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Mass Spectrometry-Based Chemical Proteomics for Drug Target Discoveries

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Abstract

—Chemical proteomics, emerging rapidly in recent years, has become a main approach to identifying interactions between the small molecules and proteins in the cells on a proteome scale and mapping the signaling and/or metabolic pathways activated and regulated by these interactions. The methods of chemical proteomics allow not only identifying proteins targeted by drugs, characterizing their toxicity and discovering possible off-target proteins, but also elucidation of the fundamental mechanisms of cell functioning under conditions of drug exposure or due to the changes in physiological state of the organism itself. Solving these problems is essential for both basic research in biology and clinical practice, including approaches to early diagnosis of various forms of serious diseases or prediction of the effectiveness of therapeutic treatment. At the same time, recent developments in high-resolution mass spectrometry have provided the technology for searching the drug targets across the whole cell proteomes. This review provides a concise description of the main objectives and problems of mass spectrometry-based chemical proteomics, the methods and approaches to their solution, and examples of implementation of these methods in biomedical research.

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Abbreviations

ABPP:

activity-based protein profiling

AS-MS:

affinity selection mass spectrometry method

CCMS:

capture compound mass spectrometry

HDX-MS:

hydrogen-deuterium exchange mass spectrometry

HPLC-MS/MS:

analysis method of complex mixtures of organic and bioorganic compounds including proteolytic peptides, based on combination of high performance liquid chromatography and tandem mass spectrometry

LiP-MS:

limited proteolysis mass spectrometry

MS:

mass spectrometry

PISA:

protein integral solubility alteration method

PREPL:

prolyl endopeptidase-like enzyme encoded by PREPL gene

TMT:

tandem mass tags for multiplex quantitative proteome analysis based on tandem mass spectrometry

TPP:

thermal proteome profiling

References

  1. Schutte, M., Ogilvie, L. A., Rieke, D. T., Lange, B. M. H., Yaspo, M. L., et al. (2017) Cancer precision medicine: why more is more and DNA is not enough, Public Health Genomics, 20, 70-80, https://doi.org/10.1159/000477157.

    Article  PubMed  Google Scholar 

  2. Frieri, M., Kumar, K., and Boutin, A. (2017) Antibiotic resistance, J. Infect. Public Health, 10, 369-378, https://doi.org/10.1016/j.jiph.2016.08.007.

    Article  PubMed  Google Scholar 

  3. Vasan, N., Baselga, J., and Hyman, D. M. (2019) A view on drug resistance in cancer, Nature, 575, 299-309, https://doi.org/10.1038/s41586-019-1730-1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Ramos, A., Sadeghi, S., and Tabatabaeian, H. (2021) Battling chemoresistance in cancer: root causes and strategies to uproot them, Int. J. Mol. Sci., 22, 9451, https://doi.org/10.3390/ijms22179451.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ashley, E. A. (2016) Towards precision medicine, Nat. Rev. Genet., 17, 507-522, https://doi.org/10.1038/nrg.2016.86.

    Article  CAS  PubMed  Google Scholar 

  6. Mroz, E. A., and Rocco, J. W. (2017) The challenges of tumor genetic diversity, Cancer, 123, 917-927, https://doi.org/10.1002/cncr.30430.

    Article  PubMed  Google Scholar 

  7. Rix, U., and Superti-Furga, G. (2009) Target profiling of small molecules by chemical proteomics, Nat. Chem. Biol., 5, 616-624, https://doi.org/10.1038/nchembio.216.

    Article  CAS  PubMed  Google Scholar 

  8. Wright, M. H., and Sieber, S. A. (2016) Chemical proteomics approaches for identifying the cellular targets of natural products, Nat. Prod. Rep., 33, 681-708, https://doi.org/10.1039/c6np00001k.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Rodriguez, E. L., Poddar, S., Iftekhar, S., Suh, K., Woolfork, A. G., et al. (2020) Affinity chromatography: a review of trends and developments over the past 50 years, J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci., 1157, 122332, https://doi.org/10.1016/j.jchromb.2020.122332.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Huang, F., Zhang, B., Zhou, S., Zhao, X., Bian, C., et al. (2012) Chemical proteomics: terra incognita for novel drug target profiling, Chinese J. Cancer, 31, 507-518, https://doi.org/10.5732/cjc.011.10377.

    Article  CAS  Google Scholar 

  11. Pfab, C., Schnobrich, L., Eldnasoury, S., Gessner, A., and El-Najjar, N. (2021) Repurposing of antimicrobial agents for cancer therapy: what do we know? Cancers (Basel), 13, 3193, https://doi.org/10.3390/cancers13133193.

    Article  CAS  Google Scholar 

  12. Kamel, H. F. M., and Al-Amodi, H. S. A. B. (2017) Exploitation of gene expression and cancer biomarkers in paving the path to era of personalized medicine, Genom. Proteom. Bioinform., 15, 220-235, https://doi.org/10.1016/j.gpb.2016.11.005.

    Article  Google Scholar 

  13. Sneha, P., and Doss, C. G. (2016) Molecular dynamics: new frontier in personalized medicine, Adv. Protein Chem. Struct. Biol., 102, 181-224, https://doi.org/10.1016/bs.apcsb.2015.09.004.

    Article  CAS  PubMed  Google Scholar 

  14. Siwy, J., Mischak, H., and Zürbig, P. (2019) Proteomics and personalized medicine: a focus on kidney disease, Exp. Rev. Proteomics, 16, 773-782, https://doi.org/10.1080/14789450.2019.1659138.

    Article  CAS  Google Scholar 

  15. Meissner, F., Geddes-McAlister, J., Mann, M., and Bantscheff, M. (2022) The emerging role of mass spectrometry-based proteomics in drug discovery, Nat. Rev. Drug Discov., https://doi.org/10.1038/s41573-022-00409-3.

    Article  PubMed  Google Scholar 

  16. Corson, T. W., and Crews, C. M. (2007) Molecular understanding and modern application of traditional medicines: triumphs and trials, Cell, 130, 769-774, https://doi.org/10.1016/j.cell.2007.08.021.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Aebersold, R., and Mann, M. (2016) Mass-spectrometric exploration of proteome structure and function, Nature, 537, 347-355, https://doi.org/10.1038/nature19949.

    Article  CAS  PubMed  Google Scholar 

  18. Chernobrovkin, A., Marin-Vicente, C., Visa, N., and Zubarev, R. A. (2015) Functional identification of target by expression proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs, Sci. Rep., 5, 11176, https://doi.org/10.1038/srep11176.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Saei, A. A., Beusch, C. M., Chernobrovkin, A., Sabatier, P., Zhang, B., et al. (2019) ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery, Nat. Commun., 10, 5715, https://doi.org/10.1038/s41467-019-13582-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ruprecht, B., Di Bernardo, J., Wang, Z., Mo, X., Ursu, O., et al. (2020) A mass spectrometry-based proteome map of drug action in lung cancer cell lines, Nat. Chem. Biol., 16, 1111-1119, https://doi.org/10.1038/s41589-020-0572-3.

    Article  CAS  PubMed  Google Scholar 

  21. Schubert, O., Röst, H., Collins, B., Rosenberger, G., and Aebersold, R. (2017) Quantitative proteomics: challenges and opportunities in basic and applied research, Nat. Protoc., 12, 1289-1294, https://doi.org/10.1038/nprot.2017.040.

    Article  CAS  PubMed  Google Scholar 

  22. Cuatrecasas, P. (1970) Protein purification by affinity chromatography. Derivatizations of agarose and polyacrylamide beads, J. Biol. Chem., 245, 3059-3065, https://doi.org/10.1016/S0021-9258(18)63022-4.

    Article  CAS  PubMed  Google Scholar 

  23. Lolli, G., Thaler, F., Valsasina, B., Roletto, F., Knapp, S., et al. (2003) Inhibitor affinity chromatography: profiling the specific reactivity of the proteome with immobilized molecules, Proteomics, 3, 1287-1298, https://doi.org/10.1002/pmic.200300431.

    Article  CAS  PubMed  Google Scholar 

  24. McMasters, D. R. (2018) Knowledge-based approaches to off-target screening, Methods Enzymol., 610, 311-323, https://doi.org/10.1016/bs.mie.2018.09.023.

    Article  CAS  PubMed  Google Scholar 

  25. Kurien, B. T., and Scofield, R. H. (2015) Western blotting: an introduction, Methods Mol. Biol., 1312, 17-30, https://doi.org/10.1007/978-1-4939-2694-7_5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Dudley, E. (2019) MALDI profiling and applications in medicine, Adv. Exp. Med. Biol., 1140, 27-43, https://doi.org/10.1007/978-3-030-15950-4_2.

    Article  CAS  PubMed  Google Scholar 

  27. Zhang, Y., Fonslow, B. R., Shan, B., Baek, M. C., and Yates, J. R. 3rd (2013) Protein analysis by shotgun/bottom-up proteomics, Chem. Rev., 113, 2343-2394, https://doi.org/10.1021/cr3003533.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Porath, J., Carlsson, J., Olsson, I., and Belfrage, G. (1975) Metal chelate affinity chromatography, a new approach to protein fractionation, Nature, 258, 598-599, https://doi.org/10.1038/258598a0.

    Article  CAS  PubMed  Google Scholar 

  29. Sun, X., Chiu, J.-F., and He, Q.-Y. (2005) Application of immobilized metal affinity chromatography in proteomics, Expert Rev. Proteomics, 2, 649-657, https://doi.org/10.1586/14789450.2.5.649.

    Article  CAS  PubMed  Google Scholar 

  30. Ong, S. E., Schenone, M., Margolin, A. A., Li, X., Do, K., et al. (2009) Identifying the proteins to which small-molecule probes and drugs bind in cells, Proc. Natl. Acad. Sci. USA, 106, 4617-4622, https://doi.org/10.1073/pnas.0900191106.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Sanman, L. E., and Bogyo, M. (2014) Activity-based profiling of proteases, Annu. Rev. Biochem., 83, 249-273, https://doi.org/10.1146/annurev-biochem-060713-035352.

    Article  CAS  PubMed  Google Scholar 

  32. Saghatelian, A., Jessani, N., Joseph, A., Humphrey, M., and Cravatt, B. F. (2004) Activity-based probes for the proteomic profiling of metalloproteases, Proc. Natl. Acad. Sci. USA, 101, 10000-10005, https://doi.org/10.1073/pnas.0402784101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Lone, A. M., Bachovchin, D. A., Westwood, D., Speers, A. E., Timothy, P., et al. (2012) A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors, J. Am. Chem. Soc., 133, 11665-11674, https://doi.org/10.1021/ja2036095.

    Article  CAS  Google Scholar 

  34. Greenbaum, D. C., Baruch, A., Grainger, M., Bozdech, Z., Medzihradszky, K. F., et al. (2002) A role for the protease falcipain 1 in host cell invasion by the human malaria parasite, Science, 298, 2002-2006, https://doi.org/10.1126/science.1077426.

    Article  CAS  PubMed  Google Scholar 

  35. Singaravelu, R., Blais, D. R., McKay, C. S., and Pezacki, J. P. (2010) Activity-based protein profiling of the hepatitis C virus replication in Huh-7 hepatoma cells using a non-directed active site probe, Proteome Sci., 8, 5, https://doi.org/10.1186/1477-5956-8-5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Torkamani, A., and Schork, N. J. (2007) Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family, Genomics, 90, 49-58, https://doi.org/10.1016/j.ygeno.2007.03.006.

    Article  CAS  PubMed  Google Scholar 

  37. Hubbard, M. J., and Cohen, P. (1993) On target with a new mechanism for the regulation of protein phosphorylation, Trends Biochem. Sci., 18, 172-177, https://doi.org/10.1016/0968-0004(93)90109-z.

    Article  CAS  PubMed  Google Scholar 

  38. Blume-Jensen, P., and Hunter, T. (2001) Oncogenic kinase signalling, Nature, 411, 355-365, https://doi.org/10.1038/35077225.

    Article  CAS  PubMed  Google Scholar 

  39. Valsasina, B., Kalisz, H. M., and Isacchi, A. (2004) Kinase selectivity profiling by inhibitor affinity chromatography, Expert Rev. Proteomics, 1, 303-315, https://doi.org/10.1586/14789450.1.3.303.

    Article  CAS  PubMed  Google Scholar 

  40. Savitski, M. M., Reinhard, F. B. M., Franken, H., Werner, T., Savitski, M. F., et al. (2014) Tracking cancer drugs in living cells by thermal profiling of the proteome, Science, 346, 1255784, https://doi.org/10.1126/science.1255784.

    Article  CAS  PubMed  Google Scholar 

  41. Köster, H., Little, D. P., Luan, P., Muller, R., Siddiqi, S. M., et al. (2007) Capture compound mass spectrometry: a technology for the investigation of small molecule protein interactions, Assay Drug Dev. Technol., 5, 381-390, https://doi.org/10.1089/adt.2006.039.

    Article  CAS  PubMed  Google Scholar 

  42. Fischer, J. J., Michaelis, S., Schrey, A. K., Graebner, O. G., Glinski, M.,et al. (2010) Capture compound mass spectrometry sheds light on the molecular mechanisms of liver toxicity of two Parkinson drugs, Toxicol. Sci., 113, 243-253, https://doi.org/10.1093/toxsci/kfp236.

    Article  CAS  PubMed  Google Scholar 

  43. Assal, F., Spahr, L., Hadengue, A., Rubbia-Brandt, L., and Burkhard, P. R. (1998) Tolcapone and fulminant hepatitis, Lancet, 352, 958, https://doi.org/10.1016/s0140-6736(05)61511-5.

    Article  CAS  PubMed  Google Scholar 

  44. Silva, T. B., Borges, F., Serrão, M. P., and Soares-da-Silva, P. (2020) Liver says no: the ongoing search for safe catechol O-methyltransferase inhibitors to replace tolcapone, Drug Discov. Today, 25, 1846-1854, https://doi.org/10.1016/j.drudis.2020.07.015.

    Article  CAS  PubMed  Google Scholar 

  45. Artusi, C. A., Sarro, L., Imbalzano, G., Fabbri, M., and Lopiano, L. (2021) Safety and efficacy of tolcapone in Parkinson’s disease: systematic review, Eur. J. Clin. Pharmacol., 77, 817-829, https://doi.org/10.1007/s00228-020-03081-x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Mateus, A., Kurzawa, N., Becher, I., Sridharan, S., Helm, D., et al. (2020) Thermal proteome profiling for interrogating protein interactions, Mol. Syst. Biol., 16, e9232, https://doi.org/10.15252/msb.20199232.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Tansey, W.P. (2006) Freeze-thaw lysis for extraction of proteins from mammalian cells, CSH Protoc., 2006, pdb.prot4614, https://doi.org/10.1101/pdb.prot4614.

    Article  PubMed  Google Scholar 

  48. De Souza, N., and Picotti, P. (2020) Mass spectrometry analysis of the structural proteome, Curr. Opin. Struct. Biol., 60, 57-65, https://doi.org/10.1016/j.sbi.2019.10.006.

    Article  CAS  PubMed  Google Scholar 

  49. James, E. I., Murphree, T. A., Vorauer, C., Engen, R., and Guttman, M. (2022) Advances in hydrogen/deuterium exchange mass spectrometry and the pursuit of challenging biological systems, Chem. Rev., 122, 7562-7623, https://doi.org/10.1021/acs.chemrev.1c00279.

    Article  CAS  PubMed  Google Scholar 

  50. Kaltashov, I. A., Bobst, C. E., and Abzalimov, R. R. (2013) Mass spectrometry-based methods to study protein architecture and dynamics, Protein Sci., 22, 530-544, https://doi.org/10.1002/pro.2238.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Kaltashov, I. A., Bobst, C. E., and Abzalimov, R. R. (2009) H/D exchange and mass spectrometry in the studies of protein conformation and dynamics: is there a need for a top-down approach? Anal. Chem., 81, 7892-7899, https://doi.org/10.1021/ac901366n.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Campobasso, N., and Huddler, D. (2015) Hydrogen deuterium mass spectrometry in drug discovery, Bioorg. Med. Chem. Lett., 25, 3771-3776, https://doi.org/10.1016/j.bmcl.2015.07.007.

    Article  CAS  PubMed  Google Scholar 

  53. Miyagi, M., Tanaka, K., Watanabe, S., Kondo, J., and Kishimoto, T. (2021) Identifying protein-drug interactions in cell lysates using histidine hydrogen deuterium exchange, Anal. Chem., 93, 14985-14995, https://doi.org/10.1021/acs.analchem.1c02283.

    Article  CAS  PubMed  Google Scholar 

  54. Schopper, S., Kahraman, A., Leuenberger, P., Feng, Y., Piazza, I., et al. (2017) Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry, Nat. Protocols, 12, 2391-2410, https://doi.org/10.1038/nprot.2017.100.

    Article  CAS  PubMed  Google Scholar 

  55. Cheng, K. W., Wong, C. C., Wang, M., He, Q. Y., and Chen, F. (2010) Identification and characterization of molecular targets of natural products by mass spectrometry, Mass Spectrom. Rev., 29, 126-155, https://doi.org/10.1002/mas.20235.

    Article  CAS  PubMed  Google Scholar 

  56. Pepelnjak, M., de Souza, N., and Picotti, P. (2020) Detecting protein-small molecule interactions Using limited proteolysis-mass spectrometry (LiP-MS), Trends Biochem. Sci., 45, 919-920, https://doi.org/10.1016/j.tibs.2020.05.006.

    Article  CAS  PubMed  Google Scholar 

  57. Thompson, A., Schafer, J., Kuhn, K., Kienle, S., Schwarz, J., et al. (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS, Anal. Chem., 75, 1895-1904, https://doi.org/10.1021/ac0262560.

    Article  CAS  PubMed  Google Scholar 

  58. Werner, T., Sweetman, G., Savitski, M. F., Mathieson, T., Bantscheff, M., et al. (2014) Ion coalescence of neutron encoded TMT 10-plex reporter ions, Anal. Chem., 86, 3594-3601, https://doi.org/10.1021/ac500140S.

    Article  CAS  PubMed  Google Scholar 

  59. Gaetani, M., Sabatier, P., Saei, A. A., Beusch, C. M., Yang, Z., et al. (2019) Proteome integral solubility alteration: a high-throughput proteomics assay for target deconvolution, J. Proteome Res., 18, 4027-4037, https://doi.org/10.1021/acs.jproteome.9b00500.

    Article  CAS  PubMed  Google Scholar 

  60. Li, J., Van Vranken, J. G., Pontano Vaites, L., Schweppe, D. K., Huttlin, E. L., et al. (2020) TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples, Nat. Methods, 17, 399-404, https://doi.org/10.1038/s41592-020-0781-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Dai, L., Prabhu, N., Yu, L. Y., Bacanu, S., Ramos, A. D., et al. (2019) Horizontal cell biology: monitoring global changes of protein interaction states with the proteome-wide Cellular Thermal Shift Assay (CETSA), Annu. Rev. Biochem., 88, 383-408, https://doi.org/10.1146/annurev-biochem-062917-012837.

    Article  CAS  PubMed  Google Scholar 

  62. Li, J., Van Vranken, J. G., Paulo, J. A., Huttlin, E. L., and Gygi, S. P. (2020) Selection of heating temperatures improves the sensitivity of the proteome integral solubility alteration assay, J. Proteome Res., 19, 2159-2166, https://doi.org/10.1021/acs.jproteome.0c00063.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Bekker-Jensen, D. B., Kelstrup, C. D., Batth, T. S., Larsen, S. C., Haldrup, C., et al. (2017) An optimized shotgun strategy for the rapid generation of comprehensive human proteomes, Cell Syst., 4, 587-599.e4, https://doi.org/10.1016/j.cels.2017.05.009.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Meier, F., Geyer, P. E., Virreira Winter, S., Cox, J., and Mann, M. (2018) BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes, Nat. Methods, 15, 440-448, https://doi.org/10.1038/s41592-018-0003-5.

    Article  CAS  PubMed  Google Scholar 

  65. Bache, N., Geyer, P. E., Bekker-Jensen, D. B., Hoerning, O., Falkenby, L., et al. (2018) A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics, Mol. Cell Proteomics, 17, 2284-2296, https://doi.org/10.1074/mcp.TIR118.000853.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Meier, F., Brunner, A. D., Koch, S., Koch, H., Lubeck, M., et al. (2018) Online parallel accumulation-serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer, Mol. Cell Proteomics, 17, 2534-2545, https://doi.org/10.1074/mcp.TIR118.000900.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Ivanov, M. V., Tarasova, I. A., Levitsky, L. I., Solovyeva, E. M., Pridatchenko, M. L., et al. (2017) MS/MS-free protein identification in complex mixtures using multiple enzymes with complementary specificity, J. Proteome Res., 16, 3989-3999, https://doi.org/10.1021/acs.jproteome.7b00365.

    Article  CAS  PubMed  Google Scholar 

  68. Teleman, J., Chawade, A., Sandin, M., Levander, F., and Malmstrom, J. (2016) Dinosaur: a refined open-source peptide MS feature detector, J. Proteome Res., 15, 2143-2151, https://doi.org/10.1021/acs.jproteome.6b00016.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Zhang, B., Pirmoradian, M., Zubarev, R.,and Käll, L. (2017) Covariation of peptide abundances accurately reflects protein concentration differences, Mol. Cell Proteomics, 16, 936-948, https://doi.org/10.1074/mcp.O117.067728.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Ivanov, M. V., Bubis, J. A., Gorshkov, V., Abdrakhimov, D. A., Kjeldsen, F., et al. (2021) Boosting MS1-only proteomics with machine learning allows 2000 protein identifications in single-shot human proteome analysis using 5 min HPLC gradient, J. Prot. Res., 20, 1864-1873, https://doi.org/10.1021/acs.jproteome.0c00863.

    Article  CAS  Google Scholar 

  71. Messner, C. B., Demichev, V., Bloomfield, N., Yu, J. S. L., White, M., et al. (2021) Ultra-fast proteomics with scanning SWATH, Nat. Biotechnol., 39, 846-854, https://doi.org/10.1038/s41587-021-00860-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S., and Ralser, M. (2020) DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput, Nat. Methods, 17, 41-44, https://doi.org/10.1038/s41592-019-0638-x.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors express their gratitude to Prof. S. A. Moshkovsky for critical discussion and long-term support of their research.

Funding

This work was financially supported by the Russian Science Foundation (grant no. 20-14-00229).

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Authors and Affiliations

  1. V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia

    Ivan I. Fedorov, Irina A. Tarasova & Mikhail V. Gorshkov

  2. Moscow Institute of Physics and Technology (National University), 141700, Dolgoprudny, Moscow Region, Russia

    Ivan I. Fedorov & Victoria I. Lineva

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  1. Ivan I. Fedorov
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  2. Victoria I. Lineva
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  3. Irina A. Tarasova
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Contributions

I. I. Federov and V. I. Lineva contributed to literature analysis and review writing; I. A. Tarasova discussed the review structure and described methods; M. V. Gorshkov has leaded the efforts for writing the review.

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Correspondence to Mikhail V. Gorshkov.

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The authors declare no conflicts of interest in financial or any other sphere. This article does not contain any studies with human participants or animals performed by any of the authors.

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Fedorov, I.I., Lineva, V.I., Tarasova, I.A. et al. Mass Spectrometry-Based Chemical Proteomics for Drug Target Discoveries. Biochemistry Moscow 87, 983–994 (2022). https://doi.org/10.1134/S0006297922090103

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