New tools for quantitative phosphoproteome analysis.

Recent advances in analytical methods, particularly in the area of mass spectrometry, have brought the field of proteomics to the forefront in biological science. The ultimate goal of proteomics--to characterize proteins expressed within a cell under a specific set of conditions--is daunting due to the complexity and dynamic nature the of protein population within the cell. While much of the effort has focused on developing methods to identify expressed proteins, the identification of posttranslational modifications is equally important for comprehensive proteome characterization. Of all the known posttranslational modifications, phosphorylation arguably plays the largest role in the context of cellular homeostasis. This review discusses some of the recent progress made in the development of techniques not only to identify, but also to quantitatively determine sites of phosphorylation.

[1]  S. Patterson,et al.  Proteomics: the industrialization of protein chemistry. , 2000, Current opinion in biotechnology.

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

[3]  K. Bennett,et al.  Phosphopeptide detection and sequencing by matrix-assisted laser desorption/ionization quadrupole time-of-flight tandem mass spectrometry. , 2002, Journal of mass spectrometry : JMS.

[4]  M. Hung,et al.  Akt activation by estrogen in estrogen receptor-negative breast cancer cells. , 2001, Cancer research.

[5]  P. Cohen,et al.  The regulation of protein function by multisite phosphorylation--a 25 year update. , 2000, Trends in biochemical sciences.

[6]  J. Yates,et al.  Matrix-assisted Laser Desorption Ionization/Quadrupole Ion Trap Mass Spectrometry of Peptides , 1997, The Journal of Biological Chemistry.

[7]  W. Cosand,et al.  Proteomics in the post-genome age. , 2001, Biopolymers.

[8]  S. Ryu,et al.  Phosphorylation-dependent Regulation of Phospholipase D2 by Protein Kinase Cδ in Rat Pheochromocytoma PC12 Cells* , 2002, The Journal of Biological Chemistry.

[9]  F. Cross,et al.  Accurate quantitation of protein expression and site-specific phosphorylation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[10]  A. Stensballe,et al.  Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off‐line mass spectrometry analysis , 2001, Proteomics.

[11]  B. Chait,et al.  Identification and characterization of posttranslational modifications of proteins by MALDI ion trap mass spectrometry. , 1997, Analytical chemistry.

[12]  R. Huganir,et al.  Identification of protein kinase C phosphorylation sites within the AMPA receptor GluR2 subunit , 2001, Neuropharmacology.

[13]  E. Pasquale,et al.  In Vivo Tyrosine Phosphorylation Sites of Activated Ephrin-B1 and EphB2 from Neural Tissue* , 2001, The Journal of Biological Chemistry.

[14]  K. H. Lee,et al.  Proteomics: a technology-driven and technology-limited discovery science. , 2001, Trends in biotechnology.

[15]  A. Schulze,et al.  Navigating gene expression using microarrays — a technology review , 2001, Nature Cell Biology.

[16]  J. Venter,et al.  Sequencing the entire genomes of free-living organisms: the foundation of pharmacology in the new millennium. , 2000, Annual review of pharmacology and toxicology.

[17]  H. Meyer,et al.  Identification of platelet proteins separated by two‐dimensional gel electrophoresis and analyzed by matrix assisted laser desorption/ionization‐time of flight‐mass spectrometry and detection of tyrosine‐phosphorylated proteins , 2000, Electrophoresis.

[18]  S. Carr,et al.  A multidimensional electrospray MS-based approach to phosphopeptide mapping. , 2001, Analytical chemistry.

[19]  S. Frank,et al.  Insulin receptor substrate-1-mediated enhancement of growth hormone-induced mitogen-activated protein kinase activation. , 2000, Endocrinology.

[20]  A. Rivett,et al.  Phosphorylation of ATPase subunits of the 26S proteasome , 1998, FEBS letters.

[21]  D. Botstein,et al.  Exploring the new world of the genome with DNA microarrays , 1999, Nature Genetics.

[22]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[23]  P. Cao,et al.  Phosphopeptide analysis by on-line immobilized metal-ion affinity chromatography-capillary electrophoresis-electrospray ionization mass spectrometry. , 1999, Journal of chromatography. A.

[24]  M. Fussenegger,et al.  Use of antibodies for detection of phosphorylated proteins separated by two‐dimensional gel electrophoresis , 2001, Proteomics.

[25]  M. Dunn Detection of total proteins on western blots of 2-D polyacrylamide gels. , 1999, Methods in molecular biology.

[26]  Richard D. Smith,et al.  Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. , 2001, Analytical chemistry.

[27]  K. Resing,et al.  Toward the phosphoproteome , 2001, Nature Biotechnology.

[28]  M. Campbell,et al.  Preparation and application of antibodies to phosphoamino acid sequences. , 2001, Biopolymers.

[29]  Professor Dr. Miklos Bodanszky,et al.  The Practice of Peptide Synthesis , 1994, Springer Lab Manual.

[30]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[31]  V. Gaberc-Porekar,et al.  Perspectives of immobilized-metal affinity chromatography. , 2001, Journal of biochemical and biophysical methods.

[32]  Mitsuaki Yanagida,et al.  Matrix assisted laser desorption/ionization‐time of flight‐mass spectrometry analysis of proteins detected by anti‐phosphotyrosine antibody on two‐dimensional‐gels of fibrolast cell lysates after tumor necrosis factor‐α stimulation , 2000 .

[33]  류성호 Phosphorylation-dependent Regulation of Phospholipase D2 by Protein Kinase Cdelta in Rat Pheochromocytoma PC12 Cells , 2001 .

[34]  P. Andrews,et al.  Phosphopeptide derivatization signatures to identify serine and threonine phosphorylated peptides by mass spectrometry. , 2001, Analytical chemistry.

[35]  Weiya Ma,et al.  Shortage of mitogen-activated protein kinase is responsible for resistance to AP-1 transactivation and transformation in mouse JB6 cells. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[36]  R. Aebersold,et al.  Mass spectrometry in proteomics. , 2001, Chemical reviews.

[37]  M. Whiteway,et al.  Molecular Characterization of Ste20p, a Potential Mitogen-activated Protein or Extracellular Signal-regulated Kinase Kinase (MEK) Kinase Kinase from Saccharomyces cerevisiae(*) , 1995, The Journal of Biological Chemistry.

[38]  R. Aebersold,et al.  A systematic approach to the analysis of protein phosphorylation , 2001, Nature Biotechnology.