2007, Proceedings of the National Academy of Sciences.

[15]  F. Regnier,et al.  An isotope coding strategy for proteomics involving both amine and carboxyl group labeling. , 2002, Methods in molecular biology.

[16]  Alejandro Garcia,et al.  UbiProt: a database of ubiquitylated proteins , 2007, BMC Bioinformatics.

[17]  Vijay H Shah,et al.  Nitric oxide synthase generates nitric oxide locally to regulate compartmentalized protein S-nitrosylation and protein trafficking , 2006, Proceedings of the National Academy of Sciences.

[18]  M. Mann,et al.  Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks , 2006, Cell.

[19]  M. Huddleston,et al.  A Quantitative Results-driven Approach to Analyzing Multisite Protein Phosphorylation , 2006, Molecular & Cellular Proteomics.

[20]  Steven P Gygi,et al.  A probability-based approach for high-throughput protein phosphorylation analysis and site localization , 2006, Nature Biotechnology.

[21]  N. Grishin,et al.  Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. , 2006, Molecular cell.

[22]  J. Shabanowitz,et al.  Cortactin phosphorylation sites mapped by mass spectrometry , 2006, Journal of Cell Science.

[23]  Brian Raught,et al.  Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software , 2006, Nature Methods.

[24]  Yu Xue,et al.  SUMOsp: a web server for sumoylation site prediction , 2006, Nucleic Acids Res..

[25]  Brendan K Faherty,et al.  Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics*S , 2006, Molecular & Cellular Proteomics.

[26]  Linfeng Wu,et al.  Absolute Quantification of Multisite Phosphorylation by Selective Reaction Monitoring Mass Spectrometry , 2006, Molecular & Cellular Proteomics.

[27]  Daniel C Liebler,et al.  Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Trairak Pisitkun,et al.  Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Mikhail M Savitski,et al.  ModifiComb, a New Proteomic Tool for Mapping Substoichiometric Post-translational Modifications, Finding Novel Types of Modifications, and Fingerprinting Complex Protein Mixtures* , 2006, Molecular & Cellular Proteomics.

[30]  Xuejun Jiang,et al.  Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain. , 2006, Molecular cell.

[31]  Cristina M Furdui,et al.  Autophosphorylation of FGFR1 kinase is mediated by a sequential and precisely ordered reaction. , 2006, Molecular cell.

[32]  Forest M White,et al.  Quantitative Analysis of Phosphotyrosine Signaling Networks Triggered by CD3 and CD28 Costimulation in Jurkat Cells1 , 2006, The Journal of Immunology.

[33]  Hye Kyong Kweon,et al.  Selective zirconium dioxide-based enrichment of phosphorylated peptides for mass spectrometric analysis. , 2006, Analytical chemistry.

[34]  Fabien Campagne,et al.  SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[35]  G. Hart,et al.  O‐GlcNAc cycling: How a single sugar post‐translational modification is changing the Way We think about signaling networks , 2006, Journal of cellular biochemistry.

[36]  Dekel Tsur,et al.  Identification of post-translational modifications by blind search of mass spectra , 2005, Nature Biotechnology.

[37]  J. Shabanowitz,et al.  Paxillin phosphorylation sites mapped by mass spectrometry , 2005, Journal of Cell Science.

[38]  K. Resing,et al.  Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics*S , 2005, Molecular & Cellular Proteomics.

[39]  H. Ulrich Mutual interactions between the SUMO and ubiquitin systems: a plea of no contest. , 2005, Trends in cell biology.

[40]  Xuedong Liu,et al.  A Method of Mapping Protein Sumoylation Sites by Mass Spectrometry Using a Modified Small Ubiquitin-like Modifier 1 (SUMO-1) and a Computational Program*S , 2005, Molecular & Cellular Proteomics.

[41]  M. Mann,et al.  Mass spectrometry–based proteomics turns quantitative , 2005, Nature chemical biology.

[42]  H. Cooper,et al.  Fourier transform ion cyclotron resonance mass spectrometry for the analysis of small ubiquitin-like modifier (SUMO) modification: identification of lysines in RanBP2 and SUMO targeted for modification during the E3 autoSUMOylation reaction. , 2005, Analytical chemistry.

[43]  D. Lauffenburger,et al.  Time-resolved Mass Spectrometry of Tyrosine Phosphorylation Sites in the Epidermal Growth Factor Receptor Signaling Network Reveals Dynamic Modules*S , 2005, Molecular & Cellular Proteomics.

[44]  Ruedi Aebersold,et al.  Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry , 2005, Nature Methods.

[45]  P. Roepstorff,et al.  Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns* , 2005, Molecular & Cellular Proteomics.

[46]  Robert J Beynon,et al.  Metabolic Labeling of Proteins for Proteomics* , 2005, Molecular & Cellular Proteomics.

[47]  Joshua J. Coon,et al.  Electron transfer dissociation of peptide anions , 2005, Journal of the American Society for Mass Spectrometry.

[48]  J. Reilly,et al.  Deamidation as a Consequence of β-Elimination of Phosphopeptides , 2005 .

[49]  A. Lin,et al.  Receptor-regulated Dynamic S-Nitrosylation of Endothelial Nitric-oxide Synthase in Vascular Endothelial Cells* , 2005, Journal of Biological Chemistry.

[50]  R. Schmidt-Ullrich,et al.  Inhibition of Protein-tyrosine Phosphatases by Mild Oxidative Stresses Is Dependent on S-Nitrosylation* , 2005, Journal of Biological Chemistry.

[51]  S. Ficarro,et al.  Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry , 2005, Nature Biotechnology.

[52]  Michael Karin,et al.  Reactive Oxygen Species Promote TNFα-Induced Death and Sustained JNK Activation by Inhibiting MAP Kinase Phosphatases , 2005, Cell.

[53]  Neil L Kelleher,et al.  Detection and localization of protein modifications by high resolution tandem mass spectrometry. , 2005, Mass spectrometry reviews.

[54]  J. A. Taylor,et al.  Informatics for protein identification by mass spectrometry. , 2005, Methods.

[55]  Guilong Cheng,et al.  Mass spectrometry of peptides and proteins. , 2005, Methods.

[56]  Steven P Gygi,et al.  Proteomic insights into ubiquitin and ubiquitin-like proteins. , 2005, Current opinion in chemical biology.

[57]  J. Rush,et al.  Immunoaffinity profiling of tyrosine phosphorylation in cancer cells , 2005, Nature Biotechnology.

[58]  J. Reilly,et al.  Deamidation as a consequence of beta-elimination of phosphopeptides. , 2005, Analytical chemistry.

[59]  D. Fushman,et al.  Polyubiquitin chains: polymeric protein signals. , 2004, Current opinion in chemical biology.

[60]  K. Parker,et al.  Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents*S , 2004, Molecular & Cellular Proteomics.

[61]  M. Wiener,et al.  Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. , 2004, Analytical chemistry.

[62]  M. Mann,et al.  Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[63]  N. Tonks,et al.  Regulation of Insulin Signaling through Reversible Oxidation of the Protein-tyrosine Phosphatases TC45 and PTP1B* , 2004, Journal of Biological Chemistry.

[64]  Steven P Gygi,et al.  Large-scale characterization of HeLa cell nuclear phosphoproteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[65]  M. Mann,et al.  Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics , 2004, Nature Biotechnology.

[66]  H. Forman,et al.  Redox signaling: thiol chemistry defines which reactive oxygen and nitrogen species can act as second messengers. , 2004, American journal of physiology. Cell physiology.

[67]  J. Shabanowitz,et al.  Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[68]  M. Sussman,et al.  An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins , 2004, Journal of the American Society for Mass Spectrometry.

[69]  A. Ciechanover,et al.  Ubiquitin as a central cellular regulator , 2004, Cell.

[70]  Wei Li,et al.  Susceptibility of the hydroxyl groups in serine and threonine to beta-elimination/Michael addition under commonly used moderately high-temperature conditions. , 2003, Analytical biochemistry.

[71]  Kap-Seok Yang,et al.  Reversible Oxidation of the Active Site Cysteine of Peroxiredoxins to Cysteine Sulfinic Acid , 2003, Journal of Biological Chemistry.

[72]  B. Chait,et al.  Improved beta-elimination-based affinity purification strategy for enrichment of phosphopeptides. , 2003, Analytical chemistry.

[73]  A. Stensballe,et al.  Large-scale Analysis of in Vivo Phosphorylated Membrane Proteins by Immobilized Metal Ion Affinity Chromatography and Mass Spectrometry* , 2003, Molecular & Cellular Proteomics.

[74]  Natalie G. Ahn,et al.  Identification of Novel Phosphorylation Sites on Xenopus laevis Aurora A and Analysis of Phosphopeptide Enrichment by Immobilized Metal-affinity Chromatography * , 2003, Molecular & Cellular Proteomics.

[75]  Richard D. Smith,et al.  Phosphoprotein isotope-coded solid-phase tag approach for enrichment and quantitative analysis of phosphopeptides from complex mixtures. , 2003, Analytical chemistry.

[76]  Richard S. Johnson,et al.  Studies of ligand-induced site-specific phosphorylation of epidermal growth factor receptor , 2003, Journal of the American Society for Mass Spectrometry.

[77]  T. Shaler,et al.  Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. , 2003, Analytical chemistry.

[78]  Steven P Gygi,et al.  A proteomics approach to understanding protein ubiquitination , 2003, Nature Biotechnology.

[79]  R. Deshaies,et al.  Context of multiubiquitin chain attachment influences the rate of Sic1 degradation. , 2003, Molecular cell.

[80]  S. Gygi,et al.  Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[81]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[82]  Birgit Schilling,et al.  Phosphospecific proteolysis for mapping sites of protein phosphorylation , 2003, Nature Biotechnology.

[83]  M. Mann,et al.  Analysis of Tyrosine Phosphorylation Sites in Signaling Molecules by a Phosphotyrosine-Specific Immonium Ion Scanning Method , 2002, Science's STKE.

[84]  Hanno Steen,et al.  A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode , 2002, Journal of the American Society for Mass Spectrometry.

[85]  P. Cohen,et al.  The origins of protein phosphorylation , 2002, Nature Cell Biology.

[86]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[87]  R. Aebersold,et al.  Direct identification of a G protein ubiquitination site by mass spectrometry. , 2002, Biochemistry.

[88]  D. Liebler,et al.  Peptide sequence motif analysis of tandem MS data with the SALSA algorithm. , 2002, Analytical chemistry.

[89]  Solomon H. Snyder,et al.  The Biotin Switch Method for the Detection of S-Nitrosylated Proteins , 2001, Science's STKE.

[90]  X. Yao,et al.  Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. , 2001, Analytical chemistry.

[91]  B. Chait,et al.  Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome , 2001, Nature Biotechnology.

[92]  Paul Tempst,et al.  Protein S-nitrosylation: a physiological signal for neuronal nitric oxide , 2001, Nature Cell Biology.

[93]  J. Olsen,et al.  Electron capture dissociation of singly and multiply phosphorylated peptides. , 2000, Rapid communications in mass spectrometry : RCM.

[94]  F. McLafferty,et al.  Electron capture dissociation for structural characterization of multiply charged protein cations. , 2000, Analytical chemistry.

[95]  M. Posewitz,et al.  Immobilized gallium(III) affinity chromatography of phosphopeptides. , 1999, Analytical chemistry.

[96]  Peter R. Baker,et al.  Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. , 1999, Analytical chemistry.

[97]  N. Ahn,et al.  Protein phosphorylation analysis by electrospray ionization-mass spectrometry. , 1997, Methods in enzymology.

[98]  S. Carr,et al.  Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry. , 1996, Analytical biochemistry.

[99]  M. Byford Rapid and selective modification of phosphoserine residues catalysed by Ba2+ ions for their detection during peptide microsequencing. , 1991, The Biochemical journal.

[100]  L. Heilmeyer,et al.  Sequence analysis of phosphoserine‐containing peptides , 1986, FEBS letters.

[101]  J. Porath,et al.  Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. , 1986, Analytical biochemistry.