1. Meier, F., Geyer, P. E., Virreira Winter, S., Cox, J. & Mann, M. BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes. Nat. Methods 15, 440–448 (2018).
2. Bekker-Jensen, D. B. et al. An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes. Cell Syst. 4, 587-599.e4 (2017).
3. Doll, S., Gnad, F. & Mann, M. The Case for Proteomics and Phospho‐ Proteomics in Personalized Cancer Medicine. PROTEOMICS – Clin. Appl. 13, 1800113 (2019).
4. Aebersold, R. et al. How many human proteoforms are there? Nat. Chem. Biol. 14, 206–214 (2018).
5. The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45, D158–D169 (2017).
6. Aken, B. L. et al. Ensembl 2017. Nucleic Acids Res. 45, D635–D642 (2017).
7. Gaudet, P. et al. The neXtProt knowledgebase on human proteins: 2017 update. Nucleic Acids Res. 45, D177–D182 (2017).
8. Pennisi, E. The Human Genome. Science (80-. ). 291, 1177–1180 (2001).
9. Uhlen, M. et al. Tissue-based map of the human proteome. Science (80-. ). 347, 1260419–1260419 (2015).
10. Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).
11. Olsen, J. V et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635–48 (2006).
12. Humphrey, S. J. et al. Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation. Trends Endocrinol. Metab. 26, 676–687 (2015).
13. Huovila, A.-P. J., Turner, A. J., Pelto-Huikko, M., Kärkkäinen, I. & Ortiz, R. M. Shedding light on ADAM metalloproteinases. Trends Biochem. Sci. 30, 413–422 (2005).
14. Lichtenthaler, S. F., Lemberg, M. K. & Fluhrer, R. Proteolytic ectodomain shedding of membrane proteins in mammals—hardware, concepts, and recent developments. EMBO J. 37, e99456 (2018).
15. Weinert, B. T., Moustafa, T., Iesmantavicius, V., Zechner, R. & Choudhary, C. Analysis of acetylation stoichiometry suggests that SIRT 3 repairs nonenzymatic acetylation lesions. EMBO J. 34, 2620–2632 (2015).
16. Wagner, G. R. & Payne, R. M. Widespread and enzyme-independent Nε-acetylation and Nε-succinylation of proteins in the chemical conditions of the mitochondrial matrix. J. Biol. Chem. 288, 29036–45 (2013).
17. Smith, L. M. & Kelleher, N. L. Proteoform: A single term describing protein complexity. Nature Methods 10, 186–187 (2013).
18. Garcia, B. A., Pesavento, J. J., Mizzen, C. A. & Kelleher, N. L. Pervasive combinatorial modification of histone H3 in human cells. Nat. Methods 4, 487– 489 (2007).
19. Olsen, J. V. & Mann, M. Status of large-scale analysis of posttranslational modifications by mass spectrometry. Molecular and Cellular Proteomics 12, 3444–3452 (2013).
20. Stenflo, J., Fernlund, P., Egan, W. & Roepstorff, P. Vitamin K dependent modifications of glutamic acid residues in prothrombin. Proc. Natl. Acad. Sci. U. S. A. 71, 2730–2733 (1974).
21. Tan, M. et al. Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. Cell Metab. 19, 605–617 (2014).
22. Zhang, Z. et al. Identification of lysine succinylation as a new post-translational modification. Nat. Chem. Biol. 7, 58–63 (2011).
23. Chen, Y. et al. Lysine propionylation and butyrylation are novel post- translational modifications in histones. Mol. Cell. Proteomics 6, 812–819 (2007).
24. Tan, M. et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146, 1016–1028 (2011).
25. Huang, H. et al. Lysine benzoylation is a histone mark regulated by SIRT2. Nat. Commun. 9, (2018).
26. Yugi, K. et al. Reconstruction of insulin signal flow from phosphoproteome and metabolome data. Cell Rep. 8, 1171–83 (2014).
27. Kawata, K. et al. Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks. iScience 7, 212–229 (2018).
28. Arrington, J. V., Hsu, C. C., Elder, S. G. & Andy Tao, W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 142, 4373– 4387 (2017).
29. Lundby, A. et al. Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns. Cell Rep. 2, 419–431 (2012).
30. Peng, C. et al. The first identification of lysine malonylation substrates and its regulatory enzyme. Mol. Cell. Proteomics 10, (2011).
31. Jiang, H. et al. SIRT6 regulates TNF-α secretion through hydrolysis of long- chain fatty acyl lysine. Nature 496, 110–113 (2013).
32. Zhang, Z.-Y., Dodd, G. T. & Tiganis, T. Protein Tyrosine Phosphatases in Hypothalamic Insulin and Leptin Signaling. Trends Pharmacol. Sci. 36, 661–674 (2015).
33. Alonso, A. et al. Protein tyrosine phosphatases in the human genome. Cell 117, 699–711 (2004).
34. Klaeger, S. et al. The target landscape of clinical kinase drugs. Science (80-. ).358, eaan4368 (2017).
35. Tong, J. et al. Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome, and tyrosine-phosphatome in acute myeloid leukemia. Proteomics 17, 1600361 (2017).
36. Weber, S. & Saftig, P. Ectodomain shedding and ADAMs in development. Development 139, 3693–3709 (2012).
37. Beard, H. A., Barniol-Xicota, M., Yang, J. & Verhelst, S. H. L. Discovery of cellular roles of intramembrane proteases. ACS Chem. Biol. 14, 2372–2388 (2019).
38. Reiss, K. & Saftig, P. The “A Disintegrin And Metalloprotease” (ADAM) family of sheddases: Physiological and cellular functions. Semin. Cell Dev. Biol. 20, 126–137 (2009).
39. Niedermaier, S. & Huesgen, P. F. Positional proteomics for identification of secreted proteoforms released by site-specific processing of membrane proteins. Biochim. Biophys. Acta - Proteins Proteomics 1867, 140138 (2019).
40. Chow, V. W., Mattson, M. P., Wong, P. C. & Gleichmann, M. An overview of APP processing enzymes and products. Neuromolecular medicine 12, 1–12 (2010).
41. Tsumagari, K. et al. Secretome analysis to elucidate metalloprotease-dependent ectodomain shedding of glycoproteins during neuronal differentiation. Genes to Cells 22, 237–244 (2017).
42. Kleifeld, O. et al. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat. Biotechnol. 28, 281–288 (2010).
43. Prudova, A., auf dem Keller, U., Butler, G. S. & Overall, C. M. Multiplex N- terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ- TAILS quantitative proteomics. Mol. Cell. Proteomics 9, 894–911 (2010).
44. Chang, C.-H., Chang, H.-Y., Rappsilber, J. & Ishihama, Y. Isolation of Acetylated and Unmodified Protein N-Terminal Peptides by Strong Cation Exchange Chromatographic Separation of TrypN-Digested Peptides. Mol. Cell. Proteomics 20, 100003 (2021).
45. Alpert, A. J. et al. Peptide orientation affects selectivity in ion-exchange chromatography. Anal. Chem. 82, 5253–9 (2010).
46. Helbig, A. O. et al. Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome. Mol. Cell. Proteomics 9, 928–939 (2010).
47. Gauci, S. et al. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal. Chem. 81, 4493– 4501 (2009).
48. Tyanova, S., Temu, T. & Cox, J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat. Protoc. 11, 2301–2319 (2016).
49. Takami, M. et al. γ-Secretase: Successive tripeptide and tetrapeptide release from the transmembrane domain of β-carboxyl terminal fragment. J. Neurosci. 29, 13042–13052 (2009).
50. Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
51. Nagano, O. & Saya, H. Mechanism and biological significance of CD44 cleavage. Cancer Science 95, 930–935 (2004).
52. Shirakabe, K., Hattori, S., Seiki, M., Koyasu, S. & Okada, Y. VIP36 protein is a target of ectodomain shedding and regulates phagocytosis in macrophage Raw 264.7 cells. J. Biol. Chem. 286, 43154–63 (2011).
53. Szklarczyk, D. et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607–D613 (2019).
54. Imamura, H. et al. Identifications of putative PKA substrates with quantitative phosphoproteomics and primary-sequence-based scoring. J. Proteome Res. 16, 1825–1830 (2017).
55. Tucher, J. et al. LC-MS based cleavage site profiling of the proteases ADAM10 and ADAM17 using proteome-derived peptide libraries. J. Proteome Res. 13, 2205–2214 (2014).
56. Eckhard, U. et al. Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses. Matrix Biol. 49, 37–60 (2016).
57. Seegar, T. C. M. et al. Structural basis for regulated proteolysis by the α- secretase ADAM10. Cell 171, 1638-1648.e7 (2017).
58. Seidah, N. G., Sadr, M. S., Chrétien, M. & Mbikay, M. The Multifaceted Proprotein Convertases: Their Unique, Redundant, Complementary, and Opposite Functions. J. Biol. Chem. 288, 21473–21481 (2013).
59. Manon-Jensen, T., Multhaupt, H. A. B. & Couchman, J. R. Mapping of matrix metalloproteinase cleavage sites on syndecan-1 and syndecan-4 ectodomains. FEBS J. 280, 2320–2331 (2013).
60. Soh, W. T. et al. ExteNDing Proteome Coverage with Legumain as a Highly Specific Digestion Protease. Anal. Chem. 92, 2961–2971 (2020).
61. Gooz, M. ADAM-17: the enzyme that does it all. Crit. Rev. Biochem. Mol. Biol. 45, 146–169 (2010).
62. Choudhary, C., Weinert, B. T., Nishida, Y., Verdin, E. & Mann, M. The growing landscape of lysine acetylation links metabolism and cell signalling. Nat. Rev. Mol. Cell Biol. 15, 536–550 (2014).
63. Choudhary, C. et al. Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions. Science (80-. ). 325, 834–840 (2009).
64. Jiang, T., Zhou, X., Taghizadeh, K., Dong, M. & Dedon, P. C. N-formylation of lysine in histone proteins as a secondary modification arising from oxidative DNA damage. Proc. Natl. Acad. Sci. 104, 60–65 (2007).
65. Hirschey, M. D. & Zhao, Y. Metabolic regulation by lysine malonylation, succinylation, and glutarylation. Mol. Cell. Proteomics 14, 2308–2315 (2015).
66. Narita, T., Weinert, B. T. & Choudhary, C. Functions and mechanisms of non- histone protein acetylation. Nat. Rev. Mol. Cell Biol. 1 (2018). doi:10.1038/s41580-018-0081-3
67. Brittain, S. M., Ficarro, S. B., Brock, A. & Peters, E. C. Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry. Nat. Biotechnol. 23, 463–468 (2005).
68. Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S. & Heck, A. J. R. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nat. Protoc. 4, 484–494 (2009).
69. Lemmon, M. A. & Schlessinger, J. Cell Signaling by Receptor Tyrosine Kinases. Cell 141, 1117–1134 (2010).
70. Lemeer, S., Zörgiebel, C., Ruprecht, B., Kohl, K. & Kuster, B. Comparing Immobilized Kinase Inhibitors and Covalent ATP Probes for Proteomic Profiling of Kinase Expression and Drug Selectivity. J. Proteome Res. 12, 1723– 1731 (2013).
71. Bantscheff, M. et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 25, 1035–1044 (2007).
72. Ranjitkar, P. et al. Affinity-Based Probes Based on Type II Kinase Inhibitors. J. Am. Chem. Soc. 134, 19017–19025 (2012).
73. Karisch, R. et al. Global Proteomic Assessment of the Classical Protein-Tyrosine Phosphatome and “Redoxome”. Cell 146, 826–840 (2011).
74. Burke, T. R. J. et al. Nonhydrolyzable Phosphotyrosyl Mimetics for the Preparation Of Phosphatase-Resistant SH2 Domain Inhibitors. Biochemistry 33, 6490–6494 (1994).
75. Chen, L. et al. Why Is Phosphonodifluoromethyl Phenylalanine a More Potent Inhibitory Moiety Than Phosphonomethyl Phenylalanine Toward Protein- Tyrosine Phosphatases. Biochem. Biophys. Res. Commun. 216, 976–984 (1995).
76. Meyer, C. et al. Development of accessible peptidic tool compounds to study the phosphatase PTP1B in intact cells. ACS Chem. Biol. 9, 769–776 (2014).
77. Meyer, C., Hoeger, B., Chatterjee, J. & Köhn, M. Azide-alkyne cycloaddition-mediated cyclization of phosphonopeptides and their evaluation as PTP1B binders and enrichment tools. Bioorganic Med. Chem. 23, 2848–2853 (2015).
78. Masuda, T., Saito, N., Tomita, M. & Ishihama, Y. Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol. Cell. Proteomics 8, 2770–7 (2009).
79. Tiganis, T. PTP1B and TCPTP - nonredundant phosphatases in insulin signaling and glucose homeostasis. FEBS J. 280, 445–458 (2013).
80. Valius, M., Bazenet, C. & Kazlauskas, A. Tyrosines 1021 and 1009 are phosphorylation sites in the carboxy terminus of the platelet-derived growth factor receptor beta subunit and are required for binding of phospholipase C gamma and a 64-kilodalton protein, respectively. Mol. Cell. Biol. 13, 133–43 (1993).
81. Jadwin, J. A., Curran, T. G., Lafontaine, A. T., White, F. M. & Mayer, B. J. Src homology 2 domains enhance tyrosine phosphorylation in vivo by protecting binding sites in their target proteins from dephosphorylation. J. Biol. Chem. 293, 623–637 (2018).
82. Lundby, A. et al. Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites. Cell 179, 543-560.e26 (2019).
83. Garton, A. J. & Tonks, N. K. PTP-PEST: a protein tyrosine phosphatase regulated by serine phosphorylation. EMBO J. 13, 3763–3771 (1994).
84. Wang, Y., Guo, W., Liang, L. & Esselman, W. J. Phosphorylation of CD45 by casein kinase 2. Modulation of activity and mutational analysis. J. Biol. Chem. 274, 7454–61 (1999).
85. Burke, T. R. et al. Cyclic Peptide Inhibitors of Phosphatidylinositol 3-Kinase p85 SH2 Domain Binding. Biochem. Biophys. Res. Commun. 201, 1148–1153 (1994).
86. Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896–1906 (2007).
87. Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nature Methods 13, 731–740 (2016).
88. Eisenberg, E. & Levanon, E. Y. Human housekeeping genes are compact. Trends Genet. 19, 362–365 (2003).
89. Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).
90. Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M. & Gilad, Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509–17 (2008).
91. Colaert, N., Helsens, K., Martens, L., Vandekerckhove, J. & Gevaert, K. Improved visualization of protein consensus sequences by iceLogo. Nature Methods 6, 786–787 (2009).
92. Crooks, G. E., Hon, G., Chandonia, J. M. & Brenner, S. E. WebLogo: A sequence logo generator. Genome Res. 14, 1188–1190 (2004).
93. Rawlings, N. D. et al. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res. 46, D624–D632 (2018).
94. Masuda, T., Sugiyama, N., Tomita, M., Ohtsuki, S. & Ishihama, Y. Mass Spectrometry-Compatible Subcellular Fractionation for Proteomics. J. Proteome Res. acs.jproteome.9b00347 (2019). doi:10.1021/acs.jproteome.9b00347
論文の公開元へ
