References

• Abdallah C, Dumas-Gaudot E, Renaut J, Sergeant K. Gel-based and gel-free quantitative proteomics approaches at a glance. Int J Plant Genomics. 2012;2012:494572. google scholar
• Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature. 2003;422(6928):198-207. google scholar
• Aebersold R, Mann M. Mass-spectrometric exploration of proteome structure and func-tion. Nature. 2016 Sep 15;537(7620):347-55. google scholar
• Aryal UK, Ross AR. Enrichment and analysis of phosphopeptides under different expe-rimental conditions using titanium dioxide affinity chromatography and mass spectro-metry. Rapid Commun Mass Spectrom. 2010;24(2):219-31. google scholar
• Bantscheff M, Lemeer S, Savitski MM, Kuster B. Quantitative mass spectrometry in pro-teomics: critical review update from 2007 to the present. Anal Bioanal Chem. 2012;404(4):939-65. google scholar
• Batth TS, Olsen JV. Offline High pH Reversed-Phase Peptide Fractionation for Deep Phosphoproteome Coverage. Methods Mol Biol. 2016;1355:179-92. google scholar
• Beltran L, Cutillas PR. Advances in phosphopeptide enrichment techniques for phosphop-roteomics. Amino Acids. 2012;43(3):1009-24. google scholar
• Blacken GR, Volný M, Diener M, Jackson KE, Ranjitkar P, Maly DJ, Turecek F. Reactive landing of gas-phase ions as a tool for the fabrication of metal oxide surfaces for in situ phosphopeptide enrichment. J Am Soc Mass Spectrom. 2009;20(6):915-26. google scholar
• Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ. In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity puri-fication and stable isotope dimethyl labeling. Mol Cell Proteomics. 2010;9(1):84-99. google scholar
• Boersema PJ, Mohammed S, Heck AJ. Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal Bioanal Chem. 2008;391(1):151-9. google scholar
• Caprioli RM, Farmer TB, Gile J. Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. Anal Chem. 1997;69(23):4751-60. google scholar
• Carruthers NJ, Rosenspire AJ, Caruso JA, Stemmer PM. Low level Hg(2+) exposure mo-dulates the B-cell cytoskeletal phosphoproteome. J Proteomics. 2018;173:107-114. google scholar
• Carson RH, Lewis CR, Erickson MN, Zagieboylo AP, Naylor BC, Li KW, Farnsworth PB, Price JC. Imaging regiospecific lipid turnover in mouse brain with desorption elect-rospray ionization mass spectrometry. J Lipid Res. 2017;58(9):1884-1892. google scholar
• Chen H, Talaty NN, Takáts Z, Cooks RG. Desorption electrospray ionization mass spect-rometry for high-throughput analysis of pharmaceutical samples in the ambient environ-ment. Anal Chem. 2005;77(21):6915-27. google scholar
• Chen SY, Juang YM, Chien MW, Li KI, Yu CS, Lai CC. Magnetic iron oxide nanopartic-le enrichment of phosphopeptides on a radiate microstructure MALDI chip. Analyst. 2011;136(21):4454-9. google scholar
• Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics. 2015;15(18):3175-92. google scholar
• Choudhary C, Mann M. Decoding signalling networks by mass spectrometry-based prote-omics. Nat Rev Mol Cell Biol. 2010;11(6):427-39. google scholar
• Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Sha-movsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014;42 (Database issue):D472-7. google scholar
• de Hoog CL, Mann M. Proteomics. Annu Rev Genomics Hum Genet. 2004;5:267-93. Drabovich Andrei P., et al. "Proteomic and mass spectrometry technologies for biomarker discovery." Proteomic and metabolomic approaches to biomarker discovery 2013; 17-37. google scholar
• Dunn JD, Reid GE, Bruening ML. Techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Mass Spectrom Rev. 2010 Jan-Feb;29(1):29-54. google scholar
• Dyballa N, Metzger S. Fast and sensitive coomassie staining in quantitative proteomics. Methods Mol Biol. 2012;893:47-59. google scholar
• Edelmann MJ. Strong cation exchange chromatography in analysis of posttranslational modifications: innovations and perspectives. J Biomed Biotechnol. 2011;2011:936508. google scholar
• Espina V, Edmiston KH, Heiby M, Pierobon M, Sciro M, Merritt B, Banks S, Deng J, VanMeter AJ, Geho DH, Pastore L, Sennesh J, Petricoin EF 3rd, Liotta LA. A portrait of tissue phosphoprotein stability in the clinical tissue procurement process. Mol Cell Proteomics. 2008;7(10):1998-2018. google scholar
• Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM. Electrospray ionization for mass spectrometry of large biomolecules. Science. 1989;246(4926):64-71. google scholar
• Fredens J, Færgeman NJ. Quantitative proteomics by amino acid labeling identifies novel NHR-49 regulated proteins in C. elegans. Worm. 2012;1(1):66-71. google scholar
• Geiger T, Velic A, Macek B, Lundberg E, Kampf C, Nagaraj N, Uhlen M, Cox J, Mann M. Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse. Mol Cell Proteomics. 2013;12(6):1709-22. google scholar
• Gouw JW, Krijgsveld J, Heck AJ. Quantitative proteomics by metabolic labeling of model organisms. Mol Cell Proteomics. 2010;9(1):11-24. google scholar
• Grandjean M, Sermeus A, Branders S, Defresne F, Dieu M, Dupont P, Raes M, De Ridder M, Feron O. Hypoxia integration in the serological proteome analysis unmasks tumor antigens and fosters the identification of anti-phospho-eEF2 antibodies as potential cancer biomarkers. PLoS One. 2013;8(10):e76508. google scholar
• Han C, Yang P. Two Dimensional Gel Electrophoresis-Based Plant Phosphoproteomics. Methods Mol Biol. 2016;1355:213-23. google scholar
• 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(7):1346-61. google scholar
• Harsha HC, Pandey A. Phosphoproteomics in cancer. Mol Oncol. 2010 Dec;4(6):482-95. Harsha HC, Pinto SM, Pandey A. Proteomic strategies to characterize signaling pathways. Methods Mol Biol. 2013;1007:359-77. google scholar
• Herring LE, Grant KG, Blackburn K, Haugh JM, Goshe MB. Development of a tandem affinity phosphoproteomic method with motif selectivity and its application in analysis of signal transduction networks. J Chromatogr B Analyt Technol Biomed Life Sci. 2015;988:166-74. google scholar
• Ho CS, Lam CW, Chan MH, Cheung RC, Law LK, Lit LC, Ng KF, Suen MW, Tai HL. Electrospray ionisation mass spectrometry: principles and clinical applications. Clin Bioc-hem Rev. 2003;24(1):3-12. google scholar
• Honarvar E, Venter AR. Ammonium Bicarbonate Addition Improves the Detection of Proteins by Desorption Electrospray Ionization Mass Spectrometry. J Am Soc Mass Spectrom. 2017;28(6):1109-1117. google scholar
• Hoos MD, Richardson BM, Foster MW, Everhart A, Thompson JW, Moseley MA, Colton CA. Longitudinal study of differential protein expression in an Alzheimer's Mouse model lacking inducible nitric oxide synthase. J Proteome Res. 2013;12(10):4462-77. google scholar
• Iliuk A, Jayasundera K, Schluttenhofer R, Tao WA. Functionalized soluble nanopolymers for phosphoproteome analysis. Methods Mol Biol. 2011;790:277-85. google scholar
• International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931-45. google scholar
• Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics. 2005;4(9):1265-72. google scholar
• Jersie-Christensen RR, Sultan A, Olsen JV. Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity. Methods Mol Biol. 2016;1355:251-60. google scholar
• Jiang J, Sun X, Li Y, Deng C, Duan G. Facile synthesis of Fe(3)O(4)@PDA core-shell microspheres functionalized with various metal ions: A systematic comparison of com-monly-used metal ions for IMAC enrichment. Talanta. 2018;178:600-607. google scholar
• Jünger MA, Aebersold R. Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic. Wiley Interdiscip Rev Dev Biol. 2014;3(1):83-112. google scholar
• Kanshin E, Giguère S, Jing C, Tyers M, Thibault P. Machine Learning of Global Phosp-hoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates. Mol Cell Proteomics. 2017;16(5):786-798. google scholar
• Karas M, Krüger R. Ion formation in MALDI: the cluster ionization mechanism. Chem Rev. 2003;103(2):427-40. google scholar
• Kinoshita-Kikuta E, Kinoshita E, Koike T. Phosphopeptide Detection with Biotin-Labeled Phos-tag. Methods Mol Biol. 2016;1355:17-29. google scholar
• Kisluk J, Ciborowski M, Niemira M, Kretowski A, Niklinski J. Proteomics biomarkers for non-small cell lung cancer. J Pharm Biomed Anal. 2014;101:40-9. google scholar
• Kuyama H, Sonomura K, Nishimura O. Sensitive detection of phosphopeptides by matrix-assisted laser desorption/ionization mass spectrometry: use of alkylphosphonic acids as matrix additives. Rapid Commun Mass Spectrom. 2008;22(8):1109-16. google scholar
• Larsen MR, Thingholm TE, Jensen ON, Roepstorff P, Jørgensen TJ. Highly selective en-richment of phosphorylated peptides from peptide mixtures using titanium dioxide micro-columns. Mol Cell Proteomics. 2005;4(7):873-86. google scholar
• Leitner A. Enrichment Strategies in Phosphoproteomics. Methods Mol Biol. 2016;1355:105-21. Li L, Wei Y, To C, Zhu CQ, Tong J, Pham NA, Taylor P, Ignatchenko V, Ignatchenko A, Zhang W, Wang D, Yanagawa N, Li M, Pintilie M, Liu G, Muthuswamy L, Shepherd FA, Tsao MS, Kislinger T, Moran MF. Integrated omic analysis of lung cancer reveals meta-bolism proteome signatures with prognostic impact. Nat Commun. 2014;5:5469. google scholar
• Li R, Liao G, Nirujogi RS, Pinto SM, Shaw PG, Huang TC, Wan J, Qian J, Gowda H, Wu X, Lv DW, Zhang K, Manda SS, Pandey A, Hayward SD. Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling. PLoS Pathog. 2015;11(12):e1005346. google scholar
• Macek B, Mann M, Olsen JV. Global and site-specific quantitative phosphoproteomics: principles and applications. Annu Rev Pharmacol Toxicol. 2009;49:199-221. google scholar
• Mann M, Hendrickson RC, Pandey A. Analysis of proteins and proteomes by mass spect-rometry. Annu Rev Biochem. 2001;70:437-73. google scholar
• Martins-de-Souza, Daniel. "Shotgun Proteomics." Methods in Molecular Biology 1156 (2014).May C, Brosseron F, Chartowski P, Meyer HE, Marcus K. Differential proteome analysis using 2D-DIGE. Methods Mol Biol. 2012;893:75-82. google scholar
• May C, Brosseron F, Pfeiffer K, Meyer HE, Marcus K. Proteome analysis with classical 2D-PAGE. Methods Mol Biol. 2012;893:37-46. google scholar
• McLachlin DT, Chait BT. Improved beta-elimination-based affinity purification strategy for enrichment of phosphopeptides. Anal Chem. 2003;75(24):6826-36. google scholar
• Nardiello D, Palermo C, Natale A, Quinto M, Centonze D. Strategies in protein sequen-cing and characterization: multi-enzyme digestion coupled with alternate CID/ETD tan-dem mass spectrometry. Anal Chim Acta. 2015;854:106-17. google scholar
• Negroni L, Claverol S, Rosenbaum J, Chevet E, Bonneu M, Schmitter JM. Comparison of IMAC and MOAC for phosphopeptide enrichment by column chromatography. J Chroma-togr B Analyt Technol Biomed Life Sci. 2012;891-892:109-12. google scholar
• Nolte H, Hölper S, Housley MP, Islam S, Piller T, Konzer A, Stainier DY, Braun T, Krü-ger M. Dynamics of zebrafish fin regeneration using a pulsed SILAC approach. Proteo-mics. 2015;15(4):739-51. google scholar
• Olsen JV, Macek B, Lange O, Makarov A, Horning S, Mann M. Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods. 2007;4(9):709-12. google scholar
• 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(5):376-86. google scholar
• Ong SE, Mann M. Mass spectrometry-based proteomics turns quantitative. Nat Chem Biol. 2005;1(5):252-62. google scholar
• Pan N, Liu P, Cui W, Tang B, Shi J, Chen H. Highly efficient ionization of phosphopepti-des at low pH by desorption electrospray ionization mass spectrometry. Analyst. 2013;138(5):1321-1324. google scholar
• Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR. Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines. J Proteomics.2015;127(Pt B):247-58. google scholar
• Premsler T, Lewandrowski U, Sickmann A, Zahedi RP. Phosphoproteome analysis of the platelet plasma membrane. Methods Mol Biol. 2011;728:279-90. google scholar
• Qi Y, Volmer DA. Electron-based fragmentation methods in mass spectrometry: An over-view. Mass Spectrom Rev. 2017;36(1):4-15. google scholar
• Ram PT, Mendelsohn J, Mills GB. Bioinformatics and systems biology. Mol Oncol. 2012;6(2):147-54. google scholar
• Ravikumar V, Macek B, Mijakovic I. Resources for Assignment of Phosphorylation Sites on Peptides and Proteins. Methods Mol Biol. 2016;1355:293-306. google scholar
• Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS. Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas. Am J Pathol. 2014;184(5):1331-42. google scholar
• Rothenberg DA, Gordon EA, White FM, Lourido S. Identification of Direct Kinase Substrates Using Analogue-Sensitive Alleles. Methods Mol Biol. 2016;1355:71-84. google scholar
• Ruprecht B, Koch H, Medard G, Mundt M, Kuster B, Lemeer S. Comprehensive and rep-roducible phosphopeptide enrichment using iron immobilized metal ion affinity chroma-tography (Fe-IMAC) columns. Mol Cell Proteomics. 2015;14(1):205-15. google scholar
• 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(1):94-101. google scholar
• Shenoy A, Geiger T. Super-SILAC: current trends and future perspectives. Expert Rev Proteomics. 2015;12(1):13-9. google scholar
• Shukla HD, Vaitiekunas P, Cotter RJ. Advances in membrane proteomics and cancer biomarker discovery: current status and future perspective. Proteomics. 2012;12(19-20):3085-104. google scholar
• Silberring, J, A. Drabik. Proteomic Profiling and Analytical Chemistry: The Crossroads (2016): 145.Silva AM, Vitorino R, Domingues MR, Spickett CM, Domingues P. Post-translational modifications and mass spectrometry detection. Free Radic Biol Med. 2013;65:925-41. google scholar
• Song L, Wang F, Dong Z, Hua X, Xia Q. Label-free quantitative phosphoproteomic profi-ling of cellular response induced by an insect cytokine paralytic peptide. J Proteomics. 2017;154:49-58. Stensballe A, Jensen ON. Phosphoric acid enhances the performance of Fe(III) affinity chromatography and matrix-assisted laser desorption/ionization tandem mass spectrometry for recovery, detection and sequencing of phosphopeptides. Rapid Commun Mass Spectrom. 2004;18(15):1721-30. google scholar
• Sury MD, Chen JX, Selbach M. In vivo stable isotope labeling by amino acids in Drosop-hila melanogaster. Methods Mol Biol. 2014;1188:85-93. google scholar
• Thaler F, Valsasina B, Baldi R, Xie J, Stewart A, Isacchi A, Kalisz HM, Rusconi L. A new approach to phosphoserine and phosphothreonine analysis in peptides and proteins: chemical modification, enrichment via solid-phase reversible binding, and analysis by mass spectrometry. Anal Bioanal Chem. 2003;376(3):366-73. google scholar
• Thingholm TE, Jensen ON, Larsen MR. Analytical strategies for phosphoproteomics. Pro-teomics. 2009;9(6):1451-68. google scholar
• 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(4):661-71. google scholar
• 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(1):685-93. google scholar
• Tsumoto H, Ra M, Samejima K, Taguchi R, Kohda K. 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. 2008;22(7):965-72. google scholar
• van der Mijn JC, Labots M, Piersma SR, Pham TV, Knol JC, Broxterman HJ, Verheul HM, Jiménez CR. Evaluation of different phospho-tyrosine antibodies for label-free phosphoproteomics. J Proteomics. 2015;127(Pt B):259-63. google scholar
• van der Wal Lennart, and Jeroen AA Demmers. "Quantitative Mass Spectrometry-based Proteomics." Recent Advances in Proteomics Research. InTech, 2015. google scholar
• Wan H, Yan J, Yu L, Zhang X, Xue X, Li X, Liang X. Zirconia layer coated mesoporous silica microspheres used for highly specific phosphopeptide enrichment. Talanta. 2010;82(5):1701-7. google scholar
• Wang G, Wu WW, Zeng W, Chou CL, Shen RF. Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes. J Proteome Res. 2006;5(5):1214-23 google scholar
• Wang J, Gao L, Lee YM, Kalesh KA, Ong YS, Lim J, Jee JE, Sun H, Lee SS, Hua ZC, Lin Q. Target identification of natural and traditional medicines with quantitative chemi-cal proteomics approaches. Pharmacol Ther. 2016;162:10-22. google scholar
• Wiśniewski JR. Filter-Aided Sample Preparation: The Versatile and Efficient Method for Proteomic Analysis. Methods Enzymol. 2017;585:15-27. google scholar
• Yu F, F. Qiu, and J. Meza. "Desıgn And Statistical Analysis Of Mass-Spectrometry-Based Quantitative Proteomics Data." Proteomic Profiling and Analytical Chemistry: The Cross-roads (2016): 211. google scholar
• Zahari MS, Wu X, Pinto SM, Nirujogi RS, Kim MS, Fetics B, Philip M, Barnes SR, Godfrey B, Gabrielson E, Nevo E, Pandey A. Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia. Sci Rep. 2015;5:13660. google scholar
• Zarei M, Sprenger A, Gretzmeier C, Dengjel J. Rapid combinatorial ERLIC-SCX solid-phase extraction for in-depth phosphoproteome analysis. J Proteome Res. 2013;12(12):5989-95. google scholar
• Zarei M, Sprenger A, Metzger F, Gretzmeier C, Dengjel J. Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches. J Proteome Res. 2011;10(8):3474-83. google scholar
• Zarei M, Sprenger A, Rackiewicz M, Dengjel J. Fast and easy phosphopeptide fractiona-tion by combinatorial ERLIC-SCX solid-phase extraction for in-depth phosphoproteome analysis. Nat Protoc. 2016;11(1):37-45. google scholar
• Zawadzka AM, Schilling B, Cusack MP, Sahu AK, Drake P, Fisher SJ, Benz CC, Gibson BW. Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma. Mol Cell Proteomics. 2014;13(4):1034-49. google scholar
• Zhang H, Xu Y, Filipovic A, Lit LC, Koo CY, Stebbing J, Giamas G. SILAC-based phosphoproteomics reveals an inhibitory role of KSR1 in p53 transcriptional activity via modulation of DBC1. Br J Cancer. 2013;109(10):2675-84. google scholar
• Zhang Y, Zhang Y, Yu Y. Global Phosphoproteomic Analysis of insulin/Akt/mTORC1/S6K Signaling in Rat Hepatocytes. J Proteome Res. 2017 4;16(8):2825-2835.Zhang Z, Wu S, Stenoien DL, Paša-Tolić L. High-throughput proteomics. Annu Rev Anal Chem (Palo Alto Calif). 2014;7:427-54. google scholar
• Zhao Z, Wu F, Ding S, Sun L, Liu Z, Ding K, Lu J. Label-free quantitative proteomic analysis reveals potential biomarkers and pathways in renal cell carcinoma. Tumour Biol. 2015;36(2):939-51. google scholar
• Zubarev RA. Electron-capture dissociation tandem mass spectrometry. Curr Opin Bio-technol. 2004;15(1):12-6. google scholar

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