Protein & Peptide Letters

Author(s): Virendra S. Gomase*, Suchita P. Dhamane and Pavan G. Kakade

DOI: 10.2174/0109298665333029240926092919

DownloadDownload PDF Flyer Cite As
Immunoproteomics: A Review of Techniques, Applications, and Advancements

Page: [827 - 849] Pages: 23

  • * (Excluding Mailing and Handling)

Abstract

Immunoproteomics is the branch of proteomics with an emphasis on the study of functional peptides and proteins related to the immune system. Combining proteomics techniques with immunological research aims to uncover the complex interactions of proteins involved in immune responses. This review discusses the methods, applications, and recent advancements in immunoproteomics, highlighting its critical role in understanding immune responses, discovering biomarkers, and developing vaccines and therapeutics. This study offers a comprehensive exploration of the methodologies, applications, and advancements within immunoproteomics. Techniques such as mass spectrometry, antibody-based assays, and computational analysis are pivotal in unraveling the complexities of the immune system at the protein level. Immunoproteomics finds diverse applications in biomarker discovery, vaccine development, autoimmune disease research, infectious disease diagnostics, and cancer immunotherapy. Challenges, including data integration, sample heterogeneity, and biomarker validation, persist, necessitating innovative approaches and interdisciplinary collaborations. In the future, immunoproteomics will likely play a major role in expanding our knowledge of immune-related diseases and accelerating the creation of targeted and precise immunotherapies.

Keywords: Immunoproteomics, immunotherapies, mass spectrometry, antibody-based assays, computational analysis, cancer immunotherapy.

Graphical Abstract

[1]
Gomase, V.; Chitlange, N.; Changbhale, S.; Kale, K. Prediction of Brugia malayi antigenic peptides: Candidates for synthetic vaccine design against lymphatic filariasis. Protein Pept. Lett., 2013, 20(8), 864-887.
[http://dx.doi.org/10.2174/0929866511320080004] [PMID: 23537185]
[2]
Gomase, V.; Changbhale, S. Antigenicity prediction in melittin: Possibilities of in drug development from Apis dorsata. Curr. Proteomics, 2007, 4(2), 107-114.
[http://dx.doi.org/10.2174/157016407782194639]
[3]
Gomase, V.; Kale, K.; Tagore, S.; Hatture, S. Proteomics: technologies for protein analysis. Curr. Drug Metab., 2008, 9(3), 213-220.
[http://dx.doi.org/10.2174/138920008783884740] [PMID: 18336224]
[4]
Gomase, V.; Kemkar, K.; Potnis, V. Intellectual property rights: Protection of biotechnological inventions in India. Recent Pat. Biotechnol., 2024, 18(2), 128-143.
[http://dx.doi.org/10.2174/1872208317666230612145600] [PMID: 38282443]
[5]
Gomase, V.; Tagore, S. Cytomics. Curr. Drug Metab., 2008, 9(3), 263-266.
[http://dx.doi.org/10.2174/138920008783884731] [PMID: 18336233]
[6]
Gomase, V.; Tagore, S. Kinomics. Curr. Drug Metab., 2008, 9(3), 255-258.
[http://dx.doi.org/10.2174/138920008783884803] [PMID: 18336231]
[7]
Fredolini, C.; Byström, S.; Pin, E.; Edfors, F.; Tamburro, D.; Iglesias, M.J.; Häggmark, A.; Hong, M.G.; Uhlen, M.; Nilsson, P.; Schwenk, J.M. Immunocapture strategies in translational proteomics. Expert Rev. Proteomics, 2016, 13(1), 83-98.
[http://dx.doi.org/10.1586/14789450.2016.1111141] [PMID: 26558424]
[8]
Becker, J.O.; Hoofnagle, A.N. Replacing immunoassays with tryptic digestion-peptide immunoaffinity enrichment and LC-MS/MS. Bioanalysis, 2012, 4(3), 281-290.
[http://dx.doi.org/10.4155/bio.11.319] [PMID: 22303832]
[9]
Kumar, V.; Barnidge, D.R.; Chen, L.S.; Twentyman, J.M.; Cradic, K.W.; Grebe, S.K.; Singh, R.J. Quantification of serum 1-84 parathyroid hormone in patients with hyperparathyroidism by immunocapture in situ digestion liquid chromatography-tandem mass spectrometry. Clin. Chem., 2010, 56(2), 306-313.
[http://dx.doi.org/10.1373/clinchem.2009.134643] [PMID: 20007860]
[10]
Melby, J.A.; Roberts, D.S.; Larson, E.J.; Brown, K.A.; Bayne, E.F.; Jin, S.; Ge, Y. Novel strategies to address the challenges in top-down proteomics. J. Am. Soc. Mass Spectrom., 2021, 32(6), 1278-1294.
[http://dx.doi.org/10.1021/jasms.1c00099] [PMID: 33983025]
[11]
Artigues, A.; Nadeau, O.W.; Rimmer, M.A.; Villar, M.T.; Du, X.; Fenton, A.W.; Carlson, G.M. Protein structural analysis via mass spectrometry-based proteomics. Adv. Exp. Med. Biol., 2016, 919, 397-431.
[http://dx.doi.org/10.1007/978-3-319-41448-5_19] [PMID: 27975228]
[12]
Darie-Ion, L.; Whitham, D.; Jayathirtha, M.; Rai, Y.; Neagu, A.N.; Darie, C.C.; Petre, B.A. Applications of MALDI-MS/MS-based proteomics in biomedical research. Molecules, 2022, 27(19), 6196.
[http://dx.doi.org/10.3390/molecules27196196] [PMID: 36234736]
[13]
Ignjatovic, V.; Geyer, P.E.; Palaniappan, K.K.; Chaaban, J.E.; Omenn, G.S.; Baker, M.S.; Deutsch, E.W.; Schwenk, J.M. Mass spectrometry-based plasma proteomics: Considerations from sample collection to achieving translational data. J. Proteome Res., 2019, 18(12), 4085-4097.
[http://dx.doi.org/10.1021/acs.jproteome.9b00503] [PMID: 31573204]
[14]
Zhang, Y.; Bottinelli, D.; Lisacek, F.; Luban, J.; Strambio-De-Castillia, C.; Varesio, E.; Hopfgartner, G. Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomic studies. Anal. Biochem., 2015, 484, 40-50.
[http://dx.doi.org/10.1016/j.ab.2015.05.007] [PMID: 25983236]
[15]
Donnell, A.M.; Lewis, S.; Abraham, S.; Subramanian, K.; Figueroa, J.L.; Deepe, G.S., Jr; Vonderheide, A.P. Investigation of an optimal cell lysis method for the study of the zinc metalloproteome of Histoplasma capsulatum. Anal. Bioanal. Chem., 2017, 409(26), 6163-6172.
[http://dx.doi.org/10.1007/s00216-017-0556-7] [PMID: 28801743]
[16]
Wada, O.Z.; Rashid, N.; Wijten, P.; Thornalley, P.; Mckay, G.; Mackey, H.R. Evaluation of cell disruption methods for protein and coenzyme Q10 quantification in purple non-sulfur bacteria. Front. Microbiol., 2024, 15, 1324099.
[http://dx.doi.org/10.3389/fmicb.2024.1324099] [PMID: 38550862]
[17]
Janecki, D.J.; Reilly, J.P. Denaturation of metalloproteins with EDTA to facilitate enzymatic digestion and mass fingerprinting. Rapid Commun. Mass Spectrom., 2005, 19(10), 1268-1272.
[http://dx.doi.org/10.1002/rcm.1924] [PMID: 15834845]
[18]
Sierra, L.S.; Dixon, C.K.; Wilken, L.R. Enzymatic cell disruption of the microalgae Chlamydomonas reinhardtii for lipid and protein extraction. Algal Res., 2017, 25, 149-159.
[http://dx.doi.org/10.1016/j.algal.2017.04.004]
[19]
Yan, Y.; Zhang, Y.; Gao, J.; Qin, L.; Liu, F.; Zeng, W.; Wan, J. Intracellular and extracellular sources, transformation process and resource recovery value of proteins extracted from wastewater treatment sludge via alkaline thermal hydrolysis and enzymatic hydrolysis. Sci. Total Environ., 2022, 852, 158512.
[http://dx.doi.org/10.1016/j.scitotenv.2022.158512] [PMID: 36063951]
[20]
Takemori, A.; Butcher, D.S.; Harman, V.M.; Brownridge, P.; Shima, K.; Higo, D.; Ishizaki, J.; Hasegawa, H.; Suzuki, J.; Yamashita, M.; Loo, J.A.; Loo, R.R.O.; Beynon, R.J.; Anderson, L.C.; Takemori, N. PEPPI-MS: Polyacrylamide-gel-based prefractionation for analysis of intact proteoforms and protein complexes by mass spectrometry. J. Proteome Res., 2020, 19(9), 3779-3791.
[http://dx.doi.org/10.1021/acs.jproteome.0c00303] [PMID: 32538093]
[21]
Demmers, L.C.; Heck, A.J.R.; Wu, W. Pre-fractionation extends but also creates a bias in the detectable HLA class Ι ligandome. J. Proteome Res., 2019, 18(4), 1634-1643.
[http://dx.doi.org/10.1021/acs.jproteome.8b00821] [PMID: 30784271]
[22]
Christopher, J.A.; Stadler, C.; Martin, C.E.; Morgenstern, M.; Pan, Y.; Betsinger, C.N.; Rattray, D.G.; Mahdessian, D.; Gingras, A.C.; Warscheid, B.; Lehtiö, J.; Cristea, I.M.; Foster, L.J.; Emili, A.; Lilley, K.S. Subcellular proteomics. Nat. Rev. Methods Primers, 2021, 1(1), 32.
[http://dx.doi.org/10.1038/s43586-021-00029-y] [PMID: 34549195]
[23]
Wiederhold, E.; Veenhoff, L.M.; Poolman, B.; Slotboom, D.J. Proteomics of Saccharomyces cerevisiae organelles. Mol. Cell. Proteomics, 2010, 9(3), 431-445.
[http://dx.doi.org/10.1074/mcp.R900002-MCP200] [PMID: 19955081]
[24]
Qing, R.; Hao, S.; Smorodina, E.; Jin, D.; Zalevsky, A.; Zhang, S. Protein design: From the aspect of water solubility and stability. Chem. Rev., 2022, 122(18), 14085-14179.
[http://dx.doi.org/10.1021/acs.chemrev.1c00757] [PMID: 35921495]
[25]
Rabani, V.; Davani, S.; Gambert-Nicot, S.; Meneveau, N.; Montange, D. Comparative lipidomics and proteomics analysis of platelet lipid rafts using different detergents. Platelets, 2016, 27(7), 634-641.
[http://dx.doi.org/10.3109/09537104.2016.1174203] [PMID: 27184886]
[26]
Shogomori, H.; Brown, D.A. Use of detergents to study membrane rafts: the good, the bad, and the ugly. Biol. Chem., 2003, 384(9), 1259-1263.
[http://dx.doi.org/10.1515/BC.2003.139] [PMID: 14515986]
[27]
Gutstein, H.B.; Morris, J.S. Laser capture sampling and analytical issues in proteomics. Expert Rev. Proteomics, 2007, 4(5), 627-637.
[http://dx.doi.org/10.1586/14789450.4.5.627] [PMID: 17941818]
[28]
Terkelsen, T.; Pernemalm, M.; Gromov, P.; Børresen-Dale, A.L.; Krogh, A.; Haakensen, V.D.; Lethiö, J.; Papaleo, E.; Gromova, I. High-throughput proteomics of breast cancer interstitial fluid: Identification of tumor subtype-specific serologically relevant biomarkers. Mol. Oncol., 2021, 15(2), 429-461.
[http://dx.doi.org/10.1002/1878-0261.12850] [PMID: 33176066]
[29]
Lin, T.T.; Zhang, T.; Kitata, R.B.; Liu, T.; Smith, R.D.; Qian, W.J.; Shi, T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. Mass Spectrom. Rev., 2023, 42(2), 796-821.
[http://dx.doi.org/10.1002/mas.21741] [PMID: 34719806]
[30]
Itkonen, H.M.; Urbanucci, A.; Martin, S.E.S.; Khan, A.; Mathelier, A.; Thiede, B.; Walker, S.; Mills, I.G. High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Theranostics, 2019, 9(8), 2183-2197.
[http://dx.doi.org/10.7150/thno.30834] [PMID: 31149037]
[31]
MacKinnon, A.L.; Garrison, J.L.; Hegde, R.S.; Taunton, J. Photo-leucine incorporation reveals the target of a cyclodepsipeptide inhibitor of cotranslational translocation. J. Am. Chem. Soc., 2007, 129(47), 14560-14561.
[http://dx.doi.org/10.1021/ja076250y] [PMID: 17983236]
[32]
Agrawal, P.; Yu, K.; Salomon, A.R.; Sedivy, J.M. Proteomic profiling of Myc-associated proteins. Cell Cycle, 2010, 9(24), 4908-4921.
[http://dx.doi.org/10.4161/cc.9.24.14199] [PMID: 21150319]
[33]
Thomas, S.; Hao, L.; Ricke, W.A.; Li, L. Biomarker discovery in mass spectrometry-based urinary proteomics. Proteomics Clin. Appl., 2016, 10(4), 358-370.
[http://dx.doi.org/10.1002/prca.201500102] [PMID: 26703953]
[34]
Lanucara, F.; Holman, S.W.; Gray, C.J.; Eyers, C.E. The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Nat. Chem., 2014, 6(4), 281-294.
[http://dx.doi.org/10.1038/nchem.1889] [PMID: 24651194]
[35]
Achour, B.; Al Feteisi, H.; Lanucara, F.; Rostami-Hodjegan, A.; Barber, J. Global proteomic analysis of human liver microsomes: Rapid characterization and quantification of hepatic drug-metabolizing enzymes. Drug Metab. Dispos., 2017, 45(6), 666-675.
[http://dx.doi.org/10.1124/dmd.116.074732] [PMID: 28373266]
[36]
Prasad, B.; Achour, B.; Artursson, P.; Hop, C.E.C.A.; Lai, Y.; Smith, P.C.; Barber, J.; Wisniewski, J.R.; Spellman, D.; Uchida, Y.; Zientek, M.A.; Unadkat, J.D.; Rostami-Hodjegan, A. Toward a consensus on applying quantitative liquid chromatography-tandem mass spectrometry proteomics in translational pharmacology research: A white paper. Clin. Pharmacol. Ther., 2019, 106(3), 525-543.
[http://dx.doi.org/10.1002/cpt.1537] [PMID: 31175671]
[37]
Dowling, P.; Zweyer, M.; Swandulla, D.; Ohlendieck, K. Characterization of contractile proteins from skeletal muscle using gel-based top-down proteomics. Proteomes, 2019, 7(2), 25.
[http://dx.doi.org/10.3390/proteomes7020025] [PMID: 31226838]
[38]
Guo, T.; Wang, X.; Li, M.; Yang, H.; Li, L.; Peng, F.; Zhan, X. Identification of glioblastoma phosphotyrosine-containing proteins with two-dimensional western blotting and tandem mass spectrometry. BioMed Res. Int., 2015, 2015, 1-21.
[http://dx.doi.org/10.1155/2015/134050] [PMID: 26090378]
[39]
Weiss, N.G.; Jarvis, J.W.; Nelson, R.W.; Hayes, M.A. Examining serum amyloid P component microheterogeneity using capillary isoelectric focusing and MALDI-MS. Proteomics, 2011, 11(1), 106-113.
[http://dx.doi.org/10.1002/pmic.201000310] [PMID: 21182198]
[40]
Babačić, H.; Lehtiö, J.; Pico de Coaña, Y.; Pernemalm, M.; Eriksson, H. In-depth plasma proteomics reveals increase in circulating PD-1 during anti-PD-1 immunotherapy in patients with metastatic cutaneous melanoma. J. Immunother. Cancer, 2020, 8(1), e000204.
[http://dx.doi.org/10.1136/jitc-2019-000204] [PMID: 32457125]
[41]
Hamza, G.M.; Bergo, V.B.; Mamaev, S.; Wojchowski, D.M.; Toran, P.; Worsfold, C.R.; Castaldi, M.P.; Silva, J.C. Affinity-bead assisted mass spectrometry (Affi-BAMS): A multiplexed microarray platform for targeted proteomics. Int. J. Mol. Sci., 2020, 21(6), 2016.
[http://dx.doi.org/10.3390/ijms21062016] [PMID: 32188029]
[42]
Ong, S.E.; Kratchmarova, I.; Mann, M. Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res., 2003, 2(2), 173-181.
[http://dx.doi.org/10.1021/pr0255708] [PMID: 12716131]
[43]
Mann, M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol., 2006, 7(12), 952-958.
[http://dx.doi.org/10.1038/nrm2067] [PMID: 17139335]
[44]
Ong, S.E.; Mann, M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protoc., 2006, 1(6), 2650-2660.
[http://dx.doi.org/10.1038/nprot.2006.427] [PMID: 17406521]
[45]
Chen, X.; Wei, S.; Ji, Y.; Guo, X.; Yang, F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics, 2015, 15(18), 3175-3192.
[http://dx.doi.org/10.1002/pmic.201500108] [PMID: 26097186]
[46]
Lau, H.T.; Suh, H.W.; Golkowski, M.; Ong, S.E. Comparing SILAC- and stable isotope dimethyl-labeling approaches for quantitative proteomics. J. Proteome Res., 2014, 13(9), 4164-4174.
[http://dx.doi.org/10.1021/pr500630a] [PMID: 25077673]
[47]
Gouw, J.W.; Krijgsveld, J.; Heck, A.J.R. Quantitative proteomics by metabolic labeling of model organisms. Mol. Cell. Proteomics, 2010, 9(1), 11-24.
[http://dx.doi.org/10.1074/mcp.R900001-MCP200] [PMID: 19955089]
[48]
Ross, P.L.; Huang, Y.N.; Marchese, J.N.; Williamson, B.; Parker, K.; Hattan, S.; Khainovski, N.; Pillai, S.; Dey, S.; Daniels, S.; Purkayastha, S.; Juhasz, P.; Martin, S.; Bartlet-Jones, M.; He, F.; Jacobson, A.; Pappin, D.J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics, 2004, 3(12), 1154-1169.
[http://dx.doi.org/10.1074/mcp.M400129-MCP200] [PMID: 15385600]
[49]
Tonack, S.; Aspinall-O`Dea, M.; Jenkins, R.E.; Elliot, V.; Murray, S.; Lane, C.S.; Kitteringham, N.R.; Neoptolemos, J.P.; Costello, E. A technically detailed and pragmatic protocol for quantitative serum proteomics using iTRAQ. J. Proteomics, 2009, 73(2), 352-356.
[http://dx.doi.org/10.1016/j.jprot.2009.07.009] [PMID: 19651253]
[50]
Thompson, A.; Schäfer, J.; Kuhn, K.; Kienle, S.; Schwarz, J.; Schmidt, G.; Neumann, T.; Hamon, C.; Mohammed, A.K.; Hamon, C. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem., 2003, 75(8), 1895-1904.
[http://dx.doi.org/10.1021/ac0262560] [PMID: 12713048]
[51]
Sinclair, J.; Timms, J.F. Quantitative profiling of serum samples using TMT protein labelling, fractionation and LC–MS/MS. Methods, 2011, 54(4), 361-369.
[http://dx.doi.org/10.1016/j.ymeth.2011.03.004] [PMID: 21397697]
[52]
Hwang, W.; Lei, W.; Katritsis, N.M.; MacMahon, M.; Chapman, K.; Han, N. Current and prospective computational approaches and challenges for developing COVID-19 vaccines. Adv. Drug Deliv. Rev., 2021, 172, 249-274.
[http://dx.doi.org/10.1016/j.addr.2021.02.004] [PMID: 33561453]
[53]
Shi, T.; Su, D.; Liu, T.; Tang, K.; Camp, D.G., II; Qian, W.J.; Smith, R.D. Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics, 2012, 12(8), 1074-1092.
[http://dx.doi.org/10.1002/pmic.201100436] [PMID: 22577010]
[54]
Huang, B.X.; Kim, H.Y. Effective identification of Akt interacting proteins by two-step chemical crosslinking, co-immuno- precipitation and mass spectrometry. PLoS One, 2013, 8(4), e61430.
[http://dx.doi.org/10.1371/journal.pone.0061430] [PMID: 23613850]
[55]
Haymond, A.; Davis, J.B.; Espina, V. Proteomics for cancer drug design. Expert Rev. Proteomics, 2019, 16(8), 647-664.
[http://dx.doi.org/10.1080/14789450.2019.1650025] [PMID: 31353977]
[56]
van Mierlo, G.; Vermeulen, M. Chromatin proteomics to study epigenetics-challenges and opportunities. Mol. Cell. Proteomics, 2021, 20, 100056.
[http://dx.doi.org/10.1074/mcp.R120.002208] [PMID: 33556626]
[57]
Geyer, P.E.; Holdt, L.M.; Teupser, D.; Mann, M. Revisiting biomarker discovery by plasma proteomics. Mol. Syst. Biol., 2017, 13(9), 942.
[http://dx.doi.org/10.15252/msb.20156297] [PMID: 28951502]
[58]
Denis, G.V.; McComb, M.E.; Faller, D.V.; Sinha, A.; Romesser, P.B.; Costello, C.E. Identification of transcription complexes that contain the double bromodomain protein Brd2 and chromatin remodeling machines. J. Proteome Res., 2006, 5(3), 502-511.
[http://dx.doi.org/10.1021/pr050430u] [PMID: 16512664]
[59]
Gomase, V.; Tagore, S. Transcriptomics. Curr. Drug Metab., 2008, 9(3), 245-249.
[http://dx.doi.org/10.2174/138920008783884759] [PMID: 18336229]
[60]
Gomase, V.; Tagore, S. Epigenomics. Curr. Drug Metab., 2008, 9(3), 232-237.
[http://dx.doi.org/10.2174/138920008783884821] [PMID: 18336226]
[61]
Wu, C.; Duan, J.; Liu, T.; Smith, R.D.; Qian, W.J. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci., 2016, 1021, 57-68.
[http://dx.doi.org/10.1016/j.jchromb.2016.01.015] [PMID: 26868616]
[62]
Moser, A.C.; Hage, D.S. Immunoaffinity chromatography: an introduction to applications and recent developments. Bioanalysis, 2010, 2(4), 769-790.
[http://dx.doi.org/10.4155/bio.10.31] [PMID: 20640220]
[63]
Fang, X.; Zhang, W.W. Affinity separation and enrichment methods in proteomic analysis. J. Proteomics, 2008, 71(3), 284-303.
[http://dx.doi.org/10.1016/j.jprot.2008.06.011] [PMID: 18619565]
[64]
Abi-Ghanem, D.A.; Berghman, L.R. Immunoaffinity Chromatography: A Review. In: Affinity Chromatography; Magdeldin, D.S., Ed.; InTech, 2012; pp. 95-103.
[65]
Gomase, V. Prediction of antigenic epitopes of neurotoxin Bmbktx1 from Mesobuthus martensii. Curr. Drug Discov. Technol., 2006, 3(3), 225-229.
[http://dx.doi.org/10.2174/157016306780136817] [PMID: 17311567]
[66]
Cossarizza, A.; Chang, H.D.; Radbruch, A.; Acs, A.; Adam, D.; Adam-Klages, S.; Agace, W.W.; Aghaeepour, N.; Akdis, M.; Allez, M. Guidelines for the use of flow cytometry and cell sorting in immunological studies. Eur. J. Immunol., 2019, 49(10), 1457-1973.
[http://dx.doi.org/10.1002/eji.201970107.]
[67]
Sheng, W.; Zhang, C.; Mohiuddin, T.M.; Al-Rawe, M.; Zeppernick, F.; Falcone, F.H.; Meinhold-Heerlein, I.; Hussain, A.F. Multiplex immunofluorescence: A powerful tool in cancer immunotherapy. Int. J. Mol. Sci., 2023, 24(4), 3086.
[http://dx.doi.org/10.3390/ijms24043086] [PMID: 36834500]
[68]
Rivest, F.; Eroglu, D.; Pelz, B.; Kowal, J.; Kehren, A.; Navikas, V.; Procopio, M.G.; Bordignon, P.; Pérès, E.; Ammann, M.; Dorel, E.; Scalmazzi, S.; Bruno, L.; Ruegg, M.; Campargue, G.; Casqueiro, G.; Arn, L.; Fischer, J.; Brajkovic, S.; Joris, P.; Cassano, M.; Dupouy, D. Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics. Sci. Rep., 2023, 13(1), 16994.
[http://dx.doi.org/10.1038/s41598-023-43435-w] [PMID: 37813886]
[69]
Tan, W.C.C.; Nerurkar, S.N.; Cai, H.Y.; Ng, H.H.M.; Wu, D.; Wee, Y.T.F.; Lim, J.C.T.; Yeong, J.; Lim, T.K.H. Overview of multiplex immunohistochemistry/immunofluorescence techniques in the era of cancer immunotherapy. Cancer Commun. (Lond.), 2020, 40(4), 135-153.
[http://dx.doi.org/10.1002/cac2.12023] [PMID: 32301585]
[70]
Bosisio, F.M.; Van, H.Y.; Messiaen, J.; Bolognesi, M.M.; Marcelis, L.; Van Haele, M.; Cattoretti, G.; Antoranz, A.; De Smet, F. Next-Generation Pathology Using Multiplexed Immunohistochemistry: Mapping Tissue Architecture at Single-Cell Level. Front. Oncol., 2022, 12, 918900.
[http://dx.doi.org/10.3389/fonc.2022.918900] [PMID: 35992810]
[71]
Shakya, R.; Nguyen, T.H.; Waterhouse, N.; Khanna, R. Immune contexture analysis in immuno-oncology: Applications and challenges of multiplex fluorescent immunohistochemistry. Clin. Transl. Immunology, 2020, 9(10), e1183.
[http://dx.doi.org/10.1002/cti2.1183] [PMID: 33072322]
[72]
Taylor, C.R.; Levenson, R.M. Quantification of immunohistochemistry-issues concerning methods, utility and semiquantitative assessment II. Histopathology, 2006, 49(4), 411-424.
[http://dx.doi.org/10.1111/j.1365-2559.2006.02513.x] [PMID: 16978205]
[73]
Blind, C.; Koepenik, A.; Pacyna-Gengelbach, M.; Fernahl, G.; Deutschmann, N.; Dietel, M.; Krenn, V.; Petersen, I. Antigenicity testing by immunohistochemistry after tissue oxidation. J. Clin. Pathol., 2008, 61(1), 79-83.
[http://dx.doi.org/10.1136/jcp.2007.047340] [PMID: 17412873]
[74]
van den Broek, L.J.C.M.; van de Vijver, M.J. Assessment of problems in diagnostic and research immunohistochemistry associated with epitope instability in stored paraffin sections. Appl. Immunohistochem. Mol. Morphol., 2000, 8(4), 316-321.
[http://dx.doi.org/10.1097/00129039-200012000-00009] [PMID: 11127924]
[75]
Hewitt, S.M.; Baskin, D.G.; Frevert, C.W.; Stahl, W.L.; Rosa-Molinar, E. Controls for immunohistochemistry. J. Histochem. Cytochem., 2014, 62(10), 693-697.
[http://dx.doi.org/10.1369/0022155414545224] [PMID: 25023613]
[76]
González-Martínez, M.Á.; Puchades, R.; Maquieira, Á. Immunoanalytical technique: Enzyme-linked immunosorbent assay (ELISA). In: Modern Techniques for Food Authentication; Elsevier, 2018; pp. 617-657.
[http://dx.doi.org/10.1016/B978-0-12-814264-6.00015-3]
[77]
Slage, K.M.; Ghosn, S.J. Immunoassays: Tools for sensitive, specific, and accurate test results. Lab. Med., 1996, 27(3), 117-183.
[78]
Wu, A.H.B. A selected history and future of immunoassay development and applications in clinical chemistry. Clin. Chim. Acta, 2006, 369(2), 119-124.
[http://dx.doi.org/10.1016/j.cca.2006.02.045] [PMID: 16701599]
[79]
David, W. The Immunoassay Handbook; Elsevier: Amsterdam, 2005.
[80]
Cox, K.L.; Devanarayan, V.; Kriauciunas, A.; Manetta, J.; Montrose, C.; Sittampalam, S. Immunoassay Methods; Eli Lilly & Company and the National Center for Advancing Translational Sciences, 2004.
[PMID: 22553884]
[81]
Ellington, A.A.; Kullo, I.J.; Bailey, K.R.; Klee, G.G. Antibody-based protein multiplex platforms: Technical and operational challenges. Clin. Chem., 2010, 56(2), 186-193.
[http://dx.doi.org/10.1373/clinchem.2009.127514] [PMID: 19959625]
[82]
Engvall, E.; Perlmann, P. Enzyme-linked immunosorbent assay (ELISA) quantitative assay of immunoglobulin G. Immunochemistry, 1971, 8(9), 871-874.
[http://dx.doi.org/10.1016/0019-2791(71)90454-X] [PMID: 5135623]
[83]
McCarthy, J. Immunological techniques: ELISA. In: Detecting Pathogens in Food; , 2003; pp. 241-258.
[http://dx.doi.org/10.1533/9781855737044.2.241.]
[84]
Ahsan, H. Monoplex and multiplex immunoassays: Approval, advancements, and alternatives. Comp. Clin. Pathol., 2021, 31(2), 333-345.
[http://dx.doi.org/10.1007/s00580-021-03302-4] [PMID: 34840549]
[85]
Song, Z.; Mao, J.; Barrero, R.; Wang, P.; Zhang, F.; Wang, T. Development of a CD63 aptamer for efficient cancer immunochemistry and immunoaffinity-based exosome isolation. Molecules, 2020, 25(23), 5585.
[http://dx.doi.org/10.3390/molecules25235585] [PMID: 33261145]
[86]
Greening, D.W.; Xu, R.; Ji, H.; Tauro, B.J.; Simpson, R.J. A protocol for exosome isolation and characterization: Evaluation of ultracentrifugation, density-gradient separation, and immunoaffinity capture methods. Methods Mol. Biol., 2015, 1295, 179-209.
[http://dx.doi.org/10.1007/978-1-4939-2550-6_15] [PMID: 25820723]
[87]
Tang, Q.; Xiao, X.; Li, R.; He, H.; Li, S.; Ma, C. Recent advances in detection for breast-cancer-derived exosomes. Molecules, 2022, 27(19), 6673.
[http://dx.doi.org/10.3390/molecules27196673] [PMID: 36235208]
[88]
Kang, Y.T.; Hadlock, T.; Lo, T.W.; Purcell, E.; Mutukuri, A.; Fouladdel, S.; Raguera, M.D.S.; Fairbairn, H.; Murlidhar, V.; Durham, A.; McLean, S.A.; Nagrath, S. Dual-isolation and profiling of circulating tumor cells and cancer exosomes from blood samples with melanoma using immunoaffinity-based microfluidic interfaces. Adv. Sci. (Weinh.), 2020, 7(19), 2001581.
[http://dx.doi.org/10.1002/advs.202001581] [PMID: 33042766]
[89]
Li, P.; Yu, X.; Han, W.; Kong, Y.; Bao, W.; Zhang, J.; Zhang, W.; Gu, Y. Ultrasensitive and reversible nanoplatform of urinary exosomes for prostate cancer diagnosis. ACS Sens., 2019, 4(5), 1433-1441.
[http://dx.doi.org/10.1021/acssensors.9b00621] [PMID: 31017389]
[90]
Gu, H.; Ren, J.M.; Jia, X.; Levy, T.; Rikova, K.; Yang, V.; Lee, K.A.; Stokes, M.P.; Silva, J.C. Quantitative profiling of post-translational modifications by immunoaffinity enrichment and LC-MS/MS in cancer serum without immunodepletion. Mol. Cell. Proteomics, 2016, 15(2), 692-702.
[http://dx.doi.org/10.1074/mcp.O115.052266] [PMID: 26635363]
[91]
Cominetti, O.; Núñez Galindo, A.; Corthésy, J.; Oller Moreno, S.; Irincheeva, I.; Valsesia, A.; Astrup, A.; Saris, W.H.M.; Hager, J.; Kussmann, M.; Dayon, L. Proteomic biomarker discovery in 1000 human plasma samples with mass spectrometry. J. Proteome Res., 2016, 15(2), 389-399.
[http://dx.doi.org/10.1021/acs.jproteome.5b00901] [PMID: 26620284]
[92]
Parker, C.E.; Borchers, C.H. Mass spectrometry based biomarker discovery, verification, and validation-Quality assurance and control of protein biomarker assays. Mol. Oncol., 2014, 8(4), 840-858.
[http://dx.doi.org/10.1016/j.molonc.2014.03.006] [PMID: 24713096]
[93]
Rifai, N.; Gillette, M.A.; Carr, S.A. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol., 2006, 24(8), 971-983.
[http://dx.doi.org/10.1038/nbt1235] [PMID: 16900146]
[94]
Skates, S.J.; Gillette, M.A.; LaBaer, J.; Carr, S.A.; Anderson, L.; Liebler, D.C.; Ransohoff, D.; Rifai, N.; Kondratovich, M.; Težak, Ž.; Mansfield, E.; Oberg, A.L.; Wright, I.; Barnes, G.; Gail, M.; Mesri, M.; Kinsinger, C.R.; Rodriguez, H.; Boja, E.S. Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies. J. Proteome Res., 2013, 12(12), 5383-5394.
[http://dx.doi.org/10.1021/pr400132j] [PMID: 24063748]
[95]
Zhou, C.; Simpson, K.L.; Lancashire, L.J.; Walker, M.J.; Dawson, M.J.; Unwin, R.D.; Rembielak, A.; Price, P.; West, C.; Dive, C.; Whetton, A.D. Statistical considerations of optimal study design for human plasma proteomics and biomarker discovery. J. Proteome Res., 2012, 11(4), 2103-2113.
[http://dx.doi.org/10.1021/pr200636x] [PMID: 22338609]
[96]
Mann, M.; Kumar, C.; Zeng, W.F.; Strauss, M.T. Artificial intelligence for proteomics and biomarker discovery. Cell Syst., 2021, 12(8), 759-770.
[http://dx.doi.org/10.1016/j.cels.2021.06.006] [PMID: 34411543]
[97]
Hochrainer, K.; Yang, W. Stroke proteomics: From discovery to diagnostic and therapeutic applications. Circ. Res., 2022, 130(8), 1145-1166.
[http://dx.doi.org/10.1161/CIRCRESAHA.122.320110] [PMID: 35420912]
[98]
Sandin, M.; Chawade, A.; Levander, F. Is label-free LC-MS/MS ready for biomarker discovery? Proteomics Clin. Appl., 2015, 9(3-4), 289-294.
[http://dx.doi.org/10.1002/prca.201400202] [PMID: 25656266]
[99]
Keshishian, H.; Burgess, M.W.; Specht, H.; Wallace, L.; Clauser, K.R.; Gillette, M.A.; Carr, S.A. Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry. Nat. Protoc., 2017, 12(8), 1683-1701.
[http://dx.doi.org/10.1038/nprot.2017.054] [PMID: 28749931]
[100]
Vellan, C.J.; Jayapalan, J.J.; Yoong, B.K.; Abdul-Aziz, A.; Mat-Junit, S.; Subramanian, P. Application of proteomics in pancreatic ductal adenocarcinoma biomarker investigations: A review. Int. J. Mol. Sci., 2022, 23(4), 2093.
[http://dx.doi.org/10.3390/ijms23042093] [PMID: 35216204]
[101]
Schiess, R.; Wollscheid, B.; Aebersold, R. Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol., 2009, 3(1), 33-44.
[http://dx.doi.org/10.1016/j.molonc.2008.12.001] [PMID: 19383365]
[102]
Radulovic, D.; Jelveh, S.; Ryu, S.; Hamilton, T.G.; Foss, E.; Mao, Y.; Emili, A. Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics, 2004, 3(10), 984-997.
[http://dx.doi.org/10.1074/mcp.M400061-MCP200] [PMID: 15269249]
[103]
Srinivas, P.R.; Verma, M.; Zhao, Y.; Srivastava, S. Proteomics for cancer biomarker discovery. Clin. Chem., 2002, 48(8), 1160-1169.
[PMID: 12142368]
[104]
Gomase, V.; Tagore, S.; Kale, K.; Bhiwgade, D. Oncogenomics. Curr. Drug Metab., 2008, 9(3), 199-206.
[http://dx.doi.org/10.2174/138920008783884713] [PMID: 18336222]
[105]
Gomase, V.; Tagore, S.; Changbhale, S.; Kale, K. Pharmacogenomics. Curr. Drug Metab., 2008, 9(3), 207-212.
[http://dx.doi.org/10.2174/138920008783884830] [PMID: 18336223]
[106]
Gomase, V.S.; Tagore, S. Vaccinomics. Gene Ther. Mol. Biol., 2008, 12, 141-146.
[107]
Gomase, V.; Tagore, S. Blood stage parasites: sufficient to induce protective immunity. Curr. Drug Metab., 2008, 9(3), 238-240.
[http://dx.doi.org/10.2174/138920008783884704] [PMID: 18336227]
[108]
Gomase, V.S.; Tagore, S.; Shyamkumar, K. Prediction of antigenic binders from C-terminal domain human papillomavirus oncoprotein E7. Gene Ther. Mol. Biol., 2008, 12, 147-166.
[109]
Gomase, V.S.; Kale, K.V. Development of MHC class nonamers from cowpea mosaic viral protein. Gene Ther. Mol. Biol., 2008, 12, 87-94.
[110]
Gomase, V.S.; Kale, K.V. Prediction of MHC binder for fragment based viral peptide vaccines from cabbage leaf curl virus. Gene Ther. Mol. Biol., 2008, 12, 83-86.
[111]
Gomase, V.S.; Tagore, S. Transgenomics. Gene Ther. Mol. Biol., 2008, 12, 77-82.
[112]
Gomase, V.S.; Kale, K.V. Antigenic epitopes of viral polyprotein: An approach for fragment based peptide vaccines from papaya ringspot virus. Gene Ther. Mol. Biol., 2008, 12, 31-38.
[113]
Ojha, R.; Pandey, R.K.; Prajapati, V.K. Vaccinomics strategy to concoct a promising subunit vaccine for visceral leishmaniasis targeting sandfly and leishmania antigens. Int. J. Biol. Macromol., 2020, 156, 548-557.
[http://dx.doi.org/10.1016/j.ijbiomac.2020.04.097] [PMID: 32311400]
[114]
Nelde, A.; Rammensee, H.G.; Walz, J.S. The peptide vaccine of the future. Mol. Cell. Proteomics, 2021, 20, 100022.
[http://dx.doi.org/10.1074/mcp.R120.002309] [PMID: 33583769]
[115]
Du, Y.; Hu, X.; Miao, L.; Chen, J. Current status and development prospects of aquatic vaccines. Front. Immunol., 2022, 13, 1040336.
[http://dx.doi.org/10.3389/fimmu.2022.1040336] [PMID: 36439092]
[116]
Gupta, M.; Wahi, A.; Sharma, P.; Nagpal, R.; Raina, N.; Kaurav, M.; Bhattacharya, J.; Rodrigues Oliveira, S.M.; Dolma, K.G.; Paul, A.K.; de Lourdes Pereira, M.; Wilairatana, P.; Rahmatullah, M.; Nissapatorn, V. Recent advances in cancer vaccines: Challenges, achievements, and futuristic prospects. Vaccines (Basel), 2022, 10(12), 2011.
[http://dx.doi.org/10.3390/vaccines10122011] [PMID: 36560420]
[117]
Zhuang, L.; Ye, Z.; Li, L.; Yang, L.; Gong, W.; Next-Generation, T.B. Next-generation TB vaccines: Progress, challenges, and prospects. Vaccines (Basel), 2023, 11(8), 1304.
[http://dx.doi.org/10.3390/vaccines11081304] [PMID: 37631874]
[118]
Stenger, S.; Grasshoff, H.; Hundt, J.E.; Lange, T. Potential effects of shift work on skin autoimmune diseases. Front. Immunol., 2023, 13, 1000951.
[http://dx.doi.org/10.3389/fimmu.2022.1000951] [PMID: 36865523]
[119]
Ma, W.T.; Gao, F.; Gu, K.; Chen, D.K. The role of monocytes and macrophages in autoimmune diseases: A comprehensive review. Front. Immunol., 2019, 10, 1140.
[http://dx.doi.org/10.3389/fimmu.2019.01140] [PMID: 31178867]
[120]
Ganesan, V.; Schmidt, B.; Avula, R.; Cooke, D.; Maggiacomo, T.; Tellin, L.; Ascherman, D.P.; Bruchez, M.P.; Minden, J. Immuno-proteomics: Development of a novel reagent for separating antibodies from their target proteins. Biochim. Biophys. Acta. Proteins Proteomics, 2015, 1854(6), 592-600.
[http://dx.doi.org/10.1016/j.bbapap.2014.10.011] [PMID: 25466873]
[121]
Zubair, M.; Wang, J.; Yu, Y.; Faisal, M.; Qi, M.; Shah, A.U.; Feng, Z.; Shao, G.; Wang, Y.; Xiong, Q. Proteomics approaches: A review regarding an importance of proteome analyses in understanding the pathogens and diseases. Front. Vet. Sci., 2022, 9, 1079359.
[http://dx.doi.org/10.3389/fvets.2022.1079359] [PMID: 36601329]
[122]
Whiteaker, J.R.; Sharma, K.; Hoffman, M.A.; Kuhn, E.; Zhao, L.; Cocco, A.R.; Schoenherr, R.M.; Kennedy, J.J.; Voytovich, U.; Lin, C.; Fang, B.; Bowers, K.; Whiteley, G.; Colantonio, S.; Bocik, W.; Roberts, R.; Hiltke, T.; Boja, E.; Rodriguez, H.; McCormick, F.; Holderfield, M.; Carr, S.A.; Koomen, J.M.; Paulovich, A.G. Targeted mass-spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP kinase, and AKT signaling. Cell Rep. Methods, 2021, 1(3), 100015.
[http://dx.doi.org/10.1016/j.crmeth.2021.100015] [PMID: 34671754]
[123]
Rebecca, V.W.; Wood, E.; Fedorenko, I.V.; Paraiso, K.H.T.; Haarberg, H.E.; Chen, Y.; Xiang, Y.; Sarnaik, A.; Gibney, G.T.; Sondak, V.K.; Koomen, J.M.; Smalley, K.S.M. Evaluating melanoma drug response and therapeutic escape with quantitative proteomics. Mol. Cell. Proteomics, 2014, 13(7), 1844-1854.
[http://dx.doi.org/10.1074/mcp.M113.037424] [PMID: 24760959]
[124]
Schoenherr, R.M.; Saul, R.G.; Whiteaker, J.R.; Yan, P.; Whiteley, G.R.; Paulovich, A.G. Anti-peptide monoclonal antibodies generated for immuno-multiple reaction monitoring-mass spectrometry assays have a high probability of supporting Western blot and ELISA. Mol. Cell. Proteomics, 2015, 14(2), 382-398.
[http://dx.doi.org/10.1074/mcp.O114.043133] [PMID: 25512614]
[125]
Perna, F.; Berman, S.H.; Soni, R.K.; Mansilla-Soto, J.; Eyquem, J.; Hamieh, M.; Hendrickson, R.C.; Brennan, C.W.; Sadelain, M. Integrating proteomics and transcriptomics for systematic combinatorial chimeric antigen receptor therapy ofAML. Cancer Cell, 2017, 32(4), 506-519.e5.
[http://dx.doi.org/10.1016/j.ccell.2017.09.004] [PMID: 29017060]
[126]
Raghunathan, R.; Turajane, K.; Wong, L.C. Biomarkers in neurodegenerative diseases: Proteomics spotlight on ALS and Parkinson’s disease. Int. J. Mol. Sci., 2022, 23(16), 9299.
[http://dx.doi.org/10.3390/ijms23169299] [PMID: 36012563]
[127]
Zhu, J.; Nie, S.; Wu, J.; Lubman, D.M. Target proteomic profiling of frozen pancreatic CD24+ adenocarcinoma tissues by immuno-laser capture microdissection and nano-LC-MS/MS. J. Proteome Res., 2013, 12(6), 2791-2804.
[http://dx.doi.org/10.1021/pr400139c] [PMID: 23679566]
[128]
MacMullan, M.A.; Dunn, Z.S.; 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), 7872-7888.
[http://dx.doi.org/10.7150/thno.37373] [PMID: 31695805]
[129]
Shi, T.; Song, E.; Nie, S.; Rodland, K.D.; Liu, T.; Qian, W.J.; Smith, R.D. Advances in targeted proteomics and applications to biomedical research. Proteomics, 2016, 16(15-16), 2160-2182.
[http://dx.doi.org/10.1002/pmic.201500449] [PMID: 27302376]
[130]
Kobeissy, F.; Goli, M.; Yadikar, H.; Shakkour, Z.; Kurup, M.; Haidar, M.A.; Alroumi, S.; Mondello, S.; Wang, K.K.; Mechref, Y. Advances in neuroproteomics for neurotrauma: Unraveling insights for personalized medicine and future prospects. Front. Neurol., 2023, 14, 1288740.
[http://dx.doi.org/10.3389/fneur.2023.1288740] [PMID: 38073638]
[131]
Vizcaíno, J.A.; Kubiniok, P.; Kovalchik, K.A.; Ma, Q.; Duquette, J.D.; Mongrain, I.; Deutsch, E.W.; Peters, B.; Sette, A.; Sirois, I.; Caron, E. The human immunopeptidome project: A roadmap to predict and treat immune diseases. Mol. Cell. Proteomics, 2020, 19(1), 31-49.
[http://dx.doi.org/10.1074/mcp.R119.001743] [PMID: 31744855]
[132]
Spira, A.; Disis, M.L.; Schiller, J.T.; Vilar, E.; Rebbeck, T.R.; Bejar, R.; Ideker, T.; Arts, J.; Yurgelun, M.B.; Mesirov, J.P.; Rao, A.; Garber, J.; Jaffee, E.M.; Lippman, S.M. Leveraging premalignant biology for immune-based cancer prevention. Proc. Natl. Acad. Sci. USA, 2016, 113(39), 10750-10758.
[http://dx.doi.org/10.1073/pnas.1608077113] [PMID: 27638202]
[133]
Jacob, M.; Masood, A.; Shinwari, Z.; Abdel Jabbar, M.; Al-Mousa, H.; Arnaout, R.; AlSaud, B.; Dasouki, M.; Alaiya, A.A.; Abdel Rahman, A.M. Proteomics profiling to distinguish DOCK8 deficiency from atopic dermatitis. Front. Allergy, 2021, 2, 774902.
[http://dx.doi.org/10.3389/falgy.2021.774902] [PMID: 35386989]
[134]
Pulendran, B.; Davis, M.M. The science and medicine of human immunology. Science, 2020, 369(6511), eaay4014.
[http://dx.doi.org/10.1126/science.aay4014] [PMID: 32973003]
[135]
Jayawardana, K.; Schramm, S.J.; Haydu, L.; Thompson, J.F.; Scolyer, R.A.; Mann, G.J.; Müller, S.; Yang, J.Y.H. Determination of prognosis in metastatic melanoma through integration of clinico-pathologic, mutation, mRNA, microRNA, and protein information. Int. J. Cancer, 2015, 136(4), 863-874.
[http://dx.doi.org/10.1002/ijc.29047] [PMID: 24975271]
[136]
Mo, Q.; Wang, S.; Seshan, V.E.; Olshen, A.B.; Schultz, N.; Sander, C.; Powers, R.S.; Ladanyi, M.; Shen, R. Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc. Natl. Acad. Sci. USA, 2013, 110(11), 4245-4250.
[http://dx.doi.org/10.1073/pnas.1208949110] [PMID: 23431203]
[137]
Wu, D.; Wang, D.; Zhang, M.Q.; Gu, J. Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: Application to cancer molecular classification. BMC Genomics, 2015, 16(1), 1022.
[http://dx.doi.org/10.1186/s12864-015-2223-8] [PMID: 26626453]
[138]
Devonshire, A.; Gautam, Y.; Johansson, E.; Mersha, T.B. Multi-omics profiling approach in food allergy. World Allergy Organ. J., 2023, 16(5), 100777.
[http://dx.doi.org/10.1016/j.waojou.2023.100777] [PMID: 37214173]
[139]
Jain, K.K. Innovations, challenges and future prospects of oncoproteomics. Mol. Oncol., 2008, 2(2), 153-160.
[http://dx.doi.org/10.1016/j.molonc.2008.05.003] [PMID: 19383334]
[140]
Punetha, A.; Kotiya, D. Advancements in oncoproteomics technologies: Treading toward translation into clinical practice. Proteomes, 2023, 11(1), 2.
[http://dx.doi.org/10.3390/proteomes11010002] [PMID: 36648960]
[141]
López Villar, E.; Wang, X.; Madero, L.; Cho, W.C. Application of oncoproteomics to aberrant signalling networks in changing the treatment paradigm in acute lymphoblastic leukaemia. J. Cell. Mol. Med., 2015, 19(1), 46-52.
[http://dx.doi.org/10.1111/jcmm.12507] [PMID: 25537633]
[142]
Karhemo, P.R.; Hyvönen, M.; Laakkonen, P. Metastasis-associated cell surface oncoproteomics. Front. Pharmacol., 2012, 3, 192.
[http://dx.doi.org/10.3389/fphar.2012.00192] [PMID: 23162466]
[143]
Cho, W.C.S. Contribution of oncoproteomics to cancer biomarker discovery. Mol. Cancer, 2007, 6(1), 25.
[http://dx.doi.org/10.1186/1476-4598-6-25] [PMID: 17407558]
[144]
Alhamdani, M.S.S.; Schröder, C.; Hoheisel, J.D. Oncoproteomic profiling with antibody microarrays. Genome Med., 2009, 1(7), 68.
[http://dx.doi.org/10.1186/gm68] [PMID: 19591665]
[145]
Jain, K.K. Recent advances in clinical oncoproteomics. J. Balkan Union Oncol., 2007, 12, S31-S38.
[PMID: 17935275]
[146]
Zhou, L.; Li, Q.; Wang, J.; Huang, C.; Nice, E.C. Oncoproteomics: Trials and tribulations. Proteomics Clin. Appl., 2016, 10(4), 516-531.
[http://dx.doi.org/10.1002/prca.201500081] [PMID: 26518147]
[147]
Cho, W.C.S.; Cheng, C.H.K. Oncoproteomics: Current trends and future perspectives. Expert Rev. Proteomics, 2007, 4(3), 401-410.
[http://dx.doi.org/10.1586/14789450.4.3.401] [PMID: 17552924]
[148]
Roboz, J. Mass spectrometry in diagnostic oncoproteomics. Cancer Invest., 2005, 23(5), 465-478.
[http://dx.doi.org/10.1081/CNV-67182] [PMID: 16193645]
[149]
Jain, K.K. Role of oncoproteomics in the personalized management of cancer. Expert Rev. Proteomics, 2004, 1(1), 49-55.
[http://dx.doi.org/10.1586/14789450.1.1.49] [PMID: 15966798]
[150]
Shukla, H.D.; Mahmood, J.; Vujaskovic, Z. Integrated proteo-genomic approach for early diagnosis and prognosis of cancer. Cancer Lett., 2015, 369(1), 28-36.
[http://dx.doi.org/10.1016/j.canlet.2015.08.003] [PMID: 26276717]
[151]
Joshi, S.; Tiwari, A.K.; Mondal, B.; Sharma, A. Oncoproteomics. Clin. Chim. Acta, 2011, 412(3-4), 217-226.
[http://dx.doi.org/10.1016/j.cca.2010.10.002] [PMID: 20955692]
[152]
Vs, G.; Krishnan, S. Phospho-onco-proteomics. Int. J. Genet., 2009, 1(1), 6-15.
[http://dx.doi.org/10.9735/0975-2862.1.1.6-15]
[153]
Fourman, L.T.; Stanley, T.L.; Ockene, M.W.; McClure, C.M.; Toribio, M.; Corey, K.E.; Chung, R.T.; Torriani, M.; Kleiner, D.E.; Hadigan, C.M.; Grinspoon, S.K. Proteomic analysis of hepatic fibrosis in human immunodeficiency virus–associated nonalcoholic fatty liver disease demonstrates up-regulation of immune response and tissue repair pathways. J. Infect. Dis., 2023, 227(4), 565-576.
[http://dx.doi.org/10.1093/infdis/jiac475] [PMID: 36461941]
[154]
Lorey, M.; Adler, B.; Yan, H.; Soliymani, R.; Ekström, S.; Yli-Kauhaluoma, J.; Laurell, T.; Baumann, M. Mass-tag enhanced immuno-laser desorption/ionization mass spectrometry for sensitive detection of intact protein antigens. Anal. Chem., 2015, 87(10), 5255-5262.
[http://dx.doi.org/10.1021/acs.analchem.5b00304] [PMID: 25867450]
[155]
Yeh, C.H.; Huang, H.H.; Chang, T.C.; Lin, H.P.; Lin, Y.C. Using an electro-microchip, a nanogold probe, and silver enhancement in an immunoassay. Biosens. Bioelectron., 2009, 24(6), 1661-1666.
[http://dx.doi.org/10.1016/j.bios.2008.08.039] [PMID: 18838263]
[156]
Yousaf, M.; Ismail, S.; Ullah, A.; Bibi, S. Immuno-informatics profiling of monkeypox virus cell surface binding protein for designing a next generation multi-valent peptide-based vaccine. Front. Immunol., 2022, 13, 1035924.
[http://dx.doi.org/10.3389/fimmu.2022.1035924] [PMID: 36405737]
[157]
Dutsch, A.; Uhlig, C.; Bock, M.; Graesser, C.; Schuchardt, S.; Uhlig, S.; Schunkert, H.; Joner, M.; Holdenrieder, S.; Lechner, K. Multi-omic candidate screening for markers of severe clinical courses of COVID-19. J. Clin. Med., 2023, 12(19), 6225.
[http://dx.doi.org/10.3390/jcm12196225] [PMID: 37834869]
[158]
Ouali, R.; Vieira, L.R.; Salmon, D.; Bousbata, S. Rhodnius prolixus hemolymph immuno-physiology: deciphering the systemic immune response triggered by Trypanosoma cruzi establishment in the vector using quantitative proteomics. Cells, 2022, 11(9), 1449.
[http://dx.doi.org/10.3390/cells11091449] [PMID: 35563760]
[159]
Moens, C.; Filée, P.; Boes, A.; Alie, C.; Dufrasne, F.; André, E.; Marché, S.; Fretin, D. Identification of new Mycobacterium bovis antigens and development of a multiplexed serological bead-immunoassay for the diagnosis of bovine tuberculosis in cattle. PLoS One, 2023, 18(10), e0292590.
[http://dx.doi.org/10.1371/journal.pone.0292590] [PMID: 37812634]
[160]
Frigerio, R.; Musicò, A.; Strada, A.; Mussida, A.; Gagni, P.; Bergamaschi, G.; Chiari, M.; Barzon, L.; Gori, A.; Cretich, M. Epitope mapping on microarrays highlights a sequence on the N protein with strong immune response in SARS-CoV-2 patients. Methods Mol. Biol., 2023, 2578, 209-217.
[http://dx.doi.org/10.1007/978-1-0716-2732-7_15] [PMID: 36152290]
[161]
Aparici-Herraiz, I.; Gualdrón-López, M.; Castro-Cavadía, C.J.; Carmona-Fonseca, J.; Yasnot, M.F.; Fernandez-Becerra, C.; del Portillo, H.A. Antigen discovery in circulating extracellular vesicles From Plasmodium vivax patients. Front. Cell. Infect. Microbiol., 2022, 11, 811390.
[http://dx.doi.org/10.3389/fcimb.2021.811390] [PMID: 35141172]
[162]
Hu, B.; Sajid, M.; Lv, R.; Liu, L.; Sun, C. A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology. Front. Immunol., 2022, 13, 996721.
[http://dx.doi.org/10.3389/fimmu.2022.996721] [PMID: 36389765]
[163]
Maus, A.; Figdore, D.; Milosevic, D.; Algeciras-Schimnich, A.; Bornhorst, J. Comparison of intact protein and digested peptide techniques for high throughput proteotyping of ApoE. Clin. Proteomics, 2022, 19(1), 42.
[http://dx.doi.org/10.1186/s12014-022-09379-5] [PMID: 36380282]
[164]
Zhang, Y.V.; Wei, B.; Zhu, Y.; Zhang, Y.; Bluth, M.H. Liquid Chromatography–Tandem Mass Spectrometry. Clin. Lab. Med., 2016, 36(4), 635-661.
[http://dx.doi.org/10.1016/j.cll.2016.07.001] [PMID: 27842783]
[165]
Hirtz, C.; Vialaret, J.; Nouadje, G.; Schraen, S.; Benlian, P.; Mary, S.; Philibert, P.; Tiers, L.; Bros, P.; Delaby, C.; Gabelle, A.; Lehmann, S. Development of new quantitative mass spectrometry and semi-automatic isofocusing methods for the determination of Apolipoprotein E typing. Clin. Chim. Acta, 2016, 454, 33-38.
[http://dx.doi.org/10.1016/j.cca.2015.12.020] [PMID: 26707914]
[166]
Signore, M.; Manganelli, V. Reverse phase protein arrays in cancer stem cells. Methods Cell Biol., 2022, 171, 33-61.
[http://dx.doi.org/10.1016/bs.mcb.2022.04.004] [PMID: 35953205]
[167]
Whiteaker, J.R.; Lundeen, R.A.; Zhao, L.; Schoenherr, R.M.; Burian, A.; Huang, D.; Voytovich, U.; Wang, T.; Kennedy, J.J.; Ivey, R.G.; Lin, C.; Murillo, O.D.; Lorentzen, T.D.; Thiagarajan, M.; Colantonio, S.; Caceres, T.W.; Roberts, R.R.; Knotts, J.G.; Reading, J.J.; Kaczmarczyk, J.A.; Richardson, C.W.; Garcia-Buntley, S.S.; Bocik, W.; Hewitt, S.M.; Murray, K.E.; Do, N.; Brophy, M.; Wilz, S.W.; Yu, H.; Ajjarapu, S.; Boja, E.; Hiltke, T.; Rodriguez, H.; Paulovich, A.G. Targeted mass spectrometry enables multiplexed quantification of immunomodulatory proteins in clinical biospecimens. Front. Immunol., 2021, 12, 765898.
[http://dx.doi.org/10.3389/fimmu.2021.765898] [PMID: 34858420]
[168]
Scarano, C.; Veneruso, I.; De Simone, R.R.; Di Bonito, G.; Secondino, A.; D’Argenio, V. The third-generation sequencing challenge: Novel insights for the omic sciences. Biomolecules, 2024, 14(5), 568.
[http://dx.doi.org/10.3390/biom14050568] [PMID: 38785975]
[169]
Dezem, F.S.; Arjumand, W.; DuBose, H.; Morosini, N.S.; Plummer, J. Spatially resolved single-cell omics: Methods, challenges, and future perspectives. Annu. Rev. Biomed. Data Sci., 2024, 7(1), 131-153.
[http://dx.doi.org/10.1146/annurev-biodatasci-102523-103640] [PMID: 38768396]
[170]
Tan, Y.C.; Low, T.Y.; Lee, P.Y.; Lim, L.C. Single-cell proteomics by mass spectrometry: Advances and implications in cancer research. Proteomics, 2024, 24(12-13), 2300210.
[http://dx.doi.org/10.1002/pmic.202300210] [PMID: 38727198]
[171]
Gomase, V.; Tagore, S. RNAi-a tool for target finding in new drug development. Curr. Drug Metab., 2008, 9(3), 241-244.
[http://dx.doi.org/10.2174/138920008783884777] [PMID: 18336228]
[172]
Gomase, V.S.; Parundekar, A.N. microRNA: human disease and development. Int. J. Bioinform. Res. Appl., 2009, 5(5), 479-500.
[http://dx.doi.org/10.1504/IJBRA.2009.028678] [PMID: 19778865]
[173]
Agioti, S.; Zaravinos, A. Immune cytolytic activity and strategies for therapeutic treatment. Int. J. Mol. Sci., 2024, 25(7), 3624.
[http://dx.doi.org/10.3390/ijms25073624] [PMID: 38612436]
[174]
Mishra, S.; Gomase, V.S. In silico insights to predict the major histocompatibility complex peptide binders from protein. Eur. J. Mol. Clin. Med., 2021, 8(2), 219-226.
[175]
Gomase, V.S.; Kale, K.V.; Chikhale, N.J.; Changbhale, S.S. Prediction of MHC binding peptides and epitopes from alfalfa mosaic virus. Curr. Drug Discov. Technol., 2007, 4(2), 117-125.
[http://dx.doi.org/10.2174/157016307781483441] [PMID: 17691913]
[176]
Mishra, S.; Gomase, V.S. Application of in silico approach in prediction of epitopes. Res. J. Biotechnol., 2021, 16(2), 206-214.
[177]
Porfetye, A.T.; Stege, P.; Rebollido-Rios, R.; Hoffmann, D.; Schrader, T.; Vetter, I.R. How do molecular tweezers bind to proteins? Lessons from x-ray crystallography. Molecules, 2024, 29(8), 1764.
[http://dx.doi.org/10.3390/molecules29081764] [PMID: 38675584]
[178]
Bock, L.V.; Igaev, M.; Grubmüller, H. Single-particle Cryo-EM and molecular dynamics simulations: A perfect match. Curr. Opin. Struct. Biol., 2024, 86, 102825.
[http://dx.doi.org/10.1016/j.sbi.2024.102825] [PMID: 38723560]
[179]
den Boon, J. A.; Nishikiori, M.; Zhan, H.; Ahlquist, P. Positive-strand RNA virus genome replication organelles: Structure, assembly, control. Trends Genet., 2024, 40(8), 681-693.
[http://dx.doi.org/10.1016/j.tig.2024.04.003.]
[180]
Gomase, V.S.; Kemkar, K.R.; Baviskar, B.A.; Mundhe, V.S.; Sakhare, A.D.; Kolsure, A.K.; Bhimanwar, A.A.; Dhamane, S.P.; Potnis, V.V. Physicochemical and immunoproteomic analysis to design synthetic peptide vaccine from naja kaouthia neurotoxin. World J. Pharm. Res., 2023, 12(4), 1286-1291.
[181]
Gomase, V.S.; Chitlange, N.R. Sensitive quantitative predictions of MHC binding peptides and fragment based peptide vaccines from taenia crassiceps. J. Vaccines Vaccin., 2012, 3(1), 131.
[182]
Gomase, V.S.; Kemkar, K.R.; Baviskar, B.A.; Mundhe, V.S.; Sakhare, A.D.; Kolsure, A.K.; Bhimanwar, A.A.; Dhamane, S.P.; Potnis, V.V. Immunoinformatics study of physical properties of scorpion neurotoxin Bmk-M8 from Mesobuthus martensii . Int. J. Med. Pharm. Res., 2023, 7(3), 13-15.
[183]
Gomase, V.S.; Pangarkar, P.R.; Kemkar, K.R. Immunoproteomics physicochemical analysis of heterodimeric neurotoxic phospholipases A2 from apis cerana. Int. J. Pharm. Res., 2023, 15(1), 118-123.
[184]
Laroche, C.; Engen, R.M. Immune monitoring in pediatric kidney transplant. Pediatr. Transplant., 2024, 28(4), e14785.
[http://dx.doi.org/10.1111/petr.14785] [PMID: 38766986]
[185]
Iyer, M.; Ravichandran, N.; Karuppusamy, P.A.; Gnanarajan, R.; Yadav, M.K.; Narayanasamy, A.; Vellingiri, B. Molecular insights and promise of oncolytic virus based immunotherapy. Adv. Protein Chem. Struct. Biol., 2024, 140, 419-492.
[http://dx.doi.org/10.1016/bs.apcsb.2023.12.007] [PMID: 38762277]
[186]
Gomase, V.; Tagore, S.; Kale, K. Microarray: An approach for current drug targets. Curr. Drug Metab., 2008, 9(3), 221-231.
[http://dx.doi.org/10.2174/138920008783884795] [PMID: 18336225]
[187]
Gomase, V.S.; Tripathi, A.K.; Tagore, S. Cellunomics: The interaction analysis of cells. Int. J. Bioinform. Res. Appl., 2009, 5(6), 674-690.
[http://dx.doi.org/10.1504/IJBRA.2009.029046] [PMID: 19887340]
[188]
Gomase, V.S.; Tagore, S. Phylogenomics: Evolution and genomics intersection. Int. J. Bioinform. Res. Appl., 2009, 5(5), 548-563.
[http://dx.doi.org/10.1504/IJBRA.2009.028682] [PMID: 19778869]
[189]
Gomase, V.; Tagore, S. Omics: An approach for drug targets. Curr. Drug Metab., 2008, 9(3), 189.
[http://dx.doi.org/10.2174/138920008783884722] [PMID: 18336219]
[190]
Gomase, V.; Tagore, S. Toxicogenomics. Curr. Drug Metab., 2008, 9(3), 250-254.
[http://dx.doi.org/10.2174/138920008783884696] [PMID: 18336230]
[191]
Gomase, V.; Changbhale, S.; Patil, S.; Kale, K. Metabolomics. Curr. Drug Metab., 2008, 9(1), 89-98.
[http://dx.doi.org/10.2174/138920008783331149] [PMID: 18220576]