Menu
Home
Log in / Register
 
Home arrow Health arrow Analysis of Protein Post-Translational Modifications by Mass Spectrometry
Source

References

  • 1 Cohen P. The role of protein phosphorylation in human health and disease. The Sir Hans Krebs Medal Lecture. Eur JBiochem 2001;268:5001-5010.
  • 2 Hunter T. The role of tyrosine phosphorylation in cell growth and disease. Harvey Lect 1998;94:81-119.
  • 3 Zhu X, Lee HG, Raina AK, Perry G, Smith MA. The role of mitogen-activated protein kinase pathways in Alzheimer's disease. Neurosignals 2002;11:270-281.
  • 4 Fischer EH, Krebs EG. Conversion of phosphorylase b to phosphorylase a in muscle extracts. J Biol Chem 1955;216:121-132.
  • 5 Sharma K, D'Souza RC, Tyanova S, Schaab C, Wisniewski JR, Cox J, Mann M. Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep 2014;8:1583-1594.
  • 6 Levene PA, Alsberg CL. The cleavage products of vitellin. J Biol Chem 1906;2:127.
  • 7 Posternak S, Posternak T. C R Acad Sci 1928;187:313.
  • 8 Levene PA, Lipmann FA. Serinephosphoric acid obtained on hydrolysis of vitellinic acid. J Biol Chem 1932;98:109-114.
  • 9 Araki M, Yonezawa T, Chin S, Kuga M, Shimada N, Imagi S, Ochiai Y. Investigation of phosphorus metabolism of Yoshida sarcoma with the aid of P32. I. Gan 1952;43:69-72.
  • 10 Williams-Ashman HG, Kennedy EP. Oxidative phosphorylation catalyzed by cytoplasmic particles isolated from malignant tissues. Cancer Res 1952;12:415-421.
  • 11 Burnett G, Kennedy EP. The enzymatic phosphorylation of proteins. J Biol Chem 1954;211:969-980.
  • 12 Krebs EG, Fischer EH. The phosphorylase b to a converting enzyme of rabbit skeletal muscle. Biochim Biophys Acta 1956;20:150-157.
  • 13 Walsh DA, Perkins JP, Krebs EG. An adenosine 3,5'-monophosphate- dependant protein kinase from rabbit skeletal muscle. J Biol Chem 1968;243:3763-3765.
  • 14 Glass DB, Krebs EG. Protein phosphorylation catalyzed by cyclic AMP- dependent and cyclic GMP-dependent protein kinases. Annu Rev Pharmacol Toxicol 1980;20:363-388.
  • 15 Hunter T, Sefton BM. Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc Natl Acad Sci U S A 1980;77:1311-1315.
  • 16 Hunter T. The genesis of tyrosine phosphorylation. Cold Spring Harb Perspect Biol 2014;6:a020644.
  • 17 Collett MS, Erikson E, Erikson RL. Structural analysis of the avian sarcoma virus transforming protein: Sites of phosphorylation. J Virol 1979;29:770-781.
  • 18 Chinkers M, Cohen S. Purified EGF receptor-kinase interacts specifically with antibodies to Rous sarcoma virus transforming protein. Nature 1981;290:516-519.
  • 19 Hunter T, Cooper JA. Epidermal growth factor induces rapid tyrosine phosphorylation of proteins in A431 human tumor cells. Cell 1981;24:741-752.
  • 20 Penhallow RC, Class K, Sonoda H, Bolen JB, Rowley RB. Temporal activation of nontransmembrane protein-tyrosine kinases following mast cell Fc epsilon RI engagement. J Biol Chem 1995;270:23362-23365.
  • 21 Oda K, Matsuoka Y, Funahashi A, Kitano H. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 2005;1:2005.
  • 22 Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002;298:1912-1934.
  • 23 Manning G, Plowman GD, Hunter T, Sudarsanam S. Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci 2002;27:514-520.
  • 24 Robinson DR, Wu YM, Lin SF. The protein tyrosine kinase family of the human genome. Oncogene 2000;19:5548-5557.
  • 25 Fedorov O, Muller S, Knapp S. The (un)targeted cancer kinome. Nat Chem Biol 2010;6:166-169.
  • 26 Knapp S, Arruda P, Blagg J, Burley S, Drewry DH, Edwards A, Fabbro D, Gillespie P, Gray NS, Kuster B, Lackey KE, Mazzafera P, Tomkinson NC, Willson TM, Workman P, Zuercher WJ. A public-private partnership to unlock the untargeted kinome. Nat Chem Biol 2013;9:3-6.
  • 27 Kilpinen S, Ojala K, Kallioniemi O. Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PLoS One 2010;5:e15068.
  • 28 Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M. PhosphoSitePlus: A comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res 2012;40:D261-D270.
  • 29 Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. PhosphoSitePlus, 2014: Mutations, PTMs and recalibrations. Nucleic Acids Res 2015;43:D512-D520.
  • 30 Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 2010;143:1174-1189.
  • 31 Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV. Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nat Commun 2012;3:876.
  • 32 Marx H, Lemeer S, Schliep JE, Matheron L, Mohammed S, Cox J, Mann M, Heck AJ, Kuster B. A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat Biotechnol 2013;31:557-564.
  • 33 Zappacosta F, Scott GF, Huddleston MJ, Annan RS. An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome.

J Proteome Res 2015;14:997-1009.

  • 34 Cohen P. The origins of protein phosphorylation. Nat Cell Biol 2002;4:E127-E130.
  • 35 Zappacosta F, Collingwood TS, Huddleston MJ, Annan RS. A quantitative results-driven approach to analyzing multisite protein phosphorylation: The phosphate-dependent phosphorylation profile of the transcription factor Pho4. Mol Cell Proteomics 2006;5:2019-2030.
  • 36 Komeili A, O'Shea EK. Roles of phosphorylation sites in regulating activity of the transcription factor Pho4. Science 1999;284:977-980.
  • 37 Springer M, Wykoff DD, Miller N, O'Shea EK. Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes. PLoS Biol 2003;1:E28.
  • 38 Verma R, Annan RS, Huddleston MJ, Carr SA, Reynard G, Deshaies RJ. Phosphorylation of Sic1p by G1 Cdk required for its degradation and entry into S phase. Science 1997;278:455-460.
  • 39 Nash P, Tang X, Orlicky S, Chen Q, Gertler FB, Mendenhall MD, Sicheri F, Pawson T, Tyers M. Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature 2001;414:514-521.
  • 40 Hao B, Oehlmann S, Sowa ME, Harper JW, Pavletich NP. Structure of a Fbw7-Skp1-cyclin E complex: Multisite-phosphorylated substrate recognition by SCF ubiquitin ligases. Mol Cell 2007;26:131-143.
  • 41 Koivomagi M, Valk E, Venta R, Iofik A, Lepiku M, Balog ER, Rubin SM, Morgan DO, Loog M. Cascades of multisite phosphorylation control Sic1 destruction at the onset of S phase. Nature 2011;480:128-131.
  • 42 Sadowski I, Stone JC, Pawson T. A noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps. Mol Cell Biol 1986;6:4396-4408.
  • 43 Anderson D, Koch CA, Grey L, Ellis C, Moran MF, Pawson T. Binding of SH2 domains of phospholipase C gamma 1, GAP, and Src to activated growth factor receptors. Science 1990;250:979-982.
  • 44 Moran MF, Koch CA, Anderson D, Ellis C, England L, Martin GS, Pawson T. Src homology region 2 domains direct protein-protein interactions in signal transduction. Proc Natl Acad Sci U S A 1990;87:8622-8626.
  • 45 Liu BA, Jablonowski K, Raina M, Arce M, Pawson T, Nash PD. The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling. Mol Cell 2006;22:851-868.
  • 46 Kavanaugh WM, Williams LT. An alternative to SH2 domains for binding tyrosine-phosphorylated proteins. Science 1994;266:1862-1865.
  • 47 Yaffe MB, Elia AE. Phosphoserine/threonine-binding domains. Curr Opin Cell Biol 2001;13:131-138.
  • 48 Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 2004;32:1037-1049.
  • 49 Wright PE, Dyson HJ. Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. JMol Biol 1999;293:321-331.
  • 50 Kim PM, Sboner A, Xia Y, Gerstein M. The role of disorder in interaction networks: A structural analysis. Mol Syst Biol 2008;4:179.
  • 51 Tompa P, Davey NE, Gibson TJ, Babu MM. A million peptide motifs for the molecular biologist. Mol Cell 2014;55:161-169.
  • 52 Meek DW, Anderson CW. Post-translational modification of p53: Cooperative integrators of function. Cold SpringHarb Perspect Biol 2009;1:a000950.
  • 53 Munoz MJ, de la Mata M, Kornblihtt AR. The carboxy terminal domain of RNA polymerase II and alternative splicing. Trends Biochem Sci 2010;35:497-504.
  • 54 Bah A, Vernon RM, Siddiqui Z, Krzeminski M, Muhandiram R, Zhao C, Sonenberg N, Kay LE, Forman-Kay JD. Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch. Nature 2015;519:106-109.
  • 55 Wright PE, Dyson HJ. Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol 2015;16:18-29.
  • 56 Mustelin T. A brief introduction to the protein phosphatase families. Methods Mol Biol 2007;365:9-22.
  • 57 Sacco F, Perfetto L, Castagnoli L, Cesareni G. The human phosphatase interactome: An intricate family portrait. FEBS Lett 2012;586:2732-2739.
  • 58 Kinexus: Systems Bioinformatics Company. http://www.kinexus.ca/ scienceTechnology/protein_phosphatases/protein_phosphatases.html (2015)
  • 59 Shi Y. Serine/threonine phosphatases: Mechanism through structure. Cell 2009;139:468-484.
  • 60 Cohen P, Cohen PT. Protein phosphatases come of age. JBiol Chem 1989;264:21435-21438.
  • 61 Sun H, Tonks NK. The coordinated action of protein tyrosine phosphatases and kinases in cell signaling. Trends Biochem Sci 1994;19:480-485.
  • 62 Kleiman LB, Maiwald T, Conzelmann H, Lauffenburger DA, Sorger PK. Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding. Mol Cell 2011;43:723-737.
  • 63 Whiteaker JR, Zhao L, Yan P, Ivey RG, Voytovich UJ, Moore HD, Lin C, Paulovich AG. Peptide immunoaffinity enrichment and targeted mass spectrometry enables multiplex, quantitative pharmacodynamic studies of phospho-signaling. Mol Cell Proteomics 2015;14:2261-2273.
  • 64 Gould KL, Woodgett JR, Cooper JA, Buss JE, Shalloway D, Hunter T. Protein kinase C phosphorylates pp60src at a novel site. Cell 1985;42:849-857.
  • 65 van der Geer P, Hunter T. Phosphopeptide mapping and phosphoamino acid analysis by electrophoresis and chromatography on thin-layer cellulose plates. Electrophoresis 1994;15:544-554.
  • 66 Barber M, Bordoli RS, Sedgwick RD, Tyler AN. Fast atom bombardment of solids (F.A.B.): A new ion source for mass spectrometry. J Chem Soc Chem Commun 1981;7:325-327.
  • 67 Morris HR, Panico M, Barber M, Bordoli RS, Sedgwick RD, Tyler A. Fast atom bombardment: A new mass spectrometric method for peptide sequence analysis. Biochem Biophys Res Commun 1981;101:623-631.
  • 68 Webster TA, Gibson BW, Keng T, Biemann K, Schimmel P. Primary structures of both subunits of Escherichia coli glycyl-tRNA synthetase. J Biol Chem 1983;258:10637-10641.
  • 69 Gibson BW, Biemann K. Strategy for the mass spectrometric verification and correction of the primary structures of proteins deduced from their DNA sequences. Proc Natl Acad Sci U S A 1984;81:1956-1960.
  • 70 Fenselau C, Heller DN, Miller MS, White HB III. Phosphorylation sites in riboflavin-binding protein characterized by fast atom bombardment mass spectrometry. Anal Biochem 1985;150:309-314.
  • 71 Hunt DF, Yates JR III, Shabanowitz J, Winston S, Hauer CR. Protein sequencing by tandem mass spectrometry. Proc Natl Acad Sci U S A 1986;83:6233-6237.
  • 72 Michel H, Hunt DF, Shabanowitz J, Bennett J. Tandem mass spectrometry reveals that three photosystem II proteins of spinach chloroplasts contain N-acetyl-O-phosphothreonine at their NH2 termini. J Biol Chem 1988;263:1123-1130.
  • 73 Holmes CF, Tonks NK, Major H, Cohen P. Analysis of the in vivo phosphorylation state of protein phosphatase inhibitor-2 from rabbit skeletal muscle by fast-atom bombardment mass spectrometry. Biochim Biophys Acta 1987;929:208-219.
  • 74 Karas M, Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 1988;60:2299-2301.
  • 75 Hillenkamp F, Karas M. Mass spectrometry of peptides and proteins by matrix-assisted ultraviolet laser desorption/ionization. Methods Enzymol 1990;193:280-295.
  • 76 Spengler B, Kirsch D, Kaufmann R, Jaeger E. Peptide sequencing by matrix- assisted laser-desorption mass spectrometry. Rapid Commun Mass Spectrom 1992;6:105-108.
  • 77 Annan RS, Carr SA. Phosphopeptide analysis by matrix-assisted laser desorption time-of-flight mass spectrometry. Anal Chem 1996;68:3413-3421.
  • 78 Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989;246:64-71.
  • 79 Yost RA, Enke CG. Triple quadrupole mass spectrometry for direct mixture analysis and structure elucidation. Anal Chem 1979;51:1251-1264.
  • 80 Payne DM, Rossomando AJ, Martino P, Erickson AK, Her JH, Shabanowitz J, Hunt DF, Weber MJ, Sturgill TW. Identification of the regulatory phosphorylation sites in pp42/mitogen-activated protein kinase (MAP kinase). EMBO J 1991;10:885-892.
  • 81 Hunt DF, Henderson RA, Shabanowitz J, Sakaguchi K, Michel H, Sevilir N,

Cox AL, Appella E, Engelhard VH. Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 1992;255:1261-1263.

  • 82 Wilm M, Mann M. Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last? Int J Mass Spectrom Ion Processes 1994;136:167-180.
  • 83 Wilm M, Mann M. Analytical properties of the nanoelectrospray ion source. Anal Chem 1996;68:1-8.
  • 84 Emmett MR, Caprioli RM. Micro-electrospray mass spectrometry: Ultra- high-sensitivity analysis of peptides and proteins. J Am Soc Mass Spectrom 1994;5:605-613.
  • 85 Davis MT, Stahl DC, Lee TD. Low flow high-performance liquid chromatography solvent delivery system designed for tandem capillary liquid chromatography-mass spectrometry. J Am Soc Mass Spectrom 1995;6:571-577.
  • 86 Davis MT, Stahl DC, Hefta SA, Lee TD. A microscale electrospray interface for on-line, capillary liquid chromatography/tandem mass spectrometry of complex peptide mixtures. Anal Chem 1995;67:4549-4556.
  • 87 Osaka I, Takayama M. Influence of hydrophobicity on positive- and negative- ion yields of peptides in electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 2014;28:2222-2226.
  • 88 Cech NB, Enke CG. Relating electrospray ionization response to nonpolar character of small peptides. Anal Chem 2000;72:2717-2723.
  • 89 Steen H, Jebanathirajah JA, Rush J, Morrice N, Kirschner MW. Phosphorylation analysis by mass spectrometry: Myths, facts, and the consequences for qualitative and quantitative measurements. Mol Cell Proteomics 2006;5:172-181.
  • 90 Gropengiesser J, Varadarajan BT, Stephanowitz H, Krause E. The relative influence of phosphorylation and methylation on responsiveness of peptides to MALDI and ESI mass spectrometry. J Mass Spectrom 2009;44:821-831.
  • 91 Carr SA, Huddleston MJ, Annan RS. Selective detection and sequencing of phosphopeptides at the femtomole level by mass spectrometry. Anal Biochem 1996;239:180-192.
  • 92 Steen H, Jebanathirajah JA, Springer M, Kirschner MW. Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc Natl Acad Sci U S A 2005;102:3948-3953.
  • 93 Hegeman AD, Harms AC, Sussman MR, Bunner AE, Harper JF. An isotope labeling strategy for quantifying the degree of phosphorylation at multiple sites in proteins. J Am Soc Mass Spectrom 2004;15:647-653.
  • 94 Guo L, Kozlosky CJ, Ericsson LH, Daniel TO, Cerretti DP, Johnson RS. Studies of ligand-induced site-specific phosphorylation of epidermal growth factor receptor. J Am Soc Mass Spectrom 2003;14:1022-1031.
  • 95 Tsay YG, Wang YH, Chiu CM, Shen BJ, Lee SC. A strategy for identification and quantitation of phosphopeptides by liquid chromatography/tandem mass spectrometry. Anal Biochem 2000;287:55-64.
  • 96 Resing KA, Ahn NG. Protein phosphorylation analysis by electrospray ionization-mass spectrometry. Methods Enzymol 1997;283:29-44.
  • 97 Marcantonio M, Trost M, Courcelles M, Desjardins M, Thibault P. Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: Application to cell signaling events of interferon-gamma-stimulated macrophages. Mol Cell Proteomics 2008;7:645-660.
  • 98 Gao Y, Wang Y. A method to determine the ionization efficiency change of peptides caused by phosphorylation. J Am Soc Mass Spectrom 2007;18:1973-1976.
  • 99 Lee KA, Craven KB, Niemi GA, Hurley JB. Mass spectrometric analysis of the kinetics of in vivo rhodopsin phosphorylation. Protein Sci 2002;11:862-874.
  • 100 Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 2003;100:6940-6945.
  • 101 Zhang X, Jin QK, Carr SA, Annan RS. 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 2002;16:2325-2332.
  • 102 Wu R, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME, Gygi SP. A large- scale method to measure absolute protein phosphorylation stoichiometries. Nat Methods 2011;8:677-683.
  • 103 Bonenfant D, Schmelzle T, Jacinto E, Crespo JL, Mini T, Hall MN, Jenoe P. Quantitation of changes in protein phosphorylation: A simple method based on stable isotope labeling and mass spectrometry. Proc Natl Acad Sci U S A 2003;100:880-885.
  • 104 Papayannopoulos I. The interpretation of collision-induced dissociation of tandem mass spectra of peptides. Mass Spectrom Rev 1995;14:49-73.
  • 105 Palumbo AM, Tepe JJ, Reid GE. Mechanistic insights into the multistage gas-phase fragmentation behavior of phosphoserine- and phosphothreonine- containing peptides. JProteome Res 2008;7:771-779.
  • 106 Brown R, Stuart SS, Houel S, Ahn NG, Old WM. Large-scale examination of factors influencing phosphopeptide neutral loss during collision induced dissociation. J Am Soc Mass Spectrom 2015;26:1128-1142.
  • 107 March RE. An introduction to quadrupole Ion trap mass spectrometry.

J Mass Spectrom 1997;32:351-369.

  • 108 DeGnore JP, Qin J. Fragmentation of phosphopeptides in an ion trap mass spectrometer. J Am Soc Mass Spectrom 1998;9:1175-1188.
  • 109 Karcher RL, Roland JT, Zappacosta F, Huddleston MJ, Annan RS, Carr SA, Gelfand VI. Cell cycle regulation of myosin-V by calcium/calmodulin- dependent protein kinase II. Science 2001;293:1317-1320.
  • 110 Palumbo AM, Reid GE. Evaluation of gas-phase rearrangement and competing fragmentation reactions on protein phosphorylation site assignment using collision induced dissociation-MS/MS and MS3. Anal Chem 2008;80:9735-9747.
  • 111 Cui L, Reid GE. Examining factors that influence erroneous phosphorylation site localization via competing fragmentation and rearrangement reactions during ion trap CID-MS/MS and -MS(3.) Proteomics 2013;13:964-973.
  • 112 Yague J, Paradela A, Ramos M, Ogueta S, Marina A, Barahona F, Lopez de Castro JA, Vazquez J. Peptide rearrangement during quadrupole ion trap fragmentation: Added complexity to MS/MS spectra. Anal Chem 2003;75:1524-1535.
  • 113 Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A 2004;101:12130-12135.
  • 114 Cui L, Yapici I, Borhan B, Reid GE. Quantification of competing H3PO4 versus HPO3 + H2O neutral losses from regioselective 18O-labeled phosphopeptides. J Am Soc Mass Spectrom 2014;25:141-148.
  • 115 Schroeder MJ, Shabanowitz J, Schwartz JC, Hunt DF, Coon JJ. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal Chem 2004;76:3590-3598.
  • 116 Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI. Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. JProteome Res 2009;8:887-899.
  • 117 Villen J, Beausoleil SA, Gygi SP. Evaluation of the utility of neutral-loss- dependent MS3 strategies in large-scale phosphorylation analysis.

Proteomics 2008;8:4444-4452.

  • 118 Olsen JV, Mann M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc Natl Acad Sci U S A 2004;101:13417-13422.
  • 119 Gruhler A, Olsen JV, Mohammed S, Mortensen P, Faergeman NJ, Mann M, Jensen ON. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 2005;4:310-327.
  • 120 Stensballe A, Jensen ON, Olsen JV, Haselmann KF, Zubarev RA. Electron capture dissociation of singly and multiply phosphorylated peptides. Rapid Commun Mass Spectrom 2000;14:1793-1800.
  • 121 Zubarev RA, Horn DM, Fridriksson EK, Kelleher NL, Kruger NA, Lewis MA, Carpenter BK, McLafferty FW. Electron capture dissociation for structural characterization of multiply charged protein cations. Anal Chem 2000;72:563-573.
  • 122 Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 2004;101:9528-9533.
  • 123 Good DM, Wirtala M, McAlister GC, Coon JJ. Performance characteristics of electron transfer dissociation mass spectrometry. Mol Cell Proteomics 2007;6:1942-1951.
  • 124 Swaney DL, McAlister GC, Coon JJ. Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods 2008;5:959-964.
  • 125 Molina H, Horn DM, Tang N, Mathivanan S, Pandey A. Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proc Natl Acad Sci U S A 2007;104:2199-2204.
  • 126 Frese CK, Zhou H, Taus T, Altelaar AF, Mechtler K, Heck AJ, Mohammed S. Unambiguous phosphosite localization using electron-transfer/higher- energy collision dissociation (EThcD). J Proteome Res 2013;12:1520-1525.
  • 127 Junger MA, Aebersold R. Mass spectrometry-driven phosphoproteomics: Patterning the systems biology mosaic. Wiley Interdiscip Rev Dev Biol 2014;3:83-112.
  • 128 Shvartsburg AA, Singer D, Smith RD, Hoffmann R. Ion mobility separation of isomeric phosphopeptides from a protein with variant modification of adjacent residues. Anal Chem 2011;83:5078-5085.
  • 129 Bridon G, Bonneil E, Muratore-Schroeder T, Caron-Lizotte O, Thibault P. Improvement of phosphoproteome analyses using FAIMS and decision tree fragmentation. application to the insulin signaling pathway in Drosophila melanogaster S2 cells. J Proteome Res 2012;11:927-940.
  • 130 Bian Y, Ye M, Song C, Cheng K, Wang C, Wei X, Zhu J, Chen R, Wang F, Zou H. Improve the coverage for the analysis of phosphoproteome of HeLa cells by a tandem digestion approach. JProteome Res 2012;11:2828-2837.
  • 131 Wisniewski JR, Mann M. Consecutive proteolytic digestion in an enzyme reactor increases depth of proteomic and phosphoproteomic analysis. Anal Chem 2012;84:2631-2637.
  • 132 Giansanti P, Aye TT, Van Den Toorn H, Peng M, van Breukelen B, Heck AJ. An augmented multiple-protease-based human phosphopeptide atlas. Cell Rep 2015;11:1834-1843.
  • 133 Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM,

Shabanowitz J, Hunt DF, White FM. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 2002;20:301-305.

  • 134 Erickson BK, Jedrychowski MP, McAlister GC, Everley RA, Kunz R, Gygi SP. Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer. Anal Chem 2015;87:1241-1249.
  • 135 Batth TS, Francavilla C, Olsen JV. Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics. J Proteome Res 2014;13:6176-6186.
  • 136 Cohen P. The regulation of protein function by multisite phosphorylation--a 25 year update. Trends Biochem Sci 2000;25:596-601.
  • 137 Ubersax JA, Ferrell JE Jr. Mechanisms of specificity in protein phosphorylation. Nat Rev Mol Cell Biol 2007;8:530-541.
  • 138 Roux PP, Thibault P. The coming of age of phosphoproteomics--from large data sets to inference of protein functions. Mol Cell Proteomics 2013;12:3453-3464.
  • 139 Liu Y, Chance MR. Integrating phosphoproteomics in systems biology. Comput Struct Biotechnol J 2014;10:90-97.
  • 140 Courcelles M, Fremin C, Voisin L, Lemieux S, Meloche S, Thibault P. Phosphoproteome dynamics reveal novel ERK1/2 MAP kinase substrates with broad spectrum of functions. Mol Syst Biol 2013;9:669.
  • 141 Hsu PP, Kang SA, Rameseder J, Zhang Y, Ottina KA, Lim D, Peterson TR, Choi Y, Gray NS, Yaffe MB, Marto JA, Sabatini DM. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science 2011;332:1317-1322.
  • 142 Yu Y, Yoon SO, Poulogiannis G, Yang Q, Ma XM, Villen J, Kubica N, Hoffman GR, Cantley LC, Gygi SP, Blenis J. Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science 2011;332:1322-1326.
  • 143 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. Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma. Mol Cell 2009;34:115-131.

144 Kim JY, Welsh EA, Oguz U, Fang B, Bai Y, Kinose F, Bronk C, Remsing Rix

LL, Beg AA, Rix U, Eschrich SA, Koomen JM, Haura EB. Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells. Proc Natl Acad Sci

U S A 2013;110:12414-12419.

  • 145 Johnson H, Lescarbeau RS, Gutierrez JA, White FM. Phosphotyrosine profiling of NSCLC cells in response to EGF and HGF reveals network specific mediators of invasion. JProteome Res 2013;12:1856-1867.
  • 146 Osinalde N, Sanchez-Quiles V, Akimov V, Guerra B, Blagoev B, Kratchmarova I. Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics. Proteomics 2015;15:520-531.
  • 147 Rust HL, Thompson PR. Kinase consensus sequences: A breeding ground for crosstalk. ACS Chem Biol 2011;6:881-892.
  • 148 Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002;1:376-386.
  • 149 Kruger M, Moser M, Ussar S, Thievessen I, Luber CA, Forner F, Schmidt S, Zanivan S, Fassler R, Mann M. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 2008;134:353-364.
  • 150 McClatchy DB, Liao L, Park SK, Venable JD, Yates JR. Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res 2007;17:1378-1388.
  • 151 Hsu JL, Huang SY, Chow NH, Chen SH. Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem 2003;75:6843-6852.
  • 152 DeSouza LV, Taylor AM, Li W, Minkoff MS, Romaschin AD, Colgan TJ, Siu

KW. Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues. J Proteome Res 2008;7:3525-3534.

  • 153 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. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004;3:1154-1169.
  • 154 Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C. Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003;75:1895-1904.
  • 155 Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE, Jaffe JD, Carr SA. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Mol Cell Proteomics 2012;11:M111.
  • 156 Chahrour O, Cobice D, Malone J. Stable isotope labelling methods in mass spectrometry-based quantitative proteomics. JPharm Biomed Anal 2015;113:2-20.
  • 157 Savitski MM, Sweetman G, Askenazi M, Marto JA, Lang M, Zinn N, Bantscheff M. Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on Orbitrap-type mass spectrometers. Anal Chem 2011;83:8959-8967.
  • 158 Ow SY, Salim M, Noirel J, Evans C, Wright PC. Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation. Proteomics 2011;11:2341-2346.
  • 159 Wenger CD, Lee MV, Hebert AS, McAlister GC, Phanstiel DH, Westphall MS, Coon JJ. Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. Nat Methods 2011;8:933-935.
  • 160 Ting L, Rad R, Gygi SP, Haas W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods 2011;8:937-940.
  • 161 McAlister GC, Nusinow DP, Jedrychowski MP, Wuhr M, Huttlin EL,

Erickson BK, Rad R, Haas W, Gygi SP. MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal Chem 2014;86:7150-7158.

  • 162 Savitski MM, Mathieson T, Zinn N, Sweetman G, Doce C, Becher I, Pachl F, Kuster B, Bantscheff M. Measuring and managing ratio compression for accurate iTRAQ/TMT quantification. J Proteome Res 2013;12:3586-3598.
  • 163 Bantscheff M, Lemeer S, Savitski MM, Kuster B. Quantitative mass spectrometry in proteomics: Critical review update from 2007 to the present. Anal Bioanal Chem 2012;404:939-965.
  • 164 Bondarenko PV, Chelius D, Shaler TA. Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem 2002;74:4741-4749.
  • 165 Sun W, Wu S, Wang X, Zheng D, Gao Y. An analysis of protein abundance suppression in data dependent liquid chromatography and tandem mass spectrometry with tryptic peptide mixtures of five known proteins. Eur J Mass Spectrom (Chichester, Eng) 2005;11:575-580.
  • 166 Neilson KA, Ali NA, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Lee A, van Sluyter SC, Haynes PA. Less label, more free: Approaches in label-free quantitative mass spectrometry. Proteomics 2011;11:535-553.
  • 167 de Graaf EL, Giansanti P, Altelaar AF, Heck AJ. Single-step enrichment by Ti-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution. Mol Cell Proteomics 2014;13:2426-2434.
  • 168 Oliveira AP, Ludwig C, Zampieri M, Weisser H, Aebersold R, Sauer U. Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis. Sci Signal 2015;8:rs4.
  • 169 Wu R, Dephoure N, Haas W, Huttlin EL, Zhai B, Sowa ME, Gygi SP. Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Mol Cell Proteomics 2011;10:1-12.
  • 170 Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods 2009;6:359-362.
  • 171 Chen EI, Cociorva D, Norris JL, Yates JR III. Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. JProteome Res 2007;6:2529-2538.
  • 172 Guo X, Trudgian DC, Lemoff A, Yadavalli S, Mirzaei H. Confetti: A multiprotease map of the HeLa proteome for comprehensive proteomics.

Mol Cell Proteomics 2014;13:1573-1584.

  • 173 Swaney DL, Wenger CD, Coon JJ. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res 2010;9:1323-1329.
  • 174 Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal Chem 2009;81:4493-4501.
  • 175 Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006;127:635-648.
  • 176 Frackelton J, Ross AH, Eisen HN. Characterization and use of monoclonal antibodies for isolation of phosphotyrosyl proteins from retrovirus-transformed cells and growth factor-stimulated cells. Mol Cell Biol 1983;3:1343-1352.
  • 177 Tinti M, Nardozza AP, Ferrari E, Sacco F, Corallino S, Castagnoli L, Cesareni G. The 4G10, pY20 and p-TYR-100 antibody specificity: Profiling by peptide microarrays. NBiotechnol 2012;29:571-577.
  • 178 Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD, Comb MJ. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 2005;23:94-101.
  • 179 Kassel DB, Consler TG, Shalaby M, Sekhri P, Gordon NNT. Direct coupling of an automated 2-dimensional microcolumn affinity chromatographycapillary HPLC system with mass spectrometry for biomolecule nalysis. Tech Protein Chem 1995;VI:39-46.
  • 180 Gold MR, Yungwirth T, Sutherland CL, Ingham RJ, Vianzon D, Chiu R, van Oostveen I, Morrison HD, Aebersold R. Purification and identification of tyrosine-phosphorylated proteins from B lymphocytes stimulated through the antigen receptor. Electrophoresis 1994;15:441-453.
  • 181 Pandey A, Podtelejnikov AV, Blagoev B, Bustelo XR, Mann M, Lodish HF. Analysis of receptor signaling pathways by mass spectrometry: Identification of Vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. Proc Natl Acad Sci U S A 2000;97:179-184.
  • 182 Steen H, Kuster B, Fernandez M, Pandey A, Mann M. Tyrosine phosphorylation mapping of the epidermal growth factor receptor signaling pathway. JBiol Chem 2002;277:1031-1039.
  • 183 Ibarrola N, Kalume DE, Gronborg M, Iwahori A, Pandey A. A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Anal Chem 2003;75:6043-6049.
  • 184 Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 2004;22:1139-1145.
  • 185 Kruger M, Kratchmarova I, Blagoev B, Tseng YH, Kahn CR, Mann M. Dissection of the insulin signaling pathway via quantitative phosphoproteomics. Proc Natl Acad Sci U S A 2008;105:2451-2456.
  • 186 Boersema PJ, Foong LY, Ding VMY, Lemeer S, Van Breukelen B, Philp R, Boekhorst J, Snel B, Hertog JD, Choo ABH, Heck AJR. In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Mol Cell Proteomics 2010;9:84-99.
  • 187 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. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 2007;131:1190-1203.
  • 188 Villen J, Beausoleil SA, Gerber SA, Gygi SP. Large-scale phosphorylation analysis of mouse liver. Proc Natl Acad Sci U S A 2007;104:1488-1493.
  • 189 Kumar N, Wolf-Yadlin A, White FM, Lauffenburger DA. Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput Biol 2007;3:e4.
  • 190 Grunborg M, Kristiansen TZ, Stensballe A, Andersen JS, Ohara O, Mann M, Jensen ON, Pandey A. 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 2002;1:517-527.
  • 191 Zhang H, Zha X, Tan Y, Hornbeck PV, Mastrangelo AJ, Alessi DR, Polakiewicz RD, Comb MJ. Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs. J Biol Chem 2002;277:39379-39387.
  • 192 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. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007;316:1160-1166.
  • 193 Andersson L, Porath J. Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal Biochem 1986;154:250-254.
  • 194 Neville DCA, Rozanas CR, Price EM, Gruis DB, Verkman AS, Townsend RR. Evidence for phosphorylation of serine 753 in CFTR using a novel metal- ion affinity resin and matrix-assisted laser desorption mass spectrometry.

Protein Sci 1997;6:2436-2445.

  • 195 Posewitz MC, Tempst P. Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal Chem 1999;71:2883-2892.
  • 196 Kokubu M, Ishihama Y, Sato T, Nagasu T, Oda Y. Specificity of immobilized metal affinity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis. Anal Chem 2005;77:5144-5154.
  • 197 Tsai CF, Wang YT, Chen YR, Lai CY, Iin PY, Pan KT, Chen JY, Khoo KH,

Chen YJ. Immobilized metal affinity chromatography revisited: PH/acid control toward high selectivity in phosphoproteomics. J Proteome Res 2008;7:4058-4069.

  • 198 Ye J, Zhang X, Young C, Zhao X, Hao Q, Cheng L, Jensen ON. Optimized IMAC-IMAC protocol for phosphopeptide recovery from complex biological samples. J Proteome Res 2010;9:3561-3573.
  • 199 Jensen SS, Larsen MR. Evaluation of the impact of some experimental procedures on different phosphopeptide enrichment techniques. Rapid Commun Mass Spectrom 2007;21:3635-3645.
  • 200 McNulty DE, Annan RS. Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection. Mol Cell Proteomics 2008;7:971-980.
  • 201 Thingholm TE, Jensen ON, Robinson PJ, Larsen MR. SIMAC (Sequential Elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics 2008;7:661-671.
  • 202 Zhou H, Ye M, Dong J, Han G, Jiang X, Wu R, Zou H. Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis. J Proteome Res 2008;7:3957-3967.
  • 203 Yu Z, Han G, Sun S, Jiang X, Chen R, Wang F, Wu R, Ye M, Zou H. Preparation of monodisperse immobilized Ti4+ affinity chromatography microspheres for specific enrichment of phosphopeptides. Anal Chim Acta 2009;636:34-41.
  • 204 Zhou H, Ye M, Dong J, Corradini E, Cristobal A, Heck AJR, Zou H, Mohammed S. Robust phosphoproteome enrichment using monodisperse microsphere-based immobilized titanium(IV) ion affinity chromatography. Nat Protoc 2013;8:461-480.
  • 205 Matheron L, Van Den Toorn H, Heck AJR, Mohammed S. Characterization of biases in phosphopeptide enrichment by Ti-immobilized metal affinity chromatography and TiO2 using a massive synthetic library and human cell digests. Anal Chem 2014;86:8312-8320.
  • 206 Pinkse MWH, Uitto PM, Hilhorst MJ, Ooms B, Heck AJR. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem 2004;76:3935-3943.
  • 207 Kuroda I, Shintani Y, Motokawa M, Abe S, Furuno M. Phosphopeptide- selective column-switching RP-HPLC with a titania precolumn. Anal Sci 2004;20:1313-1319.
  • 208 Sano A, Nakamura H. Titania as a chemo-affinity support for the columnswitching HPLC analysis of phosphopeptides: Application to the characterization of phosphorylation sites in proteins by combination with protease digestion and electrospray ionization mass spectrometry. Anal Sci 2004;20:861-864.
  • 209 Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jorgensen TJD.

Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics 2005;4:873-886.

  • 210 Thingholm TE, Jorgensen TJD, Jensen OL, Larsen MR. Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc 2006;1:1929-1935.
  • 211 Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y. Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Mol Cell Proteomics 2007;6:1103-1109.
  • 212 Wilson-Grady JT, Haas W, Gygi SP. Quantitative comparison of the fasted and re-fed mouse liver phosphoproteomes using lower pH reductive dimethylation. Methods 2013;61:277-286.
  • 213 Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R.

Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods 2007;4:231-237.

  • 214 Lai ACY, Tsai CF, Hsu CC, Sun YN, Chen YJ. Complementary Fe3+- and Ti4+-immobilized metal ion affinity chromatography for purification of acidic and basic phosphopeptides. Rapid Commun Mass Spectrom 2012;26:2186-2194.
  • 215 Tsai CF, Hsu CC, Hung JN, Wang YT, Choong WK, Zeng MY, Lin PY, Hong RW, Sung TY, Chen YJ. Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography. Anal Chem 2014;86:685-693.
  • 216 Zhou H, Low TY, Hennrich ML, van der Toorn H, Schwend T, Zou H, Mohammed S, Heck AJ. Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti(IV) based IMAC enrichment. Mol Cell Proteomics 2011;10:M110.
  • 217 Ruprecht B, Koch H, Medard G, Mundt M, Kuster B, Lemeer S. Comprehensive and reproducible phosphopeptide enrichment using iron immobilized metal ion affinity chromatography (Fe-IMAC) columns. Mol Cell Proteomics 2015;14:205-215.
  • 218 Oda Y, Nagasu T, Chait BT. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol 2001;19:379-382.
  • 219 Goshe MB, Conrads TP, Panisko EA, Angell NH, Veenstra TD, Smith RD. Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal Chem 2001;73:2578-2586.
  • 220 McLachlin DT, Chait BT. Improved beta elimination-based affinity purification strategy for enrichment of phosphopeptides. Anal Chem 2003;75:6826-6836.
  • 221 Zhou H, Watts JD, Aebersold R. A systematic approach to the analysis of protein phosphorylation. Nat Biotechnol 2001;19:375-378.
  • 222 Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts JD, Hood L, Aebersold R. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods 2005;2:591-598.
  • 223 Nuhse TS, Stensballe A, Jensen ON, Peck SC. Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics 2003;2:1234-1243.
  • 224 Washburn MP, Wolters D, Yates JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001;19:242-247.
  • 225 Wolters DA, Washburn MP, Yates JR III. An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 2001;73:5683-5690.
  • 226 Pinkse MWH, Mohammed S, Gouw JW, Van Breukelen B, Vos HR, Heck AJR. Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster. J Proteome Res 2008;7:687-697.
  • 227 Goldberg RN, Kishore N, Lennen RM. Thermodynamic quantities for the ionization reactions of buffers. J Phys Chem Ref Data 2002;31:231-370.
  • 228 Alpert AJ. Hydrophilic-interaction chromatography for the separation of peptides, nucleic acids and other polar compounds. J Chromatogr A 1990;499:177-196.
  • 229 Gilar M, Olivova P, Daly AE, Gebler JC. Orthogonality of separation in two-dimensional liquid chromatography. Anal Chem 2005;77:6426-6434.
  • 230 Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal 2010;3:ra3.
  • 231 Han G, Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J. Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography. Proteomics 2008;8:1346-1361.
  • 232 Dai J, Wang LS, Wu YB, Sheng QH, Wu JR, Shieh CH, Zeng R. Fully automatic separation and identification of phosphopeptides by continuous pH-gradient anion exchange online coupled with reversed-phase liquid chromatography mass spectrometry. JProteome Res 2009;8:133-141.
  • 233 Nie S, Dai J, Ning ZB, Cao XJ, Sheng QH, Zeng R. Comprehensive profiling of phosphopeptides based on anion exchange followed by flow-through enrichment with titanium dioxide (AFET). J Proteome Res 2010;9:4585-4594.
  • 234 Ficarro SB, Zhang Y, Carrasco-Alfonso MJ, Garg B, Adelmant G, Webber JT, Luckey CJ, Marto JA. Online nanoflow multidimensional fractionation for high efficiency phosphopeptide analysis. Mol Cell Proteomics 2011;10:6996-7005.
  • 235 Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics 2008;7:1389-1396.
  • 236 Engholm-Keller K, Birck P, Storling J, Pociot F, Mandrup-Poulsen T, Larsen MR. TiSH - a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC. J Proteomics 2012;75:5749-5761.
  • 237 Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJR, Mohammed S. Toward a comprehensive characterization of a human cancer cell phosphoproteome. J Proteome Res 2013;12:260-271.
  • 238 Alpert AJ. Electrostatic repulsion hydrophilic interaction chromatography for isocratic separation of charged solutes and selective isolation of phosphopeptides. Anal Chem 2008;80:62-76.
  • 239 Alpert AJ, Hudecz O, Mechtler K. Anion-exchange chromatography of phosphopeptides: Weak anion exchange versus strong anion exchange and anion-exchange chromatography versus electrostatic repulsion-hydrophilic interaction chromatography. Anal Chem 2015;87:4704-4711.
  • 240 Bennetzen MV, Larsen DH, Bunkenborg J, Bartek J, Lukas J, Andersen JS. Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response. Mol Cell Proteomics 2010;9:1314-1323.
  • 241 Gan CS, Guo T, Zhang H, Lim SK, Sze SK. A comparative study of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) versus SCX-IMAC-based methods for phosphopeptide isolation/enrichment. J Proteome Res 2008;7:4869-4877.
  • 242 Hao P, Guo T, Sze SK. Simultaneous analysis of proteome, phospho- and glycoproteome of rat kidney tissue with electrostatic repulsion hydrophilic interaction chromatography. PLoS One 2011;6:E16884.
  • 243 Gilar M, Olivova P, Daly AE, Gebler JC. Two-dimensional separation of peptides using RP-RP-HPLC system with different pH in first and second separation dimensions. JSep Sci 2005;28:1694-1703.
  • 244 Song C, Ye M, Han G, Jiang X, Wang F, Yu Z, Chen R, Zou H. Reversed- phase-reversed-phase liquid chromatography approach with high orthogonality for multidimensional separation of phosphopeptides. Anal Chem 2010;82:53-56.
  • 245 Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999;20:3551-3567.
  • 246 Eng JK, McCormack AL, Yates JR. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.

J Am Soc Mass Spectrom 1994;5:976-989.

  • 247 Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large- scale protein identifications by mass spectrometry. Nat Methods 2007;4:207-214.
  • 248 Chalkley RJ, Clauser KR. Modification site localization scoring: Strategies and performance. Mol Cell Proteomics 2012;11:3-14.
  • 249 Lee DC, Jones AR, Hubbard SJ. Computational phosphoproteomics: From identification to localization. Proteomics 2015;15:950-963.
  • 250 Baker PR, Trinidad JC, Chalkley RJ. Modification site localization scoring integrated into a search engine. Mol Cell Proteomics 2011; 10:

M111.

  • 251 Taus T, Kocher T, Pichler P, Paschke C, Schmidt A, Henrich C, Mechtler K. Universal and confident phosphorylation site localization using phosphoRS. JProteome Res 2011;10:5354-5362.
  • 252 Fermin D, Avtonomov D, Choi H, Nesvizhskii AI. LuciPHOr2: Site localization of generic post-translational modifications from tandem mass spectrometry data. Bioinformatics 2015;31:1141-1143.
  • 253 Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. LuciPHOr: Algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics 2013;12:3409-3419.
  • 254 Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol 2006;24:1285-1292.
  • 255 Wan Y, Cripps D, Thomas S, Campbell P, Ambulos N, Chen T, Yang A. PhosphoScan: A probability-based method for phosphorylation site prediction using MS2/MS3 pair information. J Proteome Res 2008;7:2803-2811.
  • 256 Ruttenberg BE, Pisitkun T, Knepper MA, Hoffert JD. PhosphoScore: An open-source phosphorylation site assignment tool for MSn data. J Proteome Res 2008;7:3054-3059.
  • 257 Saeed F, Pisitkun T, Hoffert JD, Rashidian S, Wang G, Gucek M, Knepper MA. PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data. Proteome Sci. 2013;11:S14.
  • 258 Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B. Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics 2011;10:Mn0.
  • 259 Bailey CM, Sweet SM, Cunningham DL, Zeller M, Heath JK, Cooper HJ. SLoMo: Automated site localization of modifications from ETD/ECD mass spectra. JProteome Res 2009;8:1965-1971.
  • 260 Vaudel M, Breiter D, Beck F, Rahnenfuhrer J, Martens L, Zahedi RP. D-score: A search engine independent MD-score. Proteomics 2013;13:1036-1041.
  • 261 Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008;26:1367-1372.
  • 262 Nesvizhskii AI. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.

J Proteomics 2010;73:2092-2123.

  • 263 Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: A database of phosphorylation sites--update 2011. Nucleic Acids Res 2011;39:D261-D267.
  • 264 Goel R, Harsha HC, Pandey A, Prasad TS. Human protein reference database and human proteinpedia as resources for phosphoproteome analysis. Mol Biosyst 2012;8:453-463.
  • 265 Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human protein reference database--2009 update. Nucleic Acids Res 2009;37:D767-D772.
  • 266 Durek P, Schmidt R, Heazlewood JL, Jones A, MacLean D, Nagel A, Kersten B, Schulze WX. PhosPhAt: The Arabidopsis thaliana phosphorylation site databaseAn update. Nucleic Acids Res 2010;38:D828-D834.
  • 267 Bodenmiller B, Campbell D, Gerrits B, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R. PhosphoPep--a database of protein phosphorylation sites in model organisms. Nat Biotechnol 2008;26:1339-1340.
  • 268 Bateman A, Martin MJ, O'Donovan C, Magrane M, Apweiler R, Alpi E, Antunes R, Arganiska J, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, Chavali G, Cibrian-Uhalte E, Silva AD, De Giorgi M, Dogan T, Fazzini F,

Gane P, Castro LG, Garmiri P, Hatton-Ellis E, Hieta R, Huntley R, Legge D, Liu W, Luo J, MacDougall A, Mutowo P, Nightingale A, Orchard S, Pichler K, Poggioli D, Pundir S, Pureza L, Qi G, Rosanoff S, Saidi R, Sawford T,

Shypitsyna A, Turner E, Volynkin V, Wardell T, Watkins X, Zellner H,

Cowley A, Figueira L, Li W, McWilliam H, Lopez R, Xenarios I,

Bougueleret L, Bridge A, Poux S, Redaschi N, Aimo L, Argoud-Puy G, Auchincloss A, Axelsen K, Bansal P, Baratin D, Blatter MC, Boeckmann B, Bolleman J, Boutet E, Breuza L, Casal-Casas C, de Castro E, Coudert E, Cuche B, Doche M, Dornevil D, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz- Gumowski N, Hinz U, Hulo C, Jungo F, Keller G, Lara V, Lemercier P, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto T, Nouspikel N, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M,

Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey AL, Wu CH, Arighi CN, Arminski L, Chen C, Chen Y, Garavelli JS, Huang H, Laiho K, McGarvey P, Natale DA, Suzek BE, Vinayaka C, Wang Q, Wang Y, Yeh LS, Yerramalla MS, Zhang J. UniProt: A hub for protein information. Nucleic Acids Res 2015;43:D204-D212.

  • 269 Gnad F, Gunawardena J, Mann M. PHOSIDA 2011: The post-translational modification database. Nucleic Acids Res 2011;39:D253-D260.
  • 270 Li J, Jia J, Li H, Yu J, Sun H, He Y, Lv D, Yang X, Glocker MO, Ma L, Yang J,

Li L, Li W, Zhang G, Liu Q, Li Y, Xie L. SysPTM 2.0: An updated systematic resource for post-translational modification. Database 2014;2014:bau025.

  • 271 Lu CT, Huang KY, Su MG, Lee TY, Bretana NA, Chang WC, Chen YJ, Chen YJ, Huang HD. DbPTM 3.0: An informative resource for investigating substrate site specificity and functional association of protein posttranslational modifications. Nucleic Acids Res 2013;41:D295-D305.
  • 272 Liu Z, Wang Y, Xue Y. Phosphoproteomics-based network medicine. FEBSJ 2013;280:5696-5704.
  • 273 Mi H, Muruganujan A, Thomas PD. PANTHER in 2013: Modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 2013;41:D377-D386.
  • 274 Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012;40:D109-D114.
  • 275 Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2015;43:D447-D452.
  • 276 Obenauer JC, Cantley LC, Yaffe MB. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 2003;31:3635-3641.
  • 277 Xue Y, Ren J, Gao X, Jin C, Wen L, Yao X. GPS 2.0, a tool to predict kinase- specific phosphorylation sites in hierarchy. Mol Cell Proteomics 2008;7:1598-1608.
  • 278 Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 2004;4:1633-1649.
  • 279 binding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T. NetworKIN: A resource for exploring cellular phosphorylation networks. Nucleic Acids Res 2008;36:D695-D699.
  • 280 Horn H, Schoof EM, Kim J, Robin X, Miller ML, Diella F, Palma A,

Cesareni G, Jensen LJ, Linding R. KinomeXplorer: An integrated platform for kinome biology studies. Nat Methods 2014;11:603-604.

  • 281 Song C, Ye M, Liu Z, Cheng H, Jiang X, Han G, Songyang Z, Tan Y, Wang H, Ren J, Xue Y, Zou H. Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Mol Cell Proteomics 2012;11:1070-1083.
  • 282 Petsalaki E, Helbig AO, Gopal A, Pasculescu A, Roth FP, Pawson T. SELPHI: Correlation-based identification of kinase-associated networks from global phospho-proteomics data sets. Nucleic Acids Res 2015;43(W1):W276-W282.
  • 283 Reimand J, Wagih O, Bader GD. The mutational landscape of phosphorylation signaling in cancer. Sci Rep 2013;3:2651.
  • 284 Balbin OA, Prensner JR, Sahu A, Yocum A, Shankar S, Malik R, Fermin D, Dhanasekaran SM, Chandler B, Thomas D, Beer DG, Cao X, Nesvizhskii AI, Chinnaiyan AM. Reconstructing targetable pathways in lung cancer by integrating diverse omics data. Nat Commun 2013;4:2617.
 
Source
Found a mistake? Please highlight the word and press Shift + Enter  
< Prev   CONTENTS   Next >
 
Subjects
Accounting
Business & Finance
Communication
Computer Science
Economics
Education
Engineering
Environment
Geography
Health
History
Language & Literature
Law
Management
Marketing
Mathematics
Political science
Philosophy
Psychology
Religion
Sociology
Travel