Subcellular phosphoproteomics

Mass Spectrometry Reviews

Volumn 29, Issue 6, 2010, Pages 962-990

  Trost, Matthias ^a,b   Bridon, Gaëlle ^a,b   Desjardins, Michel ^b   Thibault, Pierre ^a,b  

^a INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

mass spectrometry; organelle proteomics; phosphoproteomics; phosphorylation; SNARE; vesicle trafficking

Indexed keywords

BIOLOGICAL ACTIVITIES; CELL FRACTIONATION; CELL LYSATES; DYNAMIC CHANGES; IN-VITRO; LOW-ABUNDANCE PROTEINS; PHOSPHOPROTEOMICS; POST-TRANSLATIONAL MODIFICATIONS; PROTEIN FUNCTIONS; PROTEIN PHOSPHORYLATION; PROTEIN-PROTEIN INTERACTIONS; PROTEOMICS; SCAFFOLD PROTEIN; SENSITIVE METHOD; SNARE; SPATIAL SEPARATION; SPATIO-TEMPORAL RESOLUTION; STRUCTURAL CHANGE; SUB-CELLULAR; SUBCELLULAR COMPARTMENTS; SUBCELLULAR FRACTIONATION; VESICLE TRAFFICKING;

BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; LAWS AND LEGISLATION; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PHOSPHORYLATION;

PROTEINS;

PHOSPHOPROTEIN;

ARTICLE; BIOLOGY; CELL FRACTIONATION; CHEMISTRY; HUMAN; MASS SPECTROMETRY; METABOLISM;

COMPUTATIONAL BIOLOGY; HUMANS; MASS SPECTROMETRY; PHOSPHOPROTEINS; SUBCELLULAR FRACTIONS;

EID: 78149454885     PISSN: 02777037     EISSN: 10982787     Source Type: Journal    
DOI: 10.1002/mas.20297     Document Type: Article

References (296)

1. Achuthan A, Masendycz P, Lopez JA, Nguyen T, James DE, Sweet MJ, Hamilton JA, Scholz GM,. 2008. Regulation of the endosomal SNARE protein syntaxin 7 by colony-stimulating factor 1 in macrophages. Mol Cell Biol 28: 6149 - 6159.
2. Adamczyk M, Gebler JC, Wu J,. 2001. Selective analysis of phosphopeptides within a protein mixture by chemical modification, reversible biotinylation and mass spectrometry. Rapid Commun Mass Spectrom 15: 1481 - 1488.
3. Alpert AJ,. 2008. Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal Chem 80: 62 - 76.
4. Amanchy R, Periaswamy B, Mathivanan S, Reddy R, Tattikota SG, Pandey A,. 2007. A curated compendium of phosphorylation motifs. Nat Biotechnol 25: 285 - 286.
5. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI,. 2002. Directed proteomic analysis of the human nucleolus. Curr Biol 12: 1 - 11.
6. Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M,. 2005. Nucleolar proteome dynamics. Nature 433: 77 - 83.
7. Annan RS, Carr SA,. 1996. Phosphopeptide analysis by matrix-assisted laser desorption time-of-flight mass spectrometry. Anal Chem 68: 3413 - 3421.
8. Annan RS, Huddleston MJ, Verma R, Deshaies RJ, Carr SA,. 2001. A multidimensional electrospray MS-based approach to phosphopeptide mapping. Anal Chem 73: 393 - 404.
9. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G,. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25 - 29.
10. Bai F, Witzmann FA,. 2007. Synaptosome proteomics. Subcell Biochem 43: 77 - 98.
11. Bakalarski CE, Haas W, Dephoure NE, Gygi SP,. 2007. The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics. Anal Bioanal Chem 389: 1409 - 1419.
12. Baker DJ, Chen J, van Deursen JM,. 2005. The mitotic checkpoint in cancer and aging: What have mice taught us ? Curr Opin Cell Biol 17: 583 - 589.
13. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B,. 2007. Quantitative mass spectrometry in proteomics: A critical review. Anal Bioanal Chem 389: 1017 - 1031.
14. Barr JR, Maggio VL, Patterson DG, Jr., Cooper GR, Henderson LO, Turner WE, Smith SJ, Hannon WH, Needham LL, Sampson EJ,. 1996. Isotope dilution-mass spectrometric quantification of specific proteins: Model application with apolipoprotein A-I. Clin Chem 42: 1676 - 1682.
15. Bauman AL, Scott JD,. 2002. Kinase- and phosphatase-anchoring proteins: Harnessing the dynamic duo. Nat Cell Biol 4: E203 - E206.
16. Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP,. 2004. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci USA 101: 12130 - 12135.
17. Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP,. 2006. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 24: 1285 - 1292.
18. Behnia R, Munro S,. 2005. Organelle identity and the signposts for membrane traffic. Nature 438: 597 - 604.
19. Bernardes GJ, Chalker JM, Errey JC, Davis BG,. 2008. Facile conversion of cysteine and alkyl cysteines to dehydroalanine on protein surfaces: Versatile and switchable access to functionalized proteins. J Am Chem Soc 130: 5052 - 5053.
20. Blagoev B, Ong SE, Kratchmarova I, Mann M,. 2004. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 22: 1139 - 1145.
21. Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S,. 2004. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4: 1633 - 1649.
22. Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R,. 2007. Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods 4: 231 - 237.
23. Boja ES, Phillips D, French SA, Harris RA, Balaban RS,. 2009. Quantitative mitochondrial phosphoproteomics using iTRAQ on an LTQ-orbitrap with high energy collision dissociation. J Proteome Res. 8: 4665 - 4675.
24. Bornhovd C, Vogel F, Neupert W, Reichert AS,. 2006. Mitochondrial membrane potential is dependent on the oligomeric state of F1F0-ATP synthase supracomplexes. J Biol Chem 281: 13990 - 13998.
25. Bridges SM, Magee GB, Wang N, Williams WP, Burgess SC, Nanduri B,. 2007. ProtQuant: A tool for the label-free quantification of MudPIT proteomics data. BMC Bioinformatics 8 (Suppl 7): S24.
26. Brinkworth RI, Munn AL, Kobe B,. 2006. Protein kinases associated with the yeast phosphoproteome. BMC Bioinformatics 7: 47.
27. Brunet S, Thibault P, Gagnon E, Kearney P, Bergeron JJ, Desjardins M,. 2003. Organelle proteomics: Looking at less to see more. Trends Cell Biol 13: 629 - 638.
28. Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD,. 2008. Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 9: 542.
29. Bykova NV, Egsgaard H, Moller IM,. 2003. Identification of 14 new phosphoproteins involved in important plant mitochondrial processes. FEBS Lett 540: 141 - 146.
30. Caenepeel S, Charydczak G, Sudarsanam S, Hunter T, Manning G,. 2004. The mouse kinome: Discovery and comparative genomics of all mouse protein kinases. Proc Natl Acad Sci USA 101: 11707 - 11712.
31. Canut H, Bauer J, Weber G,. 1999. Separation of plant membranes by electromigration techniques. J Chromatogr B Biomed Sci Appl 722: 121 - 139.
32. Carriere A, Cargnello M, Julien LA, Gao H, Bonneil E, Thibault P, Roux PP,. 2008. Oncogenic MAPK signaling stimulates mTORC1 activity by promoting RSK-mediated raptor phosphorylation. Curr Biol 18: 1269 - 1277.
33. Cassimeris L, Spittle C,. 2001. Regulation of microtubule-associated proteins. Int Rev Cytol 210: 163 - 226.
34. Castle JD,. 2003. Purification of organelles from mammalian cells. Curr Protoc Immunol Chapter 8: Unit 8 1B.
35. Castle JD,. 2004. Overview of cell fractionation. Curr Protoc Protein Sci Chapter 4: Unit 4 1.
36. Chang L, Karin M,. 2001. Mammalian MAP kinase signalling cascades. Nature 410: 37 - 40.
37. Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF,. 2007. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci USA 104: 2193 - 2198.
38. Claros MG, Vincens P,. 1996. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241: 779 - 786.
39. Cocucci E, Racchetti G, Rupnik M, Meldolesi J,. 2008. The regulated exocytosis of enlargeosomes is mediated by a SNARE machinery that includes VAMP4. J Cell Sci 121: 2983 - 2991.
40. Cokol M, Nair R, Rost B,. 2000. Finding nuclear localization signals. EMBO Rep 1: 411 - 415.
41. Colicelli J,. 2004. Human RAS superfamily proteins and related GTPases. Sci STKE 2004 250: 13.
42. Creese AJ, Cooper HJ,. 2008. The effect of phosphorylation on the electron capture dissociation of peptide ions. J Am Soc Mass Spectrom 19: 1263 - 1274.
43. Cronshaw JM, Krutchinsky AN, Zhang W, Chait BT, Matunis MJ,. 2002. Proteomic analysis of the mammalian nuclear pore complex. J Cell Biol 158: 915 - 927.
44. Crooks GE, Hon G, Chandonia JM, Brenner SE,. 2004. WebLogo: A sequence logo generator. Genome Res 14: 1188 - 1190.
45. D'Ambrosio C, Salzano AM, Arena S, Renzone G, Scaloni A,. 2007. Analytical methodologies for the detection and structural characterization of phosphorylated proteins. J Chromatogr B Anal Technol Biomed Life Sci 849: 163 - 180.
46. Dai J, Jin WH, Sheng QH, Shieh CH, Wu JR, Zeng R,. 2007. Protein phosphorylation and expression profiling by Yin-yang multidimensional liquid chromatography (Yin-yang MDLC) mass spectrometry. J Proteome Res 6: 250 - 262.
47. Darnell JE, Jr., Kerr IM, Stark GR,. 1994. Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. Science 264: 1415 - 1421.
48. Dass C, Mahalakshmi P,. 1995. Amino acid sequence determination of phosphoenkephalins using liquid secondary ionization mass spectrometry. Rapid Commun Mass Spectrom 9: 1148 - 1154.
49. Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M,. 2008. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle. Mol Cell 31: 438 - 448.
50. de Araujo ME, Huber LA, Stasyk T,. 2008. Isolation of endocytic organelles by density gradient centrifugation. Methods Mol Biol 424: 317 - 331.
51. De Duve C,. 1965. The separation and characterization of subcellular particles. Harvey Lect 59: 49 - 87.
52. de la Fuente van Bentem S, Anrather D, Roitinger E, Djamei A, Hufnagl T, Barta A, Csaszar E, Dohnal I, Lecourieux D, Hirt H,. 2006. Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA metabolism. Nucleic Acids Res 34: 3267 - 3278.
53. Decker T, Kovarik P,. 2000. Serine phosphorylation of STATs. Oncogene 19: 2628 - 2637.
54. DeGnore JP, Qin J,. 1998. Fragmentation of phosphopeptides in an ion trap mass spectrometer. J Am Soc Mass Spectrom 9: 1175 - 1188.
55. Dengjel J, Akimov V, Olsen JV, Bunkenborg J, Mann M, Blagoev B, Andersen JS,. 2007. Quantitative proteomic assessment of very early cellular signaling events. Nat Biotechnol 25: 566 - 568.
56. Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP,. 2008. A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci USA 105: 10762 - 10767.
57. Desjardins M, Celis JE, van Meer G, Dieplinger H, Jahraus A, Griffiths G, Huber LA,. 1994. Molecular characterization of phagosomes. J Biol Chem 269: 32194 - 32200.
58. Desjardins M, Griffiths G,. 2003. Phagocytosis: Latex leads the way. Curr Opin Cell Biol 15: 498 - 503.
59. Dreger M,. 2003. Subcellular proteomics. Mass Spectrom Rev 22: 27 - 56.
60. Dubois T, Kerai P, Learmonth M, Cronshaw A, Aitken A,. 2002. Identification of syntaxin-1A sites of phosphorylation by casein kinase I and casein kinase II. Eur J Biochem 269: 909 - 914. (Pubitemid 34175411)
61. Dunn JD, Reid GE, Bruening ML,. 2009. Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Mass Spectrom Rev 29: 29 - 51.
62. Edelson-Averbukh M, Pipkorn R, Lehmann WD,. 2007. 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. Anal Chem 79: 3476 - 3486.
63. Edgar RC,. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792 - 1797.
64. Emanuelsson O, Brunak S, von Heijne G, Nielsen H,. 2007. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2: 953 - 971.
65. Feldmann A, Winterstein C, White R, Trotter J, Kramer-Albers EM,. 2009. Comprehensive analysis of expression, subcellular localization, and cognate pairing of SNARE proteins in oligodendrocytes. J Neurosci Res 87: 1760 - 1772.
66. Fenselau C, Yao X,. 2009. 18O2-labeling in quantitative proteomic strategies: A status report. J Proteome Res 8: 2140 - 2143.
67. Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J, Hunt DF, White FM,. 2002. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 20: 301 - 305.
68. Ficarro SB, Parikh JR, Blank NC, Marto JA,. 2008. Niobium(V) oxide (Nb2O5): Application to phosphoproteomics. Anal Chem 80: 4606 - 4613.
69. Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K, Teasdale MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Teasdale RD,. 2006. LOCATE: A mouse protein subcellular localization database. Nucleic Acids Res 34: D213 - D217.
70. Finley MF, Scheller RH, Madison DV,. 2003. SNAP-25 Ser187 does not mediate phorbol ester enhancement of hippocampal synaptic transmission. Neuropharmacology 45: 857 - 862.
71. Foletti DL, Lin R, Finley MA, Scheller RH,. 2000. Phosphorylated syntaxin 1 is localized to discrete domains along a subset of axons. J Neurosci 20: 4535 - 4544.
72. Forner F, Foster LJ, Campanaro S, Valle G, Mann M,. 2006. Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver. Mol Cell Proteomics 5: 608 - 619.
73. Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, Mann M,. 2006. A mammalian organelle map by protein correlation profiling. Cell 125: 187 - 199.
74. Frackelton AR, Jr., Ross AH, Eisen HN,. 1983. Characterization and use of monoclonal antibodies for isolation of phosphotyrosyl proteins from retrovirus-transformed cells and growth factor-stimulated cells. Mol Cell Biol 3: 1343 - 1352.
75. Fukuda R, McNew JA, Weber T, Parlati F, Engel T, Nickel W, Rothman JE, Sollner TH,. 2000. Functional architecture of an intracellular membrane t-SNARE. Nature 407: 198 - 202.
76. Gagnon E, Duclos S, Rondeau C, Chevet E, Cameron PH, Steele-Mortimer O, Paiement J, Bergeron JJ, Desjardins M,. 2002. Endoplasmic reticulum-mediated phagocytosis is a mechanism of entry into macrophages. Cell 110: 119 - 131.
77. Gallwitz D, Jahn R,. 2003. The riddle of the Sec1/Munc-18 proteins-New twists added to their interactions with SNAREs. Trends Biochem Sci 28: 113 - 116.
78. Gan CS, Guo T, Zhang H, Lim SK, Sze SK,. 2008. A comparative study of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) versus SCX-IMAC-based methods for phosphopeptide isolation/enrichment. J Proteome Res 7: 4869 - 4877.
79. Garin J, Diez R, Kieffer S, Dermine JF, Duclos S, Gagnon E, Sadoul R, Rondeau C, Desjardins M,. 2001. The phagosome proteome: Insight into phagosome functions. J Cell Biol 152: 165 - 180.
80. Genoud S, Pralong W, Riederer BM, Eder L, Catsicas S, Muller D,. 1999. Activity-dependent phosphorylation of SNAP-25 in hippocampal organotypic cultures. J Neurochem 72: 1699 - 1706.
81. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP,. 2003. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100: 6940 - 6945.
82. Gharib M, Marcantonio M, Lehmann SG, Courcelles M, Meloche S, Verreault A, Thibault P,. 2009. Artifactual sulfation of silver-stained proteins: Implications for the assignment of phosphorylation and sulfation sites. Mol Cell Proteomics 8: 506 - 518.
83. Gilar M, Olivova P, Daly AE, Gebler JC,. 2005. Orthogonality of separation in two-dimensional liquid chromatography. Anal Chem 77: 6426 - 6434.
84. Goshe MB, Conrads TP, Panisko EA, Angell NH, Veenstra TD, Smith RD,. 2001. Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal Chem 73: 2578 - 2586.
85. Greenlund AC, Farrar MA, Viviano BL, Schreiber RD,. 1994. Ligand-induced IFN gamma receptor tyrosine phosphorylation couples the receptor to its signal transduction system (p91). EMBO J 13: 1591 - 1600.
86. Gronborg M, Kristiansen TZ, Stensballe A, Andersen JS, Ohara O, Mann M, Jensen ON, Pandey A,. 2002. A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: Identification of a novel protein, Frigg, as a protein kinase A substrate. Mol Cell Proteomics 1: 517 - 527.
87. Grosshans BL, Ortiz D, Novick P,. 2006. Rabs and their effectors: Achieving specificity in membrane traffic. Proc Natl Acad Sci USA 103: 11821 - 11827.
88. Gruhler A, Olsen JV, Mohammed S, Mortensen P, Faergeman NJ, Mann M, Jensen ON,. 2005. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 4: 310 - 327.
89. Guermonprez P, Saveanu L, Kleijmeer M, Davoust J, Van Endert P, Amigorena S,. 2003. ER-phagosome fusion defines an MHC class I cross-presentation compartment in dendritic cells. Nature 425: 397 - 402.
90. Guo A, Villen J, Kornhauser J, Lee KA, Stokes MP, Rikova K, Possemato A, Nardone J, Innocenti G, Wetzel R, Wang Y, MacNeill J, Mitchell J, Gygi SP, Rush J, Polakiewicz RD, Comb MJ,. 2008. Signaling networks assembled by oncogenic EGFR and c-Met. Proc Natl Acad Sci USA 105: 692 - 697.
91. Han G, Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J,. 2008. Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography. Proteomics 8: 1346 - 1361.
92. Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL,. 2003. Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol Cell Proteomics 2: 299 - 314.
93. Harita Y, Kurihara H, Kosako H, Tezuka T, Sekine T, Igarashi T, Hattori S,. 2008. Neph1, a component of the kidney slit diaphragm, is tyrosine-phosphorylated by the Src family tyrosine kinase and modulates intracellular signaling by binding to Grb2. J Biol Chem 283: 9177 - 9186.
94. Harjes P, Wanker EE,. 2003. The hunt for huntingtin function: Interaction partners tell many different stories. Trends Biochem Sci 28: 425 - 433.
95. Haselmann KF, Budnik BA, Olsen JV, Nielsen ML, Reis CA, Clausen H, Johnsen AH, Zubarev RA,. 2001. Advantages of external accumulation for electron capture dissociation in Fourier transform mass spectrometry. Anal Chem 73: 2998 - 3005.
96. Hegeman AD, Harms AC, Sussman MR, Bunner AE, Harper JF,. 2004. An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins. J Am Soc Mass Spectrom 15: 647 - 653.
97. Hepp R, Puri N, Hohenstein AC, Crawford GL, Whiteheart SW, Roche PA,. 2005. Phosphorylation of SNAP-23 regulates exocytosis from mast cells. J Biol Chem 280: 6610 - 6620.
98. Herbert B, Hopwood F, Oxley D, McCarthy J, Laver M, Grinyer J, Goodall A, Williams K, Castagna A, Righetti PG,. 2003. Beta-elimination: An unexpected artefact in proteome analysis. Proteomics 3: 826 - 831.
99. Hilger M, Bonaldi T, Gnad F, Mann M,. 2009. Systems-wide analysis of a phosphatase knock down by quantitative proteomics and phosphoproteomics. Mol Cell Proteomics 8: 1908 - 1920.
100. Hinners I, Wendler F, Fei H, Thomas L, Thomas G, Tooze SA,. 2003. AP-1 recruitment to VAMP4 is modulated by phosphorylation-dependent binding of PACS-1. EMBO Rep 4: 1182 - 1189.
101. Hjerrild M, Gammeltoft S,. 2006. Phosphoproteomics toolbox: Computational biology, protein chemistry and mass spectrometry. FEBS Lett 580: 4764 - 4770.
102. Honda R, Korner R, Nigg EA,. 2003. Exploring the functional interactions between Aurora B, INCENP, and survivin in mitosis. Mol Biol Cell 14: 3325 - 3341.
103. Hong W,. 2005. SNAREs and traffic. Biochim Biophys Acta 1744: 493 - 517.
104. Hopper RK, Carroll S, Aponte AM, Johnson DT, French S, Shen RF, Witzmann FA, Harris RA, Balaban RS,. 2006. Mitochondrial matrix phosphoproteome: Effect of extra mitochondrial calcium. Biochemistry 45: 2524 - 2536.
105. Houde M, Bertholet S, Gagnon E, Brunet S, Goyette G, Laplante A, Princiotta MF, Thibault P, Sacks D, Desjardins M,. 2003. Phagosomes are competent organelles for antigen cross-presentation. Nature 425: 402 - 406.
106. Huang HD, Lee TY, Tzeng SW, Horng JT,. 2005. KinasePhos: A web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res 33: W226 - W229.
107. Hunter AP, Games DE,. 1994. Chromatographic and mass spectrometric methods for the identification of phosphorylation sites in phosphoproteins. Rapid Commun Mass Spectrom 8: 559 - 570.
108. Hunter T, Sefton BM,. 1980. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc Natl Acad Sci USA 77: 1311 - 1315.
109. Hunter T, Plowman GD,. 1997. The protein kinases of budding yeast: Six score and more. Trends Biochem Sci 22: 18 - 22.
110. Hunter T,. 2007. The age of crosstalk: Phosphorylation, ubiquitination, and beyond. Mol Cell 28: 730 - 738.
111. Igarashi K, Garotta G, Ozmen L, Ziemiecki A, Wilks AF, Harpur AG, Larner AC, Finbloom DS,. 1994. Interferon-gamma induces tyrosine phosphorylation of interferon-gamma receptor and regulated association of protein tyrosine kinases, Jak1 and Jak2, with its receptor. J Biol Chem 269: 14333 - 14336.
112. Ikeguchi Y, Nakamura H,. 1997. Determination of organic phosphates by column-switching high performance anion-exchange chromatography using on-line preconcentration on Titania. Anal. Sc 13: 479 - 483. (Pubitemid 127479861)
113. Ishihama Y, Wei FY, Aoshima K, Sato T, Kuromitsu J, Oda Y,. 2007. Enhancement of the efficiency of phosphoproteomic identification by removing phosphates after phosphopeptide enrichment. J Proteome Res 6: 1139 - 1144.
114. Jaffe H, Veeranna, Pant HC,. 1998. Characterization of serine and threonine phosphorylation sites in beta-elimination/ethanethiol addition-modified proteins by electrospray tandem mass spectrometry and database searching. Biochemistry 37: 16211 - 16224. (Pubitemid 28536257)
115. Jahn R, Scheller RH,. 2006. SNAREs-Engines for membrane fusion. Nat Rev Mol Cell Biol 7: 631 - 643.
116. Jensen SS, Larsen MR,. 2007. Evaluation of the impact of some experimental procedures on different phosphopeptide enrichment techniques. Rapid Commun Mass Spectrom 21: 3635 - 3645.
117. Jin J, Smith FD, Stark C, Wells CD, Fawcett JP, Kulkarni S, Metalnikov P, O'Donnell P, Taylor P, Taylor L, Zougman A, Woodgett JR, Langeberg LK, Scott JD, Pawson T,. 2004. Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization. Curr Biol 14: 1436 - 1450.
118. Jones AM, MacLean D, Studholme DJ, Serna-Sanz A, Andreasson E, Rathjen JP, Peck SC,. 2009. Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana. J Proteomics 72: 439 - 451.
119. Jutras I, Desjardins M,. 2005. Phagocytosis: At the crossroads of innate and adaptive immunity. Annu Rev Cell Dev Biol 21: 511 - 527.
120. Kahn RA, Fu H, Roy CR,. 2002. Cellular hijacking: A common strategy for microbial infection. Trends Biochem Sci 27: 308 - 314.
121. Kalume DE, Molina H, Pandey A,. 2003. Tackling the phosphoproteome: Tools and strategies. Curr Opin Chem Biol 7: 64 - 69.
122. Karsenti E, Vernos I,. 2001. The mitotic spindle: A self-made machine. Science 294: 543 - 547.
123. Kataoka M, Kuwahara R, Iwasaki S, Shoji-Kasai Y, Takahashi M,. 2000. Nerve growth factor-induced phosphorylation of SNAP-25 in PC12 cells: A possible involvement in the regulation of SNAP-25 localization. J Neurochem 74: 2058 - 2066.
124. Kearney P, Thibault P,. 2003. Bioinformatics meets proteomics-Bridging the gap between mass spectrometry data analysis and cell biology. J Bioinform Comput Biol 1: 183 - 200.
125. Kennelly PJ,. 2002. Protein kinases and protein phosphatases in prokaryotes: A genomic perspective. FEMS Microbiol Lett 206: 1 - 8.
126. Kholodenko BN,. 2002. MAP kinase cascade signaling and endocytic trafficking: A marriage of convenience ? Trends Cell Biol 12: 173 - 177.
127. Kleinnijenhuis AJ, Kjeldsen F, Kallipolitis B, Haselmann KF, Jensen ON,. 2007. Analysis of histidine phosphorylation using tandem MS and ion-electron reactions. Anal Chem 79: 7450 - 7456.
128. Klumpp S, Krieglstein J,. 2005. Reversible phosphorylation of histidine residues in vertebrate proteins. Biochim Biophys Acta 1754: 291 - 295.
129. Knight ZA, Schilling B, Row RH, Kenski DM, Gibson BW, Shokat KM,. 2003. Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat Biotechnol 21: 1047 - 1054.
130. Kocher T, Allmaier G, Wilm M,. 2003. Nanoelectrospray-based detection and sequencing of substoichiometric amounts of phosphopeptides in complex mixtures. J Mass Spectrom 38: 131 - 137.
131. Krijgsveld J, Ketting RF, Mahmoudi T, Johansen J, Artal-Sanz M, Verrijzer CP, Plasterk RH, Heck AJ,. 2003. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol 21: 927 - 931.
132. Kruger M, Moser M, Ussar S, Thievessen I, Luber CA, Forner F, Schmidt S, Zanivan S, Fassler R, Mann M,. 2008. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134: 353 - 364.
133. Kruger R, Kubler D, Pallisse R, Burkovski A, Lehmann WD,. 2006. Protein and proteome phosphorylation stoichiometry analysis by element mass spectrometry. Anal Chem 78: 1987 - 1994.
134. Kweon HK, Hakansson K,. 2006. Selective zirconium dioxide-based enrichment of phosphorylated peptides for mass spectrometric analysis. Anal Chem 78: 1743 - 1749.
135. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG,. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947 - 2948.
136. Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJ,. 2005. Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics 4: 873 - 886.
137. Lee J, Xu Y, Chen Y, Sprung R, Kim SC, Xie S, Zhao Y,. 2007. Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS. Mol Cell Proteomics 6: 669 - 676.
138. Lehmann WD, Kruger R, Salek M, Hung CW, Wolschin F, Weckwerth W,. 2007. Neutral loss-based phosphopeptide recognition: A collection of caveats. J Proteome Res 6: 2866 - 2873.
139. Leitner A, Foettinger A, Lindner W,. 2007. Improving fragmentation of poorly fragmenting peptides and phosphopeptides during collision-induced dissociation by malondialdehyde modification of arginine residues. J Mass Spectrom 42: 950 - 959.
140. Lemeer S, Heck AJ,. 2009. The phosphoproteomics data explosion. Curr Opin Chem Biol 13: 414 - 420.
141. Li H, Coghlan A, Ruan J, Coin LJ, Heriche JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R,. 2006. TreeFam: A curated database of phylogenetic trees of animal gene families. Nucleic Acids Res 34: D572 - D580.
142. Li KW, Jimenez CR,. 2008. Synapse proteomics: Current status and quantitative applications. Expert Rev Proteomics 5: 353 - 360.
143. Lim KB, Kassel DB,. 2006. Phosphopeptides enrichment using on-line two-dimensional strong cation exchange followed by reversed-phase liquid chromatography/mass spectrometry. Anal Biochem 354: 213 - 219.
144. Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T,. 2008. NetworKIN: A resource for exploring cellular phosphorylation networks. Nucleic Acids Res 36: D695 - D699.
145. Lindner H, Sarg B, Helliger W,. 1997. Application of hydrophilic- interaction liquid chromatography to the separation of phosphorylated H1 histones. J Chromatogr A 782: 55 - 62.
146. Listgarten J, Emili A,. 2005. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol Cell Proteomics 4: 419 - 434.
147. Lupashin V, Sztul E,. 2005. Golgi tethering factors. Biochim Biophys Acta 1744: 325 - 339.
148. Macek B, Mijakovic I, Olsen JV, Gnad F, Kumar C, Jensen PR, Mann M,. 2007. The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics 6: 697 - 707.
149. Macek B, Gnad F, Soufi B, Kumar C, Olsen JV, Mijakovic I, Mann M,. 2008. Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol Cell Proteomics 7: 299 - 307.
150. Malik R, Lenobel R, Santamaria A, Ries A, Nigg EA, Korner R,. 2009. Quantitative analysis of the human spindle phosphoproteome at distinct mitotic stages. J Proteome Res 8: 4553 - -4563.
151. Mallard F, Tang BL, Galli T, Tenza D, Saint-Pol A, Yue X, Antony C, Hong W, Goud B, Johannes L,. 2002. Early/recycling endosomes-to-TGN transport involves two SNARE complexes and a Rab6 isoform. J Cell Biol 156: 653 - 664.
152. Malsam J, Kreye S, Sollner TH,. 2008. Membrane fusion: SNAREs and regulation. Cell Mol Life Sci 65: 2814 - 2832.
153. Mann M,. 2006. Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 7: 952 - 958.
154. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S,. 2002. The protein kinase complement of the human genome. Science 298: 1912 - 1934.
155. Marcantonio M, Trost M, Courcelles M, Desjardins M, Thibault P,. 2008. Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: Application to cell signaling events of interferon-gamma-stimulated macrophages. Mol Cell Proteomics 7: 645 - 660.
156. Martens S, McMahon HT,. 2008. Mechanisms of membrane fusion: Disparate players and common principles. Nat Rev Mol Cell Biol 9: 543 - 556.
157. Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER III, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ,. 2007. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 316: 1160 - 1166.
158. Matthews HR,. 1995. Protein kinases and phosphatases that act on histidine, lysine, or arginine residues in eukaryotic proteins: A possible regulator of the mitogen-activated protein kinase cascade. Pharmacol Ther 67: 323 - 350.
159. Mazanek M, Mituloviae G, Herzog F, Stingl C, Hutchins JR, Peters JM, Mechtler K,. 2007. Titanium dioxide as a chemo-affinity solid phase in offline phosphopeptide chromatography prior to HPLC-MS/MS analysis. Nat Protoc 2: 1059 - 1069.
160. McLachlin DT, Chait BT,. 2003. Improved beta-elimination-based affinity purification strategy for enrichment of phosphopeptides. Anal Chem 75: 6826 - 6836.
161. McNew JA, Parlati F, Fukuda R, Johnston RJ, Paz K, Paumet F, Sollner TH, Rothman JE,. 2000. Compartmental specificity of cellular membrane fusion encoded in SNARE proteins. Nature 407: 153 - 159.
162. McNulty DE, Annan RS,. 2008. Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection. Mol Cell Proteomics 7: 971 - 980.
163. Medzihradszky KF,. 2005. Peptide sequence analysis. Methods Enzymol 402: 209 - 244.
164. Miaczynska M, Pelkmans L, Zerial M,. 2004. Not just a sink: Endosomes in control of signal transduction. Curr Opin Cell Biol 16: 400 - 406.
165. Miller ML, Blom N,. 2009. Kinase-specific prediction of protein phosphorylation sites. Methods Mol Biol 527: 299 - 310.
166. Molina H, Horn DM, Tang N, Mathivanan S, Pandey A,. 2007. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci USA 104: 2199 - 2204.
167. Monigatti F, Hekking B, Steen H,. 2006. Protein sulfation analysis-A primer. Biochim Biophys Acta 1764: 1904 - 1913.
168. Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, Stahl E, Bolouri MS, Ray HN, Sihag S, Kamal M, Patterson N, Lander ES, Mann M,. 2003. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115: 629 - 640.
169. Morandell S, Stasyk T, Grosstessner-Hain K, Roitinger E, Mechtler K, Bonn GK, Huber LA,. 2006. Phosphoproteomics strategies for the functional analysis of signal transduction. Proteomics 6: 4047 - 4056.
170. Morrison DK, Murakami MS, Cleghon V,. 2000. Protein kinases and phosphatases in the Drosophila genome. J Cell Biol 150: F57 - F62.
171. Moser K, White FM,. 2006. Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS. J Proteome Res 5: 98 - 104.
172. Mueller LN, Brusniak MY, Mani DR, Aebersold R,. 2008. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res 7: 51 - 61.
173. Mueller P, Pieters J,. 2006. Modulation of macrophage antimicrobial mechanisms by pathogenic mycobacteria. Immunobiology 211: 549 - 556.
174. Mullock BM, Hinton RH, Peppard JV, Slot JW, Luzio JP,. 1987. The preparative isolation of endosome fractions: A review. Cell Biochem Funct 5: 235 - 243.
175. Munton RP, Tweedie-Cullen R, Livingstone-Zatchej M, Weinandy F, Waidelich M, Longo D, Gehrig P, Potthast F, Rutishauser D, Gerrits B, Panse C, Schlapbach R, Mansuy IM,. 2007. Qualitative and quantitative analyses of protein phosphorylation in naive and stimulated mouse synaptosomal preparations. Mol Cell Proteomics 6: 283 - 293.
176. Nagy G, Matti U, Nehring RB, Binz T, Rettig J, Neher E, Sorensen JB,. 2002. Protein kinase C-dependent phosphorylation of synaptosome-associated protein of 25 kDa at Ser187 potentiates vesicle recruitment. J Neurosci 22: 9278 - 9286.
177. Nagy G, Reim K, Matti U, Brose N, Binz T, Rettig J, Neher E, Sorensen JB,. 2004. Regulation of releasable vesicle pool sizes by protein kinase A-dependent phosphorylation of SNAP-25. Neuron 41: 417 - 429.
178. Ndassa YM, Orsi C, Marto JA, Chen S, Ross MM,. 2006. Improved immobilized metal affinity chromatography for large-scale phosphoproteomics applications. J Proteome Res 5: 2789 - 2799.
179. Neubauer G, King A, Rappsilber J, Calvio C, Watson M, Ajuh P, Sleeman J, Lamond A, Mann M,. 1998. Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex. Nat Genet 20: 46 - 50.
180. Newmeyer DD, Ferguson-Miller S,. 2003. Mitochondria: Releasing power for life and unleashing the machineries of death. Cell 112: 481 - 490.
181. Nielander HB, Onofri F, Valtorta F, Schiavo G, Montecucco C, Greengard P, Benfenati F,. 1995. Phosphorylation of VAMP/synaptobrevin in synaptic vesicles by endogenous protein kinases. J Neurochem 65: 1712 - 1720.
182. Niittyla T, Fuglsang AT, Palmgren MG, Frommer WB, Schulze WX,. 2007. Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis. Mol Cell Proteomics 6: 1711 - 1726.
183. Nousiainen M, Sillje HH, Sauer G, Nigg EA, Korner R,. 2006. Phosphoproteome analysis of the human mitotic spindle. Proc Natl Acad Sci USA 103: 5391 - 5396.
184. Nuhse TS, Stensballe A, Jensen ON, Peck SC,. 2003. Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics 2: 1234 - 1243.
185. Nuhse TS, Bottrill AR, Jones AM, Peck SC,. 2007. Quantitative phosphoproteomic analysis of plasma membrane proteins reveals regulatory mechanisms of plant innate immune responses. Plant J 51: 931 - 940.
186. Obenauer JC, Cantley LC, Yaffe MB,. 2003. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31: 3635 - 3641.
187. Oda Y, Nagasu T, Chait BT,. 2001. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol 19: 379 - 382.
188. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG,. 2005. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4: 1487 - 1502.
189. Old WM, Shabb JB, Houel S, Wang H, Couts KL, Yen CY, Litman ES, Croy CH, Meyer-Arendt K, Miranda JG, Brown RA, Witze ES, Schweppe RE, Resing KA, Ahn NG,. 2009. Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma. Mol Cell 34: 115 - 131.
190. Olsen JV, Mann M,. 2004. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci USA 101: 13417 - 13422.
191. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M,. 2006. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127: 635 - 648.
192. Ong SE, Kratchmarova I, Mann M,. 2003. Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res 2: 173 - 181.
193. Ono M, Shitashige M, Honda K, Isobe T, Kuwabara H, Matsuzuki H, Hirohashi S, Yamada T,. 2006. Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol Cell Proteomics 5: 1338 - 1347.
194. Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, Hill DE, Vidal M, Evans JG, Thorburn DR, Carr SA, Mootha VK,. 2008. A mitochondrial protein compendium elucidates complex I disease biology. Cell 134: 112 - 123.
195. Palmgren MG,. 2001. Plant plasma membrane H+-ATPases: Powerhouses for nutrient uptake. Annu Rev Plant Physiol Plant Mol Biol 52: 817 - 845.
196. Palumbo AM, Reid GE,. 2008. Evaluation of Gas-phase rearrangement and competing fragmentation reactions on protein phosphorylation site assignment using collision induced dissociation-MS/MS and MS(3). Anal Chem 80: 9735 - 9747.
197. Palumbo AM, Tepe JJ, Reid GE,. 2008. Mechanistic insights into the multistage gas-phase fragmentation behavior of phosphoserine- and phosphothreonine-containing peptides. J Proteome Res 7: 771 - 779.
198. Parlati F, McNew JA, Fukuda R, Miller R, Sollner TH, Rothman JE,. 2000. Topological restriction of SNARE-dependent membrane fusion. Nature 407: 194 - 198.
199. Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V,. 2008. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J Proteome Res 7: 3373 - 3381.
200. Pfeffer SR,. 2007. Unsolved mysteries in membrane traffic. Annu Rev Biochem 76: 629 - 645.
201. Pinkse MW, Uitto PM, Hilhorst MJ, Ooms B, Heck AJ,. 2004. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem 76: 3935 - 3943.
202. Polgar J, Lane WS, Chung SH, Houng AK, Reed GL,. 2003. Phosphorylation of SNAP-23 in activated human platelets. J Biol Chem 278: 44369 - 44376.
203. Pollard TD, Earnshaw WC, Lippincott-Schwartz J,. 2007. Cell biology, 2nd edition. Elsevier.
204. Posewitz MC, Tempst P,. 1999. Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal Chem 71: 2883 - 2892.
205. Pozzi D, Condliffe S, Bozzi Y, Chikhladze M, Grumelli C, Proux-Gillardeaux V, Takahashi M, Franceschetti S, Verderio C, Matteoli M,. 2008. Activity-dependent phosphorylation of Ser187 is required for SNAP-25-negative modulation of neuronal voltage-gated calcium channels. Proc Natl Acad Sci USA 105: 323 - 328.
206. Prokisch H, Scharfe C, Camp DG II, Xiao W, David L, Andreoli C, Monroe ME, Moore RJ, Gritsenko MA, Kozany C, Hixson KK, Mottaz HM, Zischka H, Ueffing M, Herman ZS, Davis RW, Meitinger T, Oefner PJ, Smith RD, Steinmetz LM,. 2004. Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol 2: e160.
207. Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferre F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Kuster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ,. 2003. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 31: 3625 - 3630.
208. Puttick J, Baker EN, Delbaere LT,. 2008. Histidine phosphorylation in biological systems. Biochim Biophys Acta 1784: 100 - 105.
209. Qian WJ, Goshe MB, Camp DG II, Yu LR, Tang K, Smith RD,. 2003. Phosphoprotein isotope-coded solid-phase tag approach for enrichment and quantitative analysis of phosphopeptides from complex mixtures. Anal Chem 75: 5441 - 5450.
210. Rappsilber J, Ryder U, Lamond AI, Mann M,. 2002. Large-scale proteomic analysis of the human spliceosome. Genome Res 12: 1231 - 1245. (Pubitemid 41264425)
211. Reinders J, Sickmann A,. 2005. State-of-the-art in phosphoproteomics. Proteomics 5: 4052 - 4061.
212. Reinders J, Wagner K, Zahedi RP, Stojanovski D, Eyrich B, van der Laan M, Rehling P, Sickmann A, Pfanner N, Meisinger C,. 2007. Profiling phosphoproteins of yeast mitochondria reveals a role of phosphorylation in assembly of the ATP synthase. Mol Cell Proteomics 6: 1896 - 1906.
213. Reynolds KJ, Yao X, Fenselau C,. 2002. Proteolytic 18O labeling for comparative proteomics: Evaluation of endoprotease Glu-C as the catalytic agent. J Proteome Res 1: 27 - 33.
214. Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ,. 2007. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131: 1190 - 1203.
215. Risinger C, Bennett MK,. 1999. Differential phosphorylation of syntaxin and synaptosome-associated protein of 25 kDa (SNAP-25) isoforms. J Neurochem 72: 614 - 624.
216. Rizo J, Chen X, Arac D,. 2006. Unraveling the mechanisms of synaptotagmin and SNARE function in neurotransmitter release. Trends Cell Biol 16: 339 - 350.
217. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ,. 2004. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3: 1154 - 1169.
218. Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT,. 2000. The yeast nuclear pore complex: Composition, architecture, and transport mechanism. J Cell Biol 148: 635 - 651.
219. Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD, Comb MJ,. 2005. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 23: 94 - 101.
220. Ruttenberg BE, Pisitkun T, Knepper MA, Hoffert JD,. 2008. PhosphoScore: An open-source phosphorylation site assignment tool for MS(n) data. J Proteome Res 7: 3054 - 3059.
221. Salek M, Alonso A, Pipkorn R, Lehmann WD,. 2003. Analysis of protein tyrosine phosphorylation by nanoelectrospray ionization high-resolution tandem mass spectrometry and tyrosine-targeted product ion scanning. Anal Chem 75: 2724 - 2729.
222. Sauer G, Korner R, Hanisch A, Ries A, Nigg EA, Sillje HH,. 2005. Proteome analysis of the human mitotic spindle. Mol Cell Proteomics 4: 35 - 43.
223. Saunders NF, Brinkworth RI, Huber T, Kemp BE, Kobe B,. 2008. Predikin and PredikinDB: A computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. BMC Bioinformatics 9: 245.
224. Savitski MM, Falth M,. 2007. Peptide fragmentation and phospho-site detection. Expert Rev Proteomics 4: 445 - 446.
225. Schirmer EC, Florens L, Guan T, Yates JR III, Gerace L,. 2003. Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science 301: 1380 - 1382.
226. Schlosser A, Vanselow JT, Kramer A,. 2007. Comprehensive phosphorylation site analysis of individual phosphoproteins applying scoring schemes for MS/MS data. Anal Chem 79: 7439 - 7449.
227. Schmelzle K, White FM,. 2006. Phosphoproteomic approaches to elucidate cellular signaling networks. Curr Opin Biotechnol 17: 406 - 414.
228. Schmidt A, Kellermann J, Lottspeich F,. 2005. A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5: 4 - 15.
229. Schon EA,. 2000. Mitochondrial genetics and disease. Trends Biochem Sci 25: 555 - 560.
230. Schwartz D, Gygi SP,. 2005. An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol 23: 1391 - 1398.
231. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T,. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498 - 2504.
232. Shimazaki Y, Nishiki T, Omori A, Sekiguchi M, Kamata Y, Kozaki S, Takahashi M,. 1996. Phosphorylation of 25-kDa synaptosome-associated protein. Possible involvement in protein kinase C-mediated regulation of neurotransmitter release. J Biol Chem 271: 14548 - 14553.
233. Shu Y, Liu X, Yang Y, Takahashi M, Gillis KD,. 2008. Phosphorylation of SNAP-25 at Ser187 mediates enhancement of exocytosis by a phorbol ester in INS-1 cells. J Neurosci 28: 21 - 30.
234. Sickmann A, Reinders J, Wagner Y, Joppich C, Zahedi R, Meyer HE, Schonfisch B, Perschil I, Chacinska A, Guiard B, Rehling P, Pfanner N, Meisinger C,. 2003. The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci USA 100: 13207 - 13212.
235. Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P,. 2002. PROSITE: A documented database using patterns and profiles as motif descriptors. Brief Bioinform 3: 265 - 274.
236. Sillje HH, Nigg EA,. 2006. Purification of mitotic spindles from cultured human cells. Methods 38: 25 - 28.
237. Sleno L, Volmer DA,. 2004. Ion activation methods for tandem mass spectrometry. J Mass Spectrom 39: 1091 - 1112.
238. Smith JC, Figeys D,. 2008. Recent developments in mass spectrometry-based quantitative phosphoproteomics. Biochem Cell Biol 86: 137 - 148.
239. Smolka MB, Albuquerque CP, Chen SH, Schmidt KH, Wei XX, Kolodner RD, Zhou H,. 2005. Dynamic changes in protein-protein interaction and protein phosphorylation probed with amine-reactive isotope tag. Mol Cell Proteomics 4: 1358 - 1369.
240. Snyder DA, Kelly ML, Woodbury DJ,. 2006. SNARE complex regulation by phosphorylation. Cell Biochem Biophys 45: 111 - 123.
241. Soufi B, Gnad F, Jensen PR, Petranovic D, Mann M, Mijakovic I, Macek B,. 2008. The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins. Proteomics 8: 3486 - 3493.
242. Stasyk T, Schiefermeier N, Skvortsov S, Zwierzina H, Peranen J, Bonn GK, Huber LA,. 2007. Identification of endosomal epidermal growth factor receptor signaling targets by functional organelle proteomics. Mol Cell Proteomics 6: 908 - 922.
243. Steegmaier M, Klumperman J, Foletti DL, Yoo JS, Scheller RH,. 1999. Vesicle-associated membrane protein 4 is implicated in trans-Golgi network vesicle trafficking. Mol Biol Cell 10: 1957 - 1972.
244. Steen H, Mann M,. 2002. A new derivatization strategy for the analysis of phosphopeptides by precursor ion scanning in positive ion mode. J Am Soc Mass Spectrom 13: 996 - 1003.
245. Steen H, Mann M,. 2004. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 5: 699 - 711.
246. Steen H, Jebanathirajah JA, Springer M, Kirschner MW,. 2005. Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc Natl Acad Sci USA 102: 3948 - 3953.
247. Steen JA, Steen H, Georgi A, Parker K, Springer M, Kirchner M, Hamprecht F, Kirschner MW,. 2008. Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: A quantitative proteomic analysis. Proc Natl Acad Sci USA 105: 6069 - 6074.
248. Stein A, Weber G, Wahl MC, Jahn R,. 2009. Helical extension of the neuronal SNARE complex into the membrane. Nature 460: 525 - 528.
249. Steinberg TH, Agnew BJ, Gee KR, Leung WY, Goodman T, Schulenberg B, Hendrickson J, Beechem JM, Haugland RP, Patton WF,. 2003. Global quantitative phosphoprotein analysis using Multiplexed Proteomics technology. Proteomics 3: 1128 - 1144.
250. Sudhof TC, Rothman JE,. 2009. Membrane fusion: Grappling with SNARE and SM proteins. Science 323: 474 - 477.
251. Suzuki K, Verma IM,. 2008. Phosphorylation of SNAP-23 by IkappaB kinase 2 regulates mast cell degranulation. Cell 134: 485 - 495.
252. Swaney DL, McAlister GC, Wirtala M, Schwartz JC, Syka JE, Coon JJ,. 2007. Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors. Anal Chem 79: 477 - 485.
253. Swaney DL, McAlister GC, Coon JJ,. 2008. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods 5: 959 - 964.
254. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF,. 2004. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101: 9528 - 9533.
255. Sztul E, Lupashin V,. 2006. Role of tethering factors in secretory membrane traffic. Am J Physiol Cell Physiol 290: C11 - C26.
256. Takahashi M, Itakura M, Kataoka M,. 2003. New aspects of neurotransmitter release and exocytosis: Regulation of neurotransmitter release by phosphorylation. J Pharmacol Sci 93: 41 - 45.
257. Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts JD, Hood L, Aebersold R,. 2005. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods 2: 591 - 598.
258. Taouatas N, Drugan MM, Heck AJ, Mohammed S,. 2008. Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase. Nat Methods 5: 405 - 407.
259. Taylor AM, Holst O, Thomas-Oates J,. 2006. Mass spectrometric profiling of O-linked glycans released directly from glycoproteins in gels using in-gel reductive beta-elimination. Proteomics 6: 2936 - 2946.
260. Thingholm TE, Jorgensen TJ, Jensen ON, Larsen MR,. 2006. Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc 1: 1929 - 1935.
261. Thingholm TE, Jensen ON, Robinson PJ, Larsen MR,. 2008a. SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics 7: 661 - 671.
262. Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON,. 2008b. TiO2-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment. J Proteome Res 7: 3304 - 3313.
263. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C,. 2003a. Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75: 1895 - 1904.
264. Thompson AJ, Hart SR, Franz C, Barnouin K, Ridley A, Cramer R,. 2003b. Characterization of protein phosphorylation by mass spectrometry using immobilized metal ion affinity chromatography with on-resin beta-elimination and Michael addition. Anal Chem 75: 3232 - 3243.
265. Tian JH, Das S, Sheng ZH,. 2003. Ca2+-dependent phosphorylation of syntaxin-1A by the death-associated protein (DAP) kinase regulates its interaction with Munc18. J Biol Chem 278: 26265 - 26274.
266. Tran TH, Zeng Q, Hong W,. 2007. VAMP4 cycles from the cell surface to the trans-Golgi network via sorting and recycling endosomes. J Cell Sci 120: 1028 - 1041.
267. Trinidad JC, Specht CG, Thalhammer A, Schoepfer R, Burlingame AL,. 2006. Comprehensive identification of phosphorylation sites in postsynaptic density preparations. Mol Cell Proteomics 5: 914 - 922.
268. Trost M, English L, Lemieux S, Courcelles M, Desjardins M, Thibault P,. 2009. The phagosomal proteome in interferon-gamma-activated macrophages. Immunity 30: 143 - 154.
269. Tsumoto H, Ra M, Samejima K, Taguchi R, Kohda K,. 2008. Chemical derivatization of peptides containing phosphorylated serine/threonine for efficient ionization and quantification in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 22: 965 - 972.
270. Tsybin YO, Hakansson P, Budnik BA, Haselmann KF, Kjeldsen F, Gorshkov M, Zubarev RA,. 2001. Improved low-energy electron injection systems for high rate electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun Mass Spectrom 15: 1849 - 1854.
271. Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI,. 2008. Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. J Proteome Res 8: 887 - 899.
272. Ungar D, Hughson FM,. 2003. SNARE protein structure and function. Annu Rev Cell Dev Biol 19: 493 - 517.
273. Villen J, Beausoleil SA, Gerber SA, Gygi SP,. 2007. Large-scale phosphorylation analysis of mouse liver. Proc Natl Acad Sci USA 104: 1488 - 1493.
274. Villen J, Beausoleil SA, Gygi SP,. 2008. Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics 8: 4444 - 4452.
275. Villen J, Gygi SP,. 2008. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat Protoc 3: 1630 - 1638.
276. Virshup DM, Shenolikar S,. 2009. From promiscuity to precision: Protein phosphatases get a makeover. Mol Cell 33: 537 - 545.
277. von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P,. 2007. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315: 1126 - 1130.
278. Wang Y, Chen W, Wu J, Guo Y, Xia X,. 2007. Highly efficient and selective enrichment of phosphopeptides using porous anodic alumina membrane for MALDI-TOF MS analysis. J Am Soc Mass Spectrom 18: 1387 - 1395.
279. Wells JM, McLuckey SA,. 2005. Collision-induced dissociation (CID) of peptides and proteins. Methods Enzymol 402: 148 - 185.
280. Wickner W, Schekman R,. 2008. Membrane fusion. Nat Struct Mol Biol 15: 658 - 664.
281. Wolschin F, Wienkoop S, Weckwerth W,. 2005. Enrichment of phosphorylated proteins and peptides from complex mixtures using metal oxide/hydroxide affinity chromatography (MOAC). Proteomics 5: 4389 - 4397.
282. Xu X, Sarikas A, Dias-Santagata DC, Dolios G, Lafontant PJ, Tsai SC, Zhu W, Nakajima H, Nakajima HO, Field LJ, Wang R, Pan ZQ,. 2008. The CUL7 E3 ubiquitin ligase targets insulin receptor substrate 1 for ubiquitin-dependent degradation. Mol Cell 30: 403 - 414.
283. Yao PJ,. 2004. Synaptic frailty and clathrin-mediated synaptic vesicle trafficking in Alzheimer's disease. Trends Neurosci 27: 24 - 29.
284. Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C,. 2001. Proteolytic 18O labeling for comparative proteomics: Model studies with two serotypes of adenovirus. Anal Chem 73: 2836 - 2842.
285. Yates JR III, Gilchrist A, Howell KE, Bergeron JJ,. 2005. Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol 6: 702 - 714.
286. Zappacosta F, Annan RS,. 2004. N-terminal isotope tagging strategy for quantitative proteomics: Results-driven analysis of protein abundance changes. Anal Chem 76: 6618 - 6627.
287. Zhang G, Spellman DS, Skolnik EY, Neubert TA,. 2006. Quantitative phosphotyrosine proteomics of EphB2 signaling by stable isotope labeling with amino acids in cell culture (SILAC). J Proteome Res 5: 581 - 588.
288. Zhang H, Zha X, Tan Y, Hornbeck PV, Mastrangelo AJ, Alessi DR, Polakiewicz RD, Comb MJ,. 2002a. Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. J Biol Chem 277: 39379 - 39387.
289. Zhang X, Jin QK, Carr SA, Annan RS,. 2002b. N-Terminal peptide labeling strategy for incorporation of isotopic tags: A method for the determination of site-specific absolute phosphorylation stoichiometry. Rapid Commun Mass Spectrom 16: 2325 - 2332.
290. Zhang X, Ye J, Jensen ON, Roepstorff P,. 2007. Highly efficient phosphopeptide enrichment by calcium phosphate precipitation combined with subsequent IMAC enrichment. Mol Cell Proteomics 6: 2032 - 2042.
291. Zhang Y, Wolf-Yadlin A, Ross PL, Pappin DJ, Rush J, Lauffenburger DA, White FM,. 2005. Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol Cell Proteomics 4: 1240 - 1250.
292. Zhou H, Watts JD, Aebersold R,. 2001. A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol 19: 375 - 378.
293. Zhou H, Tian R, Ye M, Xu S, Feng S, Pan C, Jiang X, Li X, Zou H,. 2007. Highly specific enrichment of phosphopeptides by zirconium dioxide nanoparticles for phosphoproteome analysis. Electrophoresis 28: 2201 - 2215. (Pubitemid 47065147)
294. Zischka H, Lichtmannegger J, Jagemann N, Jennen L, Hamoller D, Huber E, Walch A, Summer KH, Gottlicher M,. 2008. Isolation of highly pure rat liver mitochondria with the aid of zone-electrophoresis in a free flow device (ZE-FFE). Methods Mol Biol 424: 333 - 348.
295. Zubarev RA, Kelleher NL, McLafferty FW,. 1998. Electron capture dissociation of multiply charged protein cations. J Am Chem Soc 120: 3265 - 3266.
296. Zwilling D, Cypionka A, Pohl WH, Fasshauer D, Walla PJ, Wahl MC, Jahn R,. 2007. Early endosomal SNAREs form a structurally conserved SNARE complex and fuse liposomes with multiple topologies. EMBO J 26: 9 - 18.