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Proteomic approaches beyond expression profiling and PTM analysis

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Abstract

Essentially, all cellular functions are executed by proteins. Different physiological and pathological conditions dynamically control various properties of proteins, including expression levels, post-translational modifications (PTMs), protein–protein interactions, enzymatic activity, etc. Thus far, the vast majority of proteomic efforts have been focused on quantitative profiling of protein abundance/expression and their PTMs. In this article, we review some recent exciting progress in the development of proteomic approaches to examine protein functions from perspectives other than expression levels and PTMs. Specifically, we discuss advancements in proximity-based labeling, analysis of protein termini and newly synthesized proteins, and activity-based protein profiling.

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References

  1. Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, et al. A draft map of the human proteome. Nature. 2014;509:575–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Wilhelm M, Schlegl J, Hahne H, Gholami AM, Lieberenz M, Savitski MM, et al. Mass-spectrometry-based draft of the human proteome. Nature. 2014;509:582–7.

    Article  CAS  PubMed  Google Scholar 

  3. Lin Z, Sun L, Liu W, Xia Z, Yang H, Chen G. Synthesis of boronic acid-functionalized molecularly imprinted silica nanoparticles for glycoprotein recognition and enrichment. J Mater Chem B. 2014;2:637–43.

    Article  CAS  Google Scholar 

  4. Xing R, Wang S, Bie Z, He H, Liu Z. Preparation of molecularly imprinted polymers specific to glycoproteins, glycans and monosaccharides via boronate affinity controllable-oriented surface imprinting. Nat Protoc. 2017;12:964–87.

    Article  CAS  PubMed  Google Scholar 

  5. Ye J, Chen Y, Liu Z. A boronate affinity sandwich assay: an appealing alternative to immunoassays for the determination of glycoproteins. Angew Chem Int Ed Engl. 2014;53:10386–9.

    Article  CAS  PubMed  Google Scholar 

  6. Bie Z, Chen Y, Ye J, Wang S, Liu Z. Boronate-affinity glycan-oriented surface imprinting: a new strategy to mimic lectins for the recognition of an intact glycoprotein and its characteristic fragments. Angew Chem Int Ed Engl. 2015;54:10211–5.

    Article  CAS  PubMed  Google Scholar 

  7. Chen Y, Sprung R, Tang Y, Ball H, Sangras B, Kim SC, et al. Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics. 2007;6:812–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Xie Z, Dai J, Dai L, Tan M, Cheng Z, Wu Y, et al. Lysine succinylation and lysine malonylation in histones. Mol Cell Proteomics. 2012;11:100–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Zhang Z, Tan M, Xie Z, Dai L, Chen Y, Zhao Y. Identification of lysine succinylation as a new post-translational modification. Nat Chem Biol. 2011;7:58–63.

    Article  CAS  PubMed  Google Scholar 

  10. Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell. 2011;146:1016–28.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Xie Z, Zhang D, Chung D, Tang Z, Huang H, Dai L, et al. Metabolic regulation of gene expression by histone lysine β-hydroxybutyrylation. Mol Cell. 2016;62:194–206.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Boersema PJ, Kahraman A, Picotti P. Proteomics beyond large-scale protein expression analysis. Curr Opin Biotechnol. 2015;34:162–70.

    Article  CAS  PubMed  Google Scholar 

  13. Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature. 1989;340:245–6.

    Article  CAS  PubMed  Google Scholar 

  14. Gingras A, Gstaiger M, Raught B, Aebersold R. Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol. 2007;8:645–54.

    Article  CAS  PubMed  Google Scholar 

  15. Kim DI, Roux KJ. Filling the void: proximity-based labeling of proteins in living cells. Trend Cell Biol. 2016;26:804–17.

    Article  CAS  Google Scholar 

  16. Li P, Li J, Wang L, Di LJ. Proximity labeling of interacting proteins: application of BioID as a discovery tool. Proteomics. 2017; https://doi.org/10.1002/pmic.201700002.

  17. Roux KJ, Kim DI, Raida M, Burke B. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol. 2012;196:801–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Coyaud E, Mis M, Laurent EM, Dunham WH, Couzens AL, Robitaille M, et al. BioID-based identification of Skp Cullin F-box (SCF)β-TrCP1/2 E3 ligase substrates. Mol Cell Proteom. 2015;14:1781–195.

    Article  CAS  Google Scholar 

  19. Chojnowski A, Ong PF, Wong ES, Lim JS, Mutalif RA, Navasankari R, et al. Progerin reduces LAP2α-telomere association in Hutchinson-Gilford progeria. Elife. 2015;4. https://doi.org/10.7554/eLife.07759.

  20. Kim DI, Birendra KC, Zhu W, Motamedchaboki K, Doye V, Roux KJ. Probing nuclear pore complex architecture with proximity-dependent biotinylation. Proc Natl Acad Sci USA. 2014;111:2453–61.

    Article  CAS  Google Scholar 

  21. Kim DI, Jensen SC, Noble KA, Kc B, Roux KH, Motamedchaboki K, et al. An improved smaller biotin ligase for BioID proximity labeling. Mol Biol Cell. 2016;27:1188–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ramanathan M, Majzoub K, Rao DS, Neela PH, Zarnegar BJ, Mondal S, et al. RNA–protein interaction detection in living cells. Nat Methods. 2018; https://doi.org/10.1038/nmeth.4601.

  23. Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, et al. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science. 2013;339:1328–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Chen CL, Hu Y, Udeshi ND, Lau TY, Wirtz-Peitz F, He L, et al. Proteomic mapping in live drosophila tissues using an engineered ascorbate peroxidase. Proc Natl Acad Sci USA. 2015;112:12093–8.

    Article  CAS  PubMed  Google Scholar 

  25. Mick DU, Rodriques RB, Leib RD, Adams CM, Chien AS, Gygi SP, et al. Proteomics of primary cilia by proximity labeling. Dev Cell. 2015;35:497–512.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Lam SS, Martell JD, Kamer KJ, Deerink TJ, Ellisman MH, Mootha UK, et al. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat Methods. 2015;12:51–4.

    Article  CAS  PubMed  Google Scholar 

  27. Jing J, He L, Sun A, Quintana A, Ding Y, Ma G, et al. Proteomic mapping of ER-PM junctions identifies STIMATE as a regulator of Ca2+ influx. Nat Cell Biol. 2015;17:1339–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Paek J, Kalocsay M, Staus DP, Winqler L, Pascolutti R, Paulo JA, et al. Multidimensional tracking of GPCR signaling via peroxidase-catalyzed proximity labeling. Cell. 2017;169:338–49.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, et al. An approach to spatiotemporally resolve protein interaction networks in living cells. Cell. 2017;169:350–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Loh KH, Stawski PS, Draycott AS, Udeshi ND, Lehrman EK, Wilton DK, et al. Proteomic analysis of unbounded cellular compartments: synaptic clefts. Cell. 2016;166:1295–307.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Hopkins C, Gibson A, Stinchcombe J, Futter C. Chimeric molecules employing horseradish peroxidase as reporter enzyme for protein localization in the electron microscope. Methods Enzymol. 2000;327:35–45.

    Article  CAS  PubMed  Google Scholar 

  32. Hollebeke J, Van Damme P, Gevaert K. N terminal acetylation and other functions of N-α-acetyltransferases. Biol Chem. 2012;393:291–8.

    Article  CAS  PubMed  Google Scholar 

  33. Xu GQ, Shin SB, Jaffrey SR. Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini. Proc Natl Acad Sci USA. 2009;106:19310–5.

    Article  PubMed  Google Scholar 

  34. Timmer JC, Enoksson M, Wildfang E, Zhu WH, Igarashi Y, Denault JB, et al. Profiling constitutive proteolytic events in vivo. Biochem J. 2007;407:41–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell. 2008;134:866–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Brown JL, Roberts WK. Evidence that approximately eighty percent of the soluble proteins from Ehrlich ascites cells are N-α-acetylated. J Biol Chem. 1976;251:1009–14.

    CAS  PubMed  Google Scholar 

  37. Gevaert K, Goethals M, Martens L, Damme JV, Staes A, Thomas GR, et al. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol. 2003;21:566–9.

    Article  CAS  PubMed  Google Scholar 

  38. Staes A, Damme PV, Helsens K, Demol H, Vandekercjhove J, Gevaert K. Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics. 2008;8:1362–70.

    Article  CAS  PubMed  Google Scholar 

  39. Venne AS, Vögtle FN, Meisinger C, Sickmann A, Zahedi RP. Novel highly sensitive, specific, and straightforward strategy for comprehensive N-terminal proteomics reveals unknown substrates of the mitochondrial peptidase Icp55. J Proteome Res. 2013;12:3823–30.

    Article  CAS  PubMed  Google Scholar 

  40. Kleifeld O, Doucet A, auf dem Keller U, Prudova A, Schilling O, Kainthan RK, et al. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat Biotechnol. 2010;28:281–8.

    Article  CAS  PubMed  Google Scholar 

  41. Prudova A, auf dem Keller U, Butler GS, Overall CM. Multiplex N-terminome analysis of MMP-2 and MMP-9 substrate degradomes by iTRAQ-TAILS quantitative proteomics. Mol Cell Proteomics. 2010;9:894–911.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Klein T, Fung SY, Renner F, Blank MA, Dufour A, Kang S, et al. The paracaspase MALT1 cleaves HOIL1 reducing linear ubiquitination by LUBAC to dampen lymphocyte NF-κB signaling. Nat Commun. 2015;6:8777. https://doi.org/10.1038/ncomms9777.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Elton L, Carpentier I, Staal J, Driege Y, Haegman M, Beyaert R. MALT1 cleaves the E3 ubiquitin ligase HOIL-1 in activated T cells, generating a dominant negative inhibitor of LUBAC-induced NFkappaB signaling. FEBS J. 2015; https://doi.org/10.1111/febs.13597.

  44. Mommen GP, van de Waterbeemd B, Meiring HD, Kersten G, Heck AJ, de Jong AP. Unbiased selective isolation of protein N-terminal peptides from complex proteome samples using phospho tagging (PTAG) and TiO(2)-based depletion. Mol Cell Proteomics. 2012;11:832–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Chen L, Shan Y, Weng Y, Sui Z, Zhang X, Liang Z, et al. Hydrophobic tagging-assisted N-termini enrichment for in-depth N-terminome analysis. Anal Chem. 2016;88:8390–5.

    Article  CAS  PubMed  Google Scholar 

  46. Tanco S, Gevaert K, Van Damme P. C-terminomics: targeted analysis of natural and posttranslationally modified protein and peptide C-termini. Protemics. 2015;15:903–14.

    Article  CAS  Google Scholar 

  47. Xu G, Shin SB, Jaffrey SR. Chemoenzymatic labeling of protein C-termini for positive selection of C-terminal peptides. ACS Chem Biol. 2011;6:1015–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Liu M, Fang C, Pan X, Jiang H, Zhang L, Zhang L, et al. Positive enrichment of C-terminal peptides using oxazolone chemistry and biotinylation. Anal Chem. 2015;87:9916–22.

    Article  CAS  PubMed  Google Scholar 

  49. Van Damme P, Staes A, Bronsoms S, Helsens K, Colaert N, Timmerman E, et al. Complementary positional proteomics for screening substrates of endo- and exoproteases. Nat Methods. 2010;7:512–5.

    Article  CAS  PubMed  Google Scholar 

  50. Schilling O, Barre O, Huesgen PF, Overall CM. Proteome-wide analysis of protein carboxy termini: C terminomics. Nat Methods. 2010;7:508–11.

    Article  CAS  PubMed  Google Scholar 

  51. Dieterich DC, Link AJ, Graumann J, Tirrell DA, Schuman EM. Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc Natl Acad Sci USA. 2006;103:9482–7.

    Article  CAS  PubMed  Google Scholar 

  52. Debarba JA, Monteiro KM, Moura H, Barr JR, Ferreira HB, Zaha A. Identification of newly synthesized proteins by Echinococcus granulosus Protoscoleces upon induction of strobilation. PLoS Negl Trop Dis. 2015;9:e0004085.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Hodas JJ, Nehring A, Höche N, Sweredoski MJ, Pielot R. Dopaminergic modulation of the hippocampal neuropil proteome identified by bioorthogonal noncanonical amino acid tagging (BONCAT). Proteomics. 2012;12:2464–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Hinz FI, Dieterich DC, Tirrell DA, Schuman EM. Non-canonical amino acid labeling in vivo to visualize and affinity purify newly synthesized proteins in larval zebrafish. ACS Chem Neurosci. 2012;3:40–9.

    Article  CAS  PubMed  Google Scholar 

  55. Eichelbaum K, Winter M, Diaz MB, Herzig S, Krijgsveld J. Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nat Biotechnol. 2012;30:984–90.

    Article  CAS  PubMed  Google Scholar 

  56. Howden A, Geoghegan V, Katsch K, Efstathiou G, Bhushan B, Boutureira O, et al. QuaNCAT: quantitating proteome dynamics in primary cells. Nat Methods. 2013;10:343–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Tanrikulu IC, Schmitt E, Mechulam Y, Goddard WA III, Tirrell DA. Discovery of Escherichia coli methionyl-tRNA synthetase mutants for efficient labeling of proteins with azidonorleucine in vivo. Proc Natl Acad Sci USA. 2009;106:15285–90.

    Article  PubMed  Google Scholar 

  58. Ngo JT, Champion JA, Mahdavi A, Tanrikulu IC, Beatty KE, Connor RE, et al. Cell-selective metabolic labeling of proteins. Nat Chem Biol. 2009;5:715–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Grammel M, Zhang MM, Hang HC. Orthogonal alkynyl amino acid reporter for selective labeling of bacterial proteomes during infection. Angew Chem Int Ed Engl. 2010;49:5970–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Truong F, Yoo TH, Lampo TJ, Tirrell DA. Two-strain, cell-selective protein labeling in mixed bacterial cultures. J Am Chem Soc. 2012;134:8551–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Liu J, Xu Y, Stoleru D, Salica A. Imaging protein synthesis in cells and tissues with an alkyne analog of puromycin. Proc Natl Acad Sci USA. 2011;109:413–8.

    Article  PubMed  Google Scholar 

  62. Ngo JT, Schuman EM, Tirrell DA. Mutant methionyl-tRNA synthetase from bacteria enables site-selective N-terminal labeling of proteins expressed in mammalian cells. Proc Natl Acad Sci USA. 2013;110:4992–7.

    Article  PubMed  Google Scholar 

  63. Cravatt BF, Wright AT, Kozarich JW. Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu Rev Biochem. 2008;77:383–414.

    Article  CAS  PubMed  Google Scholar 

  64. Speers AE, Adam GC, Cravatt BF. Activity-based protein profiling in vivo using a copper(I)-catalyzed azide-alkyne 3+2. cycloaddition. J Am Chem Soc. 2003;125:4686–7.

    Article  CAS  PubMed  Google Scholar 

  65. Liu Y, Patricelli MP, Cravatt BF. Activity-based protein profiling: the serine hydrolases. Proc Natl Acad Sci USA. 1999;96:14694–9.

    Article  CAS  PubMed  Google Scholar 

  66. Powers JC, Asgian JL, Ekici OD, James KE. Irreversible inhibitors of serine, cysteine, and threonine proteases. Chem Rev. 2002;102:4639–750.

    Article  CAS  PubMed  Google Scholar 

  67. Kidd D, Liu Y, Cravatt BF. Profiling serine hydrolase activities in complex proteomes. Biochemistry. 2001;40:4005–15.

    Article  CAS  PubMed  Google Scholar 

  68. Jessani N, Liu Y, Humphrey M, Cravatt BF. Enzyme activity profiles of the secreted and membrane proteome that depict cancer cell invasiveness. Proc Natl Acad Sci USA. 2002;99:10335–40.

    Article  CAS  PubMed  Google Scholar 

  69. Patricelli MP, Szardenings AK, Liyanage M, Nomanbhoy TK, Wu M, Weissig H, et al. Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry. 2007;46:350–8.

    Article  CAS  PubMed  Google Scholar 

  70. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science. 2002;298:1912–34.

    Article  CAS  PubMed  Google Scholar 

  71. Villamor JG, Kaschani F, Colby T, Oeljeklaus J, Zhao D, Kaiser M, et al. Profiling protein kinases and other ATP binding proteins in Arabidopsis using acyl-ATP probes. Mol Cell Proteom. 2013;12:2481–96.

    Article  CAS  Google Scholar 

  72. Wolfe LM, Veeraraghavan U, Idicula-Thomas S, Schurer S, Wennerberg K, Reynolds R, et al. A chemical proteomics approach to profiling the ATP binding proteome of Mycobacterium tuberculosis. Mol Cell Proteom. 2013;12:1644–60.

    Article  CAS  Google Scholar 

  73. Xiao Y, Guo L, Wang Y. Isotope-coded, ATP probe for quantitative affinity profiling of ATP-binding proteins. Anal Chem. 2013;85:7478–86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Xiao Y, Guo L, Wang Y. A targeted quantitative proteomics strategy for global kinome profiling of cancer cells and tissues. Mol Cell Proteom. 2014;13:1065–75.

    Article  CAS  Google Scholar 

  75. Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MB, et al. Quantitative reactivity profiling predicts functional cysteins in proteomics. Nature. 2010;468:790–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Vocadlo DJ, Bertozzi CR. A strategy for functional proteomic analysis of glycosidase activity from cell lysates. Angew Chem Int Ed Engl. 2004;43:5338–42.

    Article  CAS  PubMed  Google Scholar 

  77. Vocadlo DJ, Hang HC, Kim EJ, Hanover JA, Bertozzi CR. A chemical approach for identifying O-GlcNAc modified proteins in cells. Proc Natl Acad Sci USA. 2003;100:9116–21.

    Article  CAS  PubMed  Google Scholar 

  78. Saghatelian A, Jessani N, Joseph A, Humphrey M, Cravatt BF. Activity-based probes for the proteomic profiling of metalloproteases. Proc Natl Acad Sci USA. 2004;101:10000–5.

    Article  CAS  PubMed  Google Scholar 

  79. Sieber SA, Niessen S, Hoover HS, Cravatt BF. Proteomic profiling of metalloprotease activities with cocktails of active-site probes. Nat Chem Biol. 2006;2:274–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Alfonso LF, Srivenugopal KS, Bhat GJ. Does aspirin acetylate multiple cellular proteins? Mol Med Rep. 2009;2:533–7.

    CAS  PubMed  Google Scholar 

  81. Leslie AB, Balyn WZ, Stephanie MM, Matthew RP. An alkyne–aspirin chemical reporter for the detection of aspirin-dependent protein modification in living cells. J Am Chem Soc. 2013;135:14568–73.

    Article  CAS  Google Scholar 

  82. Yang PY, Liu K, Ngai MH, Lear MJ, Wenk MR, Yao SQ. Activity-based proteome profiling of potential cellular targets of Orlistat - an FDA-approved drug with anti-tumor activities. J Am Chem Soc. 2010;132:656–66.

    Article  CAS  PubMed  Google Scholar 

  83. Zhuang S, Li Q, Cai L, Wang C, Lei X. Chemoproteomic profiling of bile acid interacting proteins. ACS Cent Sci. 2017;3:501–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was financially supported by grants from the National Natural Science Foundation of China (21475005 and 21622501), Clinical Medicine Plus X-Young Scholars Project of Peking University and the Thousand Young Talents program of the Chinese government.

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Fu, J., Wu, M. & Liu, X. Proteomic approaches beyond expression profiling and PTM analysis. Anal Bioanal Chem 410, 4051–4060 (2018). https://doi.org/10.1007/s00216-018-1021-y

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