Allergy, asthma, and proteomics: opportunities with immediate impact

Main Article Content

Renata Harumi Cruz
Leticia Gomes de Pontes
Antonio Condino-Neto


Allergy, atopic diseases, bioinformatics, mass spectrometry, peptidomics


Allergy is widely discussed by researchers due to its complex mechanism that leads to disorders and injuries, but the reason behind the allergic status remains unclear. Current treatments are insufficient to improve the patient’s quality of life significantly. New technologies in scientific and technological development are emerging. For instance, the union between allergy and peptidomics and bioinformatics tools may help fill the gaps in this field, diagnosis, and treatment. In this review, we look at peptidomics and address some findings, such as target proteins or biomarkers that help better understand mechanisms that lead to inflammation, organ damage, and, consequently, poor quality of life or even death.

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1. Jafari R, Ranjbar AR,Hosseini RF. A biographical history of some Iranian pioneers in medical immunology and allergy. Arch Iranian Med. 2019;22(6): 344–52.

2. Cooke A, Zaccone P, Raine T, Phillips JM, Dunne DW. Infection and autoimmunity: are we winning the war, only to lose the peace? Trends Parasitol.2004; 20(7): 316–21. 10.1016/

3. Palomares O, Akdis M, Martín-Fontecha M, Akdis CA. Mechanisms of immune regulation in allergic diseases: the role of regulatory T and B cells. Immunol Rev. 2017;278(1): 219–36. 10.1111/imr.12555

4. Valenta R, Karaulov A, Niederberger V, Gattinger P, van Hage M, Flicker S, et al. Molecular Aspects of allergens and allergy. In Advances in Immunology. 1st ed, vol. 138. Elsevier Inc; 2018.

5. Thomsen SF. Epidemiology and natural history of atopic diseases. Eur Clin Respir J. 2015; 1: 279–341. 10.3402/ecrj.v2.24642

6. Joan O, Stephan A. Recent advances in experimental allergy. Int Arch Allergy Immunol.2018; 177(4):281–89. 10.1159/000494440

7. Verschoor D, Gunten S Von. Allergyand atopic diseases: an update on experimental evidence. Int Arch Allergy Immunol. 2019; 180(4): 235–43. 10.1159/000504439

8. Macchiaverni P, Arslanian C, Frazão JB, Palmeira P, Russo M, Verhasselt V, Condino-Neto A. Mother to child transfer of IgG and IgA antibodies against dermatophagoides pteronyssinus. Scand J Immunol.2011; 74(6): 619–27. 10.1111/j.1365-3083.2011.02615.x

9. Holgate ST, Polosa R. Treatment strategies for allergy and asthma. Nat RevImmunol.2008; 8(3): 218–30. 10.1038/nri2262

10. Galli SJ, Tsai M, Piliponsky AM. The development of allergic inflammation. Nature. 2013;454: 445–54. 10.1038/nature07204

11. Yoo Y, Perzanowski MS. Allergic sensitization and the environment: latest update. Curr Allergy Asthma Rep. 2014;14(1): 465. 10.1007/s11882-014-0465-1

12. Gaurav R, Agrawal DK, Science T. Clinical view on the importance of the dendritic cells in asthma. Expert Rev Clin Immunol. 2015; 9(10): 899–919. 10.1586/1744666X.2013.837260

13. Humeniuk P, Dubiela P, Hoffmann-Sommergruber K. Dendritic cells and their role in allergy: uptake, proteolytic processing and presentation of allergens. Int JMolSci. 2017;18(7): 1491. 10.3390/ijms18071491

14. Hill DA, Spergel J. The atopic march: critical evidence and clinical relevance. Ann Allergy Asthma Immunol.2019;120(2): 131–37. 10.1016/j.anai.2017.10.037

15. Lowe AJ, Leung DYM, Tang MLK., Su JC, Allen KJ. The skin as a target for prevention of the atopic march. Ann Allergy Asthma Immunol. 2018;120(2): 145–51. 10.1016/j.anai.2017.11.023

16. Spergel JM. Epidemiology of atopic dermatitis and atopic march in children. Immunol Allergy Clin North Am. 2010;30(3): 269–80. 10.1016/j.iac.2010.06.003

17. Boonpiyathad T, Sözener ZC, Satitsuksanoa P, Akdis CA. Immunologic mechanisms in asthma. Semin Immunol. 2019; 46: 101333. 10.1016/j.smim.2019.101333

18. Holgate ST. The epidemic of allergy and asthma. Nature. 1999; 402(6760): 2–4. 10.1038/35037000

19. Shea KM, Truckner RT, Weber RW, Peden DB. Climate change and allergic disease. J Allergy Clin Immunol.2008;122(3): 443–53. 10.1016/j.jaci.2008.06.032

20. Pawankar R. Allergic diseases and asthma: a global public health concern and a call to action. World Allergy Organ J. 2014; 7(1):1–3. 10.1186/1939-4551-7-12

21. Pawankar R, Canonica GW, ST Holgate ST, Lockey RF, Blaiss M. White Book on Allergy. World Allergy Organization; 2013.

22. Ebert CS, Pillsbury HC. Epidemiology of allergy. Otolaryngol Clin North Am. 2011; 44(3): 537–48. 10.1016/j.otc.2011.03.001

23. Simon D. Recent advances in clinical allergy and immunology. Int Arch Allergy Immunol. 2018; 177(4): 324–33. 10.1159/000494931

24. Camelo-Nunes, IC, Solé D. Allergic rhinitis: indicators of quality of life. J Bras Pneumol. 2010;36(1): 124–33. 10.1590/s1806-37132010000100017

25. Wangberg H, Woessner K. Choice of biologics in asthma endotypes. Curr Opin Allergy Clin Immunol. 2021; 21(1): 79–85. 10.1097/ACI.0000000000000708

26. Doroudchi A, Pathria M, Modena BD. Asthma biologics: comparing trial designs, patient cohort and study results. Ann Allergy Asthma Immunol. 2020; 124: 44–56. 10.1016/j.anai.2019.10.016

27. Fitzpatrick AM, Chipps BE, Holguin F, Woodruff PG. T-2 ‘Low’ asthma: overview and management strategies. J Allergy Clin Immunol Pract. 2020; 8: 452–63. 10.1016/j.jaip.2019.11.006

28. Fahy JV. Type 2 inflammation in asthma–present in most, absent in many. Nat Rev Immunol. 2015; 15(1): 57–65. 10.1038/nri3786

29. Kuruvilla ME, Lee FE, Lee GB. Understanding asthma phenotypes, endotypes, and mechanisms of disease. Clin Rev Allergy Immunol. 2019; 56: 219–33. 10.1007/s12016-018-8712-1

30. Principe S, Porsbjerg C, Ditlev SB, Klein DK, Golebski K, Dyhre-Petersen N, et al. Treating severe asthma: targeting the IL-5 pathway. Clin Exp Allergy. 2021; 51: 992–1005. 10.1111/cea.13885

31. Pelaia C, Crimi C, Vatrella A, Tinello C, Terracciano R, Pelaia G. Molecular targets for biological therapies of severe asthma. Front Immunol. 2020; 11(603312): 1–11. 10.3389/fimmu.2020.603312

32. Kocher T, Superti-Furga G. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat Methods. 2007; 4(10): 807–15. 10.1038/nmeth1093

33. McDonald WH, Yates III JR. Shotgun proteomics and biomarker discovery. Dis Markers. 2002; 18(2): 99–105. 10.1155/2002/505397

34. Eng JK, McCormack AL, Yates I JR. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc of Mass Spectrom. 1994; 5: 976–89. 10.1016/1044-0305(94)80016-2

35. Han X, Aslanian A, Yates III JR. Mass spectrometry for proteomics. Curr Opin Chem Biol. 2008; 12(5): 483–90. 10.1016/j.cbpa.2008.07.024

36. MacCoss MJ, Yates III JR. Proteomics: analytical tools a technique. Curr Opin Clin Nutr Metab Care. 2001; 4: 369–75. 10.1097/00075197-200109000-00006

37. Tabb DL, Fernando CG, Chambers MC. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res. 2007; 6(2): 654–61. 10.1021/pr0604054

38. Tabb DL, Narasimhan C, Strader MB, Hettich RL. DBDigger: reorganized proteomic database identification that improves flexibility and speed. Anal Chem. 2005; 77(8): 2464–474. 10.1021/ac0487000

39. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999; 20(18): 3551–567. 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

40. Liu K, Zhang J, Wang J, Zhao L, Peng X, Jia W, et al Relationship between sample loading amount and peptide identification and its effects on quantitative proteomics. Anal Chem. 2009; 81(4): 1307–14. 10.1021/ac801466k

41. Moberg M, Bergquist J, Bylund D. A generic stepwise optimization strategy for liquid chromatography electrospray ionization tandem mass spectrometry methods. J Mass Spectrom. 2006; 41(10): 1334–345. 10.1002/jms.1108

42. Venable JD, Yates I JR. Impact of ion trap tandem mass spectra variability on the identification of peptides. Anal Chem. 2004; 76: 2928–937. 10.1021/ac0348219

43. Wenner BR, Lynn BC. Factors that affect ion trap data-dependent MS/MS in proteomics. J Am Soc Mass Spectrom. 2004; 15: 150–57. 10.1016/j.jasms.2003.10.006

44. Riter LS, Vitek O, Gooding KM, Hodge BD, Julian-Jr RK. Statistical design of experiments as a tool in mass spectrometry. J Mass Spectrom. 2005; 40(5): 565–79. 10.1002/jms.871

45. Jiang X, Jiang X, Han G, Ye M, Zou H. Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics. BMC Bioinformatics. 2007; 8(323): 1–12. 10.1186/1471-2105-8-323

46. Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics data integration, interpretation, and its application. Bioinform Biol Insights. 2020; 14: 7–9. 10.1177/1177932219899051

47. Whitley KV, Tueller JA, Weber KS. Genomics education in the era of personal genomics: academic, professional, and public considerations. Int J Mol Sci. 2020; 21(3): 1–19. 10.3390/ijms21030768

48. Suhre K, McCarthy MI, Schwenk JM. Genetics meets proteomics: perspectives for large population-based studies. Nat Rev Genet. 2021;22(1): 19–37. 10.1038/s41576-020-0268-2

49. Hedl TJ, Gil RS, Cheng F, Rayner SL, Davidson JM, Luca A De, Lee A. Proteomics approaches for biomarker and drug target discovery in als and ftd.Front Neurosci. 2019;13: 1–25. 10.3389/fnins.2019.00548

50. Vitorino R, Guedes S, da Costa JP, Kašička V. Microfluidics for peptidomics, proteomics, and cell analysis. Nanomaterials. 2021;11(5): 1–33. 10.3390/nano11051118

51. Bush A. Cytokines and chemokines as biomarkers of future asthma. Front Pediatr. 2019;7: 72. 10.3389/fped.2019.00072

52. Sun X, Hou T, Cheung E, Lu TNT, Tam VWH, Chu IMT, Wong CK. Anti-inflammatory mechanisms of the novel cytokine interleukin-38 in allergic asthma. Cell Mol Immunol.2020; 17(6): 631–46. 10.1038/s41423-019-0300-7

53. Varricchi G, Rossi FW, Galdiero MR, Granata F, Criscuolo G, Spadaro G, Marone G. Physiological roles of mast cells: collegium internationale allergologicum update 2019. Int Arch Allergy Immunol. 2019; 179(4): 247–61. 10.1159/000500088

54. MacMullan MA, Dunn ZS, Graham N, Yang L, Wang P. Quantitative proteomics and metabolomics reveal biomarkers of disease as potential immunotherapy targets and indicators of therapeutic efficacy. Theranostics. 2019;9(25): 7872–888. 10.7150/thno.37373

55. López-Pedrouso M, Lorenzo JM, Gagaoua M, Franco D. Current trends in proteomic advances for food allergen analysis. Biology. 2020;9(9): 247. 10.3390/biology9090247

56. Pilolli R, Gadaleta A, di Stasio L, Lamonaca A, de Angelis E, Nigro D, Monaci L. A comprehensive peptidomic approach to characterize the protein profile of selected durum wheat genotypes: implication for celiac disease and wheat allergy. Nutrients. 2019; 11(10): 2321. 10.3390/nu11102321

57. Aquino A, Conte-Junior CA. A systematic review of food allergy: nanobiosensor and food allergen detection. Biosensors. 2020; 10(12): 194. 10.3390/bios10120194

58. Schrader M, Schulz-Knappe P, Fricker LD. Historical perspective of peptidomics. EuPA Open Proteom. 2014;3: 171–82. 10.1016/j.euprot.2014.02.014

59. Vitorino R. Digging deep into peptidomics applied to body fluids. Proteomics. 2018; 18(2): 1–15. 10.1002/pmic.201700401

60. Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Mol Cell Proteomics. 2015; 14(3): 658–73. 10.1074/mcp.M114.042812

61. Mamone G, Picariello G, Addeo F, Ferranti P. Proteomic analysis in allergy and intolerance to wheat products. Expert Rev Proteomics. 2011; 8(1): 95–115. 10.1586/epr.10.98

62. Haenen S, Clynen E, Nemery B, Hoet PHM, Vanoirbeek JAJ. Biomarker discovery in asthma and COPD: application of proteomics techniques in human and mice. EuPA Open Proteomics. 2014; 4: 101–12. 10.1016/j.euprot.2014.04.008

63. Apostolopoulos V, Bojarska J, Chai TT, Elnagdy S, Kaczmarek K, Matsoukas J, Toth I, et al. A global review on short peptides: frontiers and perspectives. Molecules. 2021; 26(2): 1–45. 10.3390/molecules26020430

64. Malmström J, Tufvesson E, Löfdahl CG, Hansson L, Marko-Varga G, Westergren-Thorsson G. Activation of platelet-derived growth factor pathway in human asthmatic pulmonary--derived mesenchymal cells. Electrophoresis. 2003;24(1–2): 276–85. 10.1002/elps.200390024

65. Boukid F, Prandi B, Faccini A, Sforza S. A complete mass spectrometry (MS)-based peptidomic description of gluten peptides generated during in vitro gastrointestinal digestion of durum wheat: implication for celiac disease. J Am Soc Mass Spectrom. 2019; 30(8): 1481–490. 10.1007/s13361-019-02212-8

66. Pareek CS,Smoczynski R,Tretyn A. Sequencing technologies and genome sequencing. J Applied Genetics Poznań. 2011; 52(4): 413–35. 10.1007/s13353-011-0057-x

67. Bensimon A, Heck AJ, Aebersold R. Mass spectrometry-based proteomics and network biology. Annu Rev Biochem. 2012; 81(1): 379–405. 10.1146/annurev-biochem-072909-100424

68. Zhang Y, Fonslow BR, Shan B, Baek M-C, Yates III JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev. 2013; 113(4): 2343–394. 10.1021/cr3003533

69. Fuzery AK, Levin J, Chan MM, Chan DW. Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin Proteomics. 2013; 10(1): 1–14. 10.1186/1559-0275-10-13