Current applications of proteomics: a key and novel approach


  • Vipin Kumar Sharma Department of Biochemistry, Central University of Haryana, Jant Pali, Mahendergarh, Haryana, India
  • Ravi Kumar Department of Internal Medicine, Armed Forces Medical College, Pune, Maharashtra, India



Biomarkers, Biomedical applications, Mass Spectrometry, Microarray chips, Parallel reaction monitoring, Protein quantification


Proteomics represented vital applications of technologies in the identification and quantification of high to moderate proteins (cellular signalling networks) found in biological matrix such as tissues, cells and fluids. Proteomics based technical knowledge is applied and verified in several preclinical research settings such as invention of diagnostic markers for specific disease and have shown to be increased in clinical applications. Extensive studies on proteomics resulted in detection of biomarkers that have been highly advanced in using diseases for cancer, lungs, cardiovascular, renal and neuro-regenerative and Parkinson's disease by introducing human origins for biocompatibility such as urine and serum. Advancement in the proteomic methods is conferring candidate right direction for clinical usage. In this review, recent developments and widely used proteomics approaches such as Mass Spectrometry (MS), Microarray chips are elaborately addressed and also focused merits and demerits of commonly used advanced approaches such as Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and Data Independent Acquisition (DIA) and other used proteomics and that roles, in order to aid clinicians, were also discussed in the light of biomedical applications.


Lindoso RS, Kasai-Brunswick TH, Monnerat Cahli G, Collino F, Bastos Carvalho A, Campos de Carvalho AC, et al. Proteomics in the world of induced pluripotent stem cells. Cells. 2019 Jul;8(7):703.

Joubert-Caron R, Lutomski D, Caron M. Lymphoblastoid and Lymphoma Cells. Biomed Applications Proteomics. 2004 Jan 27:173.

Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH. Proteomics: technologies and their applications. J Chromatographic Sci. 2017 Feb 1;55(2):182-96.

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb;409(6822):860-921.

Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, et al. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genetic Engineering Rev. 1996 Dec 1;13(1):19-50.

Dashatan NA, Koushki M, Abbaszadeh HA, Nejad MR, Tavirani MR. proteomics applications in health: biomarker and drug discovery and food industry. Iran J Pharmaceutical Res. 2018;17(4):1523-36.

Gam LH. Breast cancer and protein biomarkers. World J Experiment Med. 2012 Oct 20;2(5):86-91.

Hamdan M. Cancer biomarkers: analytical techniques for discovery. Yale J Biol Med. 2007;80(3):137-8.

Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clini Chem. 2010 Feb 1;56(2):177-85.

Wetterhall M, Shevchenko G, Artemenko K, Sjödin MO, Bergquist J. Analysis of membrane and hydrophilic proteins simultaneously derived from the mouse brain using cloud-point extraction. Analytical Bioanalytical Chem. 2011 Jul 1;400(9):2827-36.

Tambor V, Fučíková A, Lenčo J, Kacerovský M, Řeháček V, Stulik J, et al. Application of proteomics in biomarker discovery: a primer for the clinician. Physiol Res. 2010 Aug 1;59(4):471‑97.

Zhang DY, Ye F, Gao L, Liu X, Zhao X, Che Y, et al. Proteomics, pathway array and signaling network-based medicine in cancer. Cell division. 2009 Dec;4(1):20.

Norman KC, Moore BB, Arnold KB, O'Dwyer DN. Proteomics: Clinical and research applications in respiratory diseases. Respirol. 2018 Nov;23(11):993-1003.

Lakhin AV, Tarantul VZ, Gening L. Aptamers: problems, solutions and prospects. Acta Naturae. 2013;5(4 (19)):34-43.

Mehan MR, Williams SA, Siegfried JM, Bigbee WL, Weissfeld JL, Wilson DO, et al. Validation of a blood protein signature for non-small cell lung cancer. Clini Proteom. 2014 Dec;11(1):32.

Ostroff RM, Mehan MR, Stewart A, Ayers D, Brody EN, Williams SA, et al. Early detection of malignant pleural mesothelioma in asbestos-exposed individuals with a non-invasive proteomics-based surveillance tool. PloS one. 2012 Oct 3;7(10):e46091.

De Groote MA, Nahid P, Jarlsberg L, Johnson JL, Weiner M, Muzanyi G, et al. Elucidating novel serum biomarkers associated with pulmonary tuberculosis treatment. PloS one. 2013 Apr 18;8(4):e61002.

Russell TM, Green LS, Rice T, Kruh-Garcia NA, Dobos K, De Groote MA, et al. Potential of high-affinity, slow off-rate modified aptamer reagents for Mycobacterium tuberculosis proteins as tools for infection models and diagnostic applications. J Clini Microbiol. 2017 Oct 1;55(10):3072-88.

O’Dwyer DN, Norman KC, Xia M, Huang Y, Gurczynski SJ, Ashley SL, et al. The peripheral blood proteome signature of idiopathic pulmonary fibrosis is distinct from normal and is associated with novel immunological processes. Sci Rep. 2017 Apr 25;7:46560.

Ashley SL, Xia M, Murray S, O’Dwyer DN, Grant E, White ES, et al. Six-SOMAmer index relating to immune, protease and angiogenic functions predicts progression in IPF. PLoS One. 2016 Aug 4;11(8):e0159878.

Gu S, Chen X. Precise proteomic identification using mass spectrometry coupled with stable isotope labelling. Analyst. 2005;130(9):1225-31.

McCormack AL. Mass spectrometry in proteomics. Methods. 2005;3(35):209-10.

Mallick P, Kuster B. Proteomics: a pragmatic perspective. Nat Biotechnol. 2010;28(7):695-709.

Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proceedings Nat Acad Sci. 2003 Aug 5;100(16):9440-5.

Krijgsveld J, Ketting RF, Mahmoudi T, Johansen J, Artal-Sanz M, Verrijzer CP, et al. elegans and D. melanogaster for quantitative proteomics. Nature Biotechnol. 2003 Aug;21(8):927-31.

Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR. Metabolic labelling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Analytical Chem. 2004 Sep 1;76(17):4951-9.

Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C. Proteolytic 18O labelling for comparative proteomics: model studies with two serotypes of adenovirus. Analytical Chem. 2001 Jul 1;73(13):2836-42.

Rao KS, Carruth RT, Miyagi M. Proteolytic 18O labelling by peptidyl-Lys Metallo endopeptidase for comparative proteomics. J Proteome Res. 2005 Apr 11;4(2):507-14.

Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, et al. Open mass spectrometry search algorithm. J Proteome Res. 2004 Oct 11;3(5):958-64.

Polanski M, Anderson NL. A list of candidate cancer biomarkers for targeted proteomics. Biomark Insights 2007; 1:1-48.

Lee BT, Liew L, Lim J, Tan JK, Lee TC, Veladandi PS, et al. Candidate List of yoUr Biomarker (CLUB): a web-based platform to aid cancer biomarker research. Biomarker insights. 2008 Jan;3:BMI-S467.

Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clini Chem. 2010 Feb 1;56(2):177-85.

Anderson L. Six decades searching for meaning in the proteome. J Proteomics. 2014 Jul 31;107:24-30.

Shi T, Su D, Liu T, Tang K, Camp DG, Qian WJ, et al. Advancing the sensitivity of selected reaction monitoring‐based targeted quantitative proteomics. Proteomics. 2012 Apr;12(8):1074-92.

Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Molecular Sys Biol. 2008 Jan 1;4(1):22.

Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Molecular Cel Proteomics. 2012 Dec 1;11(12):1709-23.

Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Molecular Cell Proteomics. 2012 Jun 1;11(6):O111-016717.

Aebersold R, Burlingame AL, Bradshaw RA. Western blots versus selected reaction monitoring assays: time to turn the tables? Mol. Cell. Proteomics.2013;12(9): 2381-2.

Sutandy FR, Qian J, Chen CS, Zhu H. Overview of protein microarrays. Current Protocols Protein Sci. 2013 Apr;72(1):27-1.

Yates III JR. A century of mass spectrometry: from atoms to proteomes. Nature Methods. 2011 Jul 28;8(8):633-7.

Smith JB. Peptide sequencing by Edman degradation. e LS. 2001 May 30.

Vihinen M. Bioinformatics in proteomics. Biomole Engineering. 2001 Nov 1;18(5):241-8.

Perez‐Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA. Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics. 2015 Mar;15(5-6):930-50.

Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics. 2015 Sep;15(18):3193-208.

Rosenberg JM, Utz PJ. Protein microarrays: a new tool for the study of autoantibodies in immunodeficiency. Frontiers Immunol. 2015 Apr 7;6:138.

Knezevic V, Leethanakul C, Bichsel VE, Worth JM, Prabhu VV, Gutkind JS, et al. Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics: Inter Edition. 2001 Oct;1(10):1271-8.

Popescu SC, Snyder M, Dinesh-Kumar SP. Arabidopsis protein microarrays for the high-throughput identification of protein-protein interactions. Plant Signalling Behaviour. 2007 Sep 1;2(5):416-20.

Brauer EK, Popescu SC, Popescu GV. Experimental and analytical approaches to characterize plant kinases using protein microarrays. In Methods in Molecular Biology. Springer Science Business Media 2014;217-35.

Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, et al. Global analysis of protein activities using proteome chips. science. 2001 Sep 14;293(5537):2101-5.

Ummanni R, Mannsperger HA, Sonntag J, Oswald M, Sharma AK, König R, et al. Evaluation of reverse phase protein array (RPPA)-based pathway-activation profiling in 84 non-small cell lung cancer (NSCLC) cell lines as platform for cancer proteomics and biomarker discovery. Biochimica Biophysica Acta (BBA)-Proteins and Proteomics. 2014 May 1;1844(5):950-9.

Trebunova M, Zivcak J. Biomedical Engineering and Proteomics. Acta Tecnología - International Scientific Journal about Technologies 2018; 4(1):15-19.

Dunn MJ. High-Resolution Two-dimensional Polyacrylamide-gel Electrophoresis Gel Electrophoresis of Proteins 1986;203-261

Aparadh VT, Patil Amol V, Karadge BA. Comparative analysis of seed and leaf proteins by SDS PAGE gel electrophoresis within Cleome species. Inter J Adv Life Sci. 2012;3:50-8.

Sadia M, Malik SA, Rabbani MA, Pearce SR. Electrophoretic characterization and the relationship between some Brassica species. Electronic J Biol. 2009;5(1):1-4.

Elamin BA, Al-Maleki A, Ismael MA, Ayoub MA. Purification and functional characterization of pancreatic insulin from camel (Camelus dromedarius). Saudi J Biol Sci. 2014 Dec 1;21(6):574-81.






Review Articles