Advanced search
Publication Cover
Expert Review of Proteomics Volume 17, 2020 - Issue 4
Submit an article Journal homepage
12,723
Views
47
CrossRef citations to date
0
Altmetric
Review

Analytical techniques for multiplex analysis of protein biomarkers

Alain Van Goola Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The NetherlandsView further author information
,
Fernado Corralesb Functional Proteomics Laboratory, Centro Nacional De Biotecnología, Madrid, SpainORCID Iconhttps://orcid.org/0000-0002-0231-5159View further author information
ORCID Icon,
Mirjana Čolovićc Department of Physical Chemistry, “Vinča“ Institute of Nuclear Sciences, University of Belgrade, Belgrade, SerbiaView further author information
,
Danijela Krstićd Institute of Medical Chemistry, Faculty of Medicine, University of Belgrade, Belgrade, SerbiaView further author information
,
Begona Oliver-Martose Neuroimmunology and Neuroinflammation Group. Instituto De Investigación Biomédica De Málaga-IBIMA. UGC Neurociencias, Hospital Regional Universitario De Málaga, Malaga, SpainView further author information
,
Eva Martínez-Cáceresf Immunology Division, LCMN, Germans Trias I Pujol University Hospital and Research Institute, Campus Can Ruti, Badalona, and Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma De Barcelona, Cerdanyola Del Vallès, SpainView further author information
,
Ivone Jakasag Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, CroatiaView further author information
,
Goran Gajskih Mutagenesis Unit, Institute for Medical Research and Occupational Health, Zagreb, CroatiaORCID Iconhttps://orcid.org/0000-0002-1886-1453View further author information
ORCID Icon,
Virginie Bruni Université Grenoble Alpes, CEA, Inserm, IRIG, BGE, Grenoble, FranceView further author information
,
Kyriacos Kyriacouj Department of Electron Microscopy/Molecular Biology, The Cyprus School of Molecular Medicine/The Cyprus Institute of Neurology and Genetics, Nicosia, CyprusView further author information
,
Izabela Burzynska-Pedziwiatrk Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz, Łódź, PolandView further author information
,
Lucyna Alicja Wozniakk Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz, Łódź, PolandView further author information
,
Stephan Nierkensl Center for Translational Immunology, University Medical Center Utrecht & Princess Máxima Center for Pediatric Oncology, Utrecht, The NetherlandsView further author information
,
César Pascual Garcíam Materials Research and Technology Department, Luxembourg Institute of Science and Technology (LIST), Belvaux, LuxembourgView further author information
,
Jaroslav Katrlikn Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, SlovakiaORCID Iconhttps://orcid.org/0000-0002-2876-9298View further author information
ORCID Icon,
Zanka Bojic-Trbojevico Laboratory for Biology of Reproduction, Institute for the Application of Nuclear Energy – INEP, University of Belgrade, Belgrade, SerbiaView further author information
,
Jan Vacekp Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech RepublicView further author information
,
Alicia Llorenteq Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, NorwayView further author information
,
Felicia Antoher Proteomics Department, Institute of Cellular Biology and Pathology “N. Simionescu” of the Romanian Academy, Bucharest, RomaniaView further author information
,
Viorel Suicar Proteomics Department, Institute of Cellular Biology and Pathology “N. Simionescu” of the Romanian Academy, Bucharest, RomaniaView further author information
,
Guillaume Suarezs Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, SwitzerlandView further author information
,
Ruben t’Kindtt Research Institute for Chromatography (RIC), Kortrijk, Belgium;View further author information
,
Petra Martinu Department of Medical Oncology, Midland Regional Hospital Tullamore/St. James’s Hospital, Dublin, IrelandView further author information
,
Deborah Penquev Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa, Lisbon,PortugalORCID Iconhttps://orcid.org/0000-0002-4527-7148View further author information
ORCID Icon,
Ines Lanca Martinsv Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa, Lisbon,PortugalView further author information
,
Ede Bodokiw Analytical Chemistry Department, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, RomaniaView further author information
,
Bogdan-Cezar Iacobw Analytical Chemistry Department, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, RomaniaView further author information
,
Eda Celikbasx Department of Chemistry, Graduate School of Sciences and Engineering, Koç University, Istanbul, TurkeyORCID Iconhttps://orcid.org/0000-0003-4882-6445View further author information
ORCID Icon,
Suna Timury Institute of Natural Sciences, Department of Biochemistry, Ege University, Izmir, TurkeyView further author information
,
John Allinsonz Immunologix Laboratories, Tampa, FL, USAView further author information
,
Christopher Suttonaa Institute of Cancer Therapeutics, University of Bradford, Bradford, UKView further author information
,
Theo Luiderbb Department of Neurology, Erasmus MC, Rotterdam, The NetherlandsView further author information
,
Saara Wittfoothcc Medisiina D 6 A-B, University of Turku, Turku, FinlandView further author information
&
Marei Sammardd Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel, IsraelCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0001-8369-2820View further author information
ORCID Icon show all
Pages 257-273 | Received 11 Mar 2020, Accepted 28 Apr 2020, Published online: 19 May 2020

References

  • Schork NJ. Personalized medicine: time for one-person trials. Nature. 2015Apr30;520(7549):609–611..
  • van Gool AJ, Henry B, Sprengers ED. From biomarker strategies to biomarker activities and back. Drug Discov Today. 2010 Feb;15(3–4):121–126.
  • Pegram MD, Lipton A, Hayes DF, et al. Phase II study of receptor-enhanced chemosensitivity using recombinant humanized anti-p185HER2/neu monoclonal antibody plus cisplatin in patients with HER2/neu-overexpressing metastatic breast cancer refractory to chemotherapy treatment. J Clin Oncol. 1998 Aug;16(8):2659–2671.
  • Freedman LP, Cockburn IM, Simcoe TS. The economics of reproducibility in preclinical research. PLoS Biol. 2015 Jun;13(6):e1002165.
  • van Gool AJ, Bietrix F, Caldenhoven E, et al. Bridging the translational innovation gap through good biomarker practice. Nat Rev Drug Discov. 2017 Sep;16(9):587–588.
  • Mischak H, Ioannidis JP, Argiles A, et al. Implementation of proteomic biomarkers: making it work. Eur J Clin Invest. 2012 Sep;42(9):1027–1036.
  • Rosenling T, Slim CL, Christin C, et al. The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF). J Proteome Res. 2009 Dec;8(12):5511–5522.
  • Cristobal A, van den Toorn HWP, van de Wetering M, et al. Personalized proteome profiles of healthy and tumor human colon organoids reveal both individual diversity and basic features of colorectal cancer. Cell Rep. 2017Jan3;18(1):263–274.
  • Hornbeck P, Winston SE, Fuller SA. Enzyme-linked immunosorbent assays (ELISA). Curr Protoc Mol Biol. 2001 May. Chapter 11: Unit 11.2.
  • Engvall E, Perlmann P. Enzyme-linked immunosorbent assay (ELISA). Quantitative assay of immunoglobulin G. Immunochemistry. 1971 Sep;8(9):871–874.
  • Aydin S. A short history, principles, and types of ELISA, and our laboratory experience with peptide/protein analyses using ELISA. Peptides. 2015 Oct;72:4–15.
  • Gan SD, Patel KR. Enzyme immunoassay and enzyme-linked immunosorbent assay. J Invest Dermatol. 2013 Sep;133(9):e12.
  • Revelen R, D’Arbonneau F, Guillevin L, et al. Comparison of cell-ELISA, flow cytometry and Western blotting for the detection of antiendothelial cell antibodies. Clin Exp Rheumatol. 2002 Jan-Feb;20(1):19–26.
  • Czerkinsky CC, Nilsson LA, Nygren H, et al. A solid-phase enzyme-linked immunospot (ELISPOT) assay for enumeration of specific antibody-secreting cells. J Immunol Methods. 1983 Dec 16;65(1–2):109–121.
  • Tighe PJ, Ryder RR, Todd I, et al. ELISA in the multiplex era: potentials and pitfalls. Proteomics Clin Appl. 2015 Apr;9(3–4):406–422.
  • Ma C, Fan R, Ahmad H, et al. A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells. Nat Med. 2011 Jun;17(6):738–743.
  • Huang RP. Cytokine protein arrays. Methods Mol Biol. 2004;264:215–231.
  • Fulton RJ, McDade RL, Smith PL, et al. Advanced multiplexed analysis with the FlowMetrix system. Clin Chem. 1997 Sep;43(9):1749–1756.
  • Appleyard DC, Chapin SC, Srinivas RL, et al. Bar-coded hydrogel microparticles for protein detection: synthesis, assay and scanning. Nat Protoc. 2011 Oct 20;6(11):1761–1774.
  • Hemmila I, Holttinen S, Pettersson K, et al. Double-label time-resolved immunofluorometry of lutropin and follitropin in serum. Clin Chem. 1987 Dec;33(12):2281–2283.
  • Ogata A, Tagoh H, Lee T, et al. A new highly sensitive immunoassay for cytokines by dissociation-enhanced lanthanide fluoroimmunoassay (DELFIA). J Immunol Methods. 1992 Apr 8;148(1–2):15–22.
  • Gilbert M, Livingston R, Felberg J, et al. Multiplex single molecule counting technology used to generate interleukin 4, interleukin 6, and interleukin 10 reference limits. Anal Biochem. 2016 Jun 15;503:11–20.
  • Rissin DM, Kan CW, Song L, et al. Multiplexed single molecule immunoassays. Lab Chip. 2013 Aug 7;13(15):2902–2911.
  • Gold L, Ayers D, Bertino J, et al. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One. 2010 Dec 7;5(12):e15004.
  • Ngo D, Sinha S, Shen D, et al. Aptamer-based proteomic profiling reveals novel candidate biomarkers and pathways in cardiovascular disease. Circulation. 2016 Jul 26;134(4):270–285.
  • Moody MD, Van Arsdell SW, Murphy KP, et al. Array-based ELISAs for high-throughput analysis of human cytokines. Biotechniques. 2001 Jul;31(1):186–90, 192–4.
  • Leng SX, McElhaney JE, Walston JD, et al. and multiplex technologies for cytokine measurement in inflammation and aging research. J Gerontol A Biol Sci Med Sci. 2008 Aug;63(8):879–884.
  • Esmaeili R, Zhang M, Sternberg MR, et al. The Quansys multiplex immunoassay for serum ferritin, C-reactive protein, and alpha-1-acid glycoprotein showed good comparability with reference-type assays but not for soluble transferrin receptor and retinol-binding protein. PLoS One. 2019;14(4):e0215782.
  • Roda A, Mirasoli M, Michelini E, et al. Progress in chemical luminescence-based biosensors: A critical review [review]. Biosens Bioelectron. 2016 Feb;76:164–179.
  • Miao WJ. Electrogenerated chemiluminescence and its biorelated applications [Review]. Chem Rev. 2008 Jul;108(7):2506–2553.
  • Sek S, Vacek J, Dorcak V. Electrochemistry of peptides [review]. Curr Opin Electrochem. 2019 Apr;14:166–172.
  • Ding CF, Zhang W, Wang W, et al. Amplification strategies using electrochemiluminescence biosensors for the detection of DNA, bioactive molecules and cancer biomarkers [review]. Trac-Trends Anal Chem. 2015 Feb;65:137–150.
  • Toedter G, Hayden K, Wagner C, et al. Simultaneous detection of eight analytes in human serum by two commercially available platforms for multiplex cytokine analysis. Clin Vaccine Immunol. 2008 Jan;15(1):42–48.
  • Gao WY, Saqib M, Qi LM, et al. Recent advances in electrochemiluminescence devices for point-of-care testing [review]. Curr Opin Electrochem. 2017 Jun;3(1):4–10.
  • Wu MR, Lai QY, Ju Q, et al. Paper-based fluorogenic devices for in vitro diagnostics [review]. Biosens Bioelectron. 2018 Apr;102:256–266.
  • Bouffier L, Arbault S, Kuhn A, et al. Generation of electrochemiluminescence at bipolar electrodes: concepts and applications [Review]. Anal Bioanal Chem. 2016 Oct;408(25):7003–7011.
  • Davies P, Carlisle D. Five days that shook the NHS. Health Serv J. 2008 Jul;3;Suppl:4-7. DOI:10.1016/0006-291x(75)90498-2.
  • Dzantiev BB, Byzova NA, Urusov AE, et al. Immunochromatographic methods in food analysis. Trends Analyt Chem. 2014 March 01;55:81–93.
  • Mao X, Wang W, Du T-E. Rapid quantitative immunochromatographic strip for multiple proteins test. Sens Actuators B Chem. 2013 Sep 01;186:315–320.
  • Bocoum FY, Ouedraogo H, Tarnagda G, et al. Evaluation of the diagnostic performance and operational characteristics of four rapid immunochromatographic syphilis tests in Burkina Faso. Afr Health Sci. 2015 Jun;15(2):360–367.
  • Majumder S, Deen MJ. Smartphone sensors for health monitoring and diagnosis. Sensors (Basel). 2019 May 9;19(9):2164.
  • Zhang D, Liu Q. Biosensors and bioelectronics on smartphone for portable biochemical detection. Biosens Bioelectron. 2016 Jan;15(75):273–284.
  • Li Z, Wang Y, Wang J, et al. Rapid and sensitive detection of protein biomarker using a portable fluorescence biosensor based on quantum dots and a lateral flow test strip. Anal Chem. 2010 Aug 15;82(16):7008–7014.
  • Guler E, Yilmaz Sengel T, Gumus ZP, et al. Mobile phone sensing of cocaine in a lateral flow assay combined with a biomimetic material. Anal Chem. 2017 Sep 19;89(18):9629–9632.
  • Martinez-Perez B, de la Torre-diez I, Lopez-Coronado M. Mobile health applications for the most prevalent conditions by the World Health Organization: review and analysis. J Med Internet Res. 2013 Jun 14;15(6):e120.
  • Oh H, Rizo C, Enkin M, et al. What is eHealth (3): a systematic review of published definitions. J Med Internet Res. 2005 Feb 24;7(1):e1.
  • Lundberg M, Eriksson A, Tran B, et al. Homogeneous antibody-based proximity extension assays provide sensitive and specific detection of low-abundant proteins in human blood. Nucleic Acids Res. 2011 Aug;39(15):e102.
  • Aebersold R, Mann M. Mass-spectrometric exploration of proteome structure and function. Nature. 2016Sep15;537(7620):347–355.
  • Doll S, Gnad F, Mann M. The case for proteomics and phospho-proteomics in personalized cancer medicine. Proteomics Clin Appl. 2019 Mar;13(2):e1800113.
  • Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics. 2002 Nov;1(11):845–867.
  • Wu C, Duan J, Liu T, et al. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci. 2016 May 15;1021:57–68.
  • Mulvey CM, Breckels LM, Geladaki A, et al. Using hyperLOPIT to perform high-resolution mapping of the spatial proteome. Nat Protoc. 2017 Jun;12(6):1110–1135.
  • Lemeer S, Zorgiebel C, Ruprecht B, et al. Comparing immobilized kinase inhibitors and covalent ATP probes for proteomic profiling of kinase expression and drug selectivity. J Proteome Res. 2013 Apr 5;12(4):1723–1731.
  • Sutton CW. The role of targeted chemical proteomics in pharmacology. Br J Pharmacol. 2012 May;166(2):457–475.
  • Ten HS, Boulon S, Ahmad Y, et al. Mass spectrometry-based immuno-precipitation proteomics - the user’s guide. Proteomics. 2011 Mar;11(6):1153–1159.
  • Trenchevska O, Nelson RW, Nedelkov D. Mass spectrometric immunoassays in characterization of clinically significant proteoforms. Proteomes. 2016 Mar 17;4(1):13.
  • Ducret A, James I, Wilson S, et al. Translation and evaluation of a pre-clinical 5-protein response prediction signature in a breast cancer phase Ib clinical trial. PLoS One. 2019;14(3):e0213892.
  • Collins CJ, Chang IJ, Jung S, et al. Rapid multiplexed proteomic screening for primary immunodeficiency disorders from dried blood spots. Front Immunol. 2018;9:2756.
  • Fu Q, Kowalski MP, Mastali M, et al. Highly reproducible automated proteomics sample preparation workflow for quantitative mass spectrometry. J Proteome Res. 2018 Jan 5;17(1):420–428.
  • Mbasu RJ, Heaney LM, Molloy BJ, et al. Advances in quadrupole and time-of-flight mass spectrometry for peptide MRM based translational research analysis. Proteomics. 2016 Aug;16(15–16):2206–2220.
  • Abbatiello SE, Schilling B, Mani DR, et al. Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma. Mol Cell Proteomics. 2015 Sep;14(9):2357–2374.
  • Percy AJ, Yang J, Hardie DB, et al. Precise quantitation of 136 urinary proteins by LC/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and/or verification studies. Methods. 2015 Jun 15;81:24–33.
  • Klont F, Pouwels SD, Hermans J, et al. A fully validated liquid chromatography-mass spectrometry method for the quantification of the soluble receptor of advanced glycation end-products (sRAGE) in serum using immunopurification in a 96-well plate format. Talanta. 2018 May 15;182:414–421.
  • Klont F, Joosten MR, Ten Hacken NHT, et al. Quantification of the soluble receptor of advanced glycation end-products (sRAGE) by LC-MS after enrichment by strong cation exchange (SCX) solid-phase extraction (SPE) at the protein level. Anal Chim Acta. 2018 Dec 28;1043:45–51.
  • De Marchi T, Kuhn E, Dekker LJ, et al. Targeted MS assay predicting tamoxifen resistance in estrogen-receptor-positive breast cancer tissues and sera. J Proteome Res. 2016 Apr 1;15(4):1230–1242.
  • Yang X, Naughton SX, Han Z, et al. Mass spectrometric quantitation of tubulin acetylation from pepsin-digested rat brain tissue using a novel stable-isotope standard and capture by anti-peptide antibody (SISCAPA) method. Anal Chem. 2018 Feb 6;90(3):2155–2163.
  • Hsiao YC, Chi LM, Chien KY, et al. Development of a multiplexed assay for oral cancer candidate biomarkers using peptide immunoaffinity enrichment and targeted mass spectrometry. Mol Cell Proteomics. 2017 Oct;16(10):1829–1849.
  • Chen YT, Chen HW, Wu CF, et al. Development of a multiplexed liquid chromatography multiple-reaction-monitoring mass spectrometry (LC-MRM/MS) method for evaluation of salivary proteins as oral cancer biomarkers. Mol Cell Proteomics. 2017 May;16(5):799–811.
  • Duangkumpha K, Stoll T, Phetcharaburanin J, et al. Urine proteomics study reveals potential biomarkers for the differential diagnosis of cholangiocarcinoma and periductal fibrosis. PLoS One. 2019;14(8):e0221024.
  • Mun S, Lee J, Park A, et al. Proteomics approach for the discovery of rheumatoid arthritis biomarkers using mass spectrometry. Int J Mol Sci. 2019 Sep 5;20(18). DOI:10.3390/ijms20184368.
  • Van Raemdonck GA, Osbak KK, Van Ostade X, et al. Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis. F1000Res. 2018;7:336.
  • Chen J, Tang MS, Xu LC, et al. Proteomic analysis of biomarkers predicting the response to triple therapy in patients with rheumatoid arthritis. Biomed Pharmacother. 2019 Aug;116:109026.
  • Zhang Q, Salzler R, Dore A, et al. Multiplex immuno-liquid chromatography-mass spectrometry-parallel reaction monitoring (LC-MS-PRM) quantitation of CD8A, CD4, LAG3, PD1, PD-L1, and PD-L2 in frozen human tissues. J Proteome Res. 2018 Nov 2;17(11):3932–3940.
  • Martinez-Garcia E, Lesur A, Devis L, et al. Development of a sequential workflow based on LC-PRM for the verification of endometrial cancer protein biomarkers in uterine aspirate samples. Oncotarget. 2016 Aug 16;7(33):53102–53115.
  • Henderson CM, Bollinger JG, Becker JO, et al. Quantification by nano liquid chromatography parallel reaction monitoring mass spectrometry of human apolipoprotein A-I, apolipoprotein B, and hemoglobin A1c in dried blood spots. Proteomics Clin Appl. 2017 Jul;11(7–8):1600103.
  • Guzel C, Govorukhina NI, Wisman GBA, et al. Proteomic alterations in early stage cervical cancer. Oncotarget. 2018 Apr 6;9(26):18128–18147.
  • van der Ende EL, Meeter LH, Stingl C, et al. Novel CSF biomarkers in genetic frontotemporal dementia identified by proteomics. Ann Clin Transl Neurol. 2019 Apr;6(4):698–707.
  • Skillback T, Mattsson N, Hansson K, et al. A novel quantification-driven proteomic strategy identifies an endogenous peptide of pleiotrophin as a new biomarker of Alzheimer’s disease. Sci Rep. 2017 Oct 17;7(1):13333.
  • Theodorescu D, Wittke S, Ross MM, et al. Discovery and validation of new protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol. 2006 Mar;7(3):230–240.
  • Rodriguez-Ortiz ME, Pontillo C, Rodriguez M, et al. Novel urinary biomarkers for improved prediction of progressive egfr loss in early chronic kidney disease stages and in high risk individuals without chronic kidney disease. Sci Rep. 2018 Oct 29;8(1):15940.
  • van den Broek I, Nouta J, Razavi M, et al. Quantification of serum apolipoproteins A-I and B-100 in clinical samples using an automated SISCAPA-MALDI-TOF-MS workflow. Methods. 2015 Jun 15;81:74–85.
  • Popp R, Li H, LeBlanc A, et al. Immuno-matrix-assisted laser desorption/ionization assays for quantifying AKT1 and AKT2 in breast and colorectal cancer cell lines and tumors. Anal Chem. 2017 Oct 3;89(19):10592–10600.
  • Tran JC, Zamdborg L, Ahlf DR, et al. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature. 2011 Oct 30;480(7376):254–258.
  • Schmit PO, Vialaret J, Wessels H, et al. Towards a routine application of top-down approaches for label-free discovery workflows. J Proteomics. 2018 Mar;20(175):12–26.
  • Tegtmeyer LC, Rust S, van Scherpenzeel M, et al. Multiple phenotypes in phosphoglucomutase 1 deficiency. N Engl J Med. 2014 Feb 6;370(6):533–542.
  • Blum BC, Mousavi F, Emili A. Single-platform ‘multi-omic’ profiling: unified mass spectrometry and computational workflows for integrative proteomics-metabolomics analysis. Mol Omics. 2018 Oct 8;14(5):307–319.
  • Rogers JC, Bomgarden RD. Sample preparation for mass spectrometry-based proteomics; from proteomes to peptides. Adv Exp Med Biol. 2016;919:43–62.
  • Lange V, Picotti P, Domon B, et al. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 2008;4(1):222.
  • Gallien S, Domon B. Detection and quantification of proteins in clinical samples using high resolution mass spectrometry. Methods. 2015 Jun 15;81:15–23.
  • Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat Methods. 2012 May 30;9(6):555–566.
  • Brun V, Masselon C, Garin J, et al. Isotope dilution strategies for absolute quantitative proteomics. J Proteomics. 2009 Jul 21;72(5):740–749.
  • Gerber SA, Rush J, Stemman O, et al. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6940–6945.
  • Kushnir MM, Rockwood AL, Roberts WL, et al. Measurement of thyroglobulin by liquid chromatography-tandem mass spectrometry in serum and plasma in the presence of antithyroglobulin autoantibodies. Clin Chem. 2013 Jun;59(6):982–990.
  • Beynon RJ, Doherty MK, Pratt JM, et al. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods. 2005 Aug;2(8):587–589.
  • Zeiler M, Straube WL, Lundberg E, et al. A protein epitope signature tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol Cell Proteomics. 2012 Mar;11(3):O111 009613.
  • Brun V, Dupuis A, Adrait A, et al. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol Cell Proteomics. 2007 Dec;6(12):2139–2149.
  • Hanke S, Besir H, Oesterhelt D, et al. Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J Proteome Res. 2008 Mar;7(3):1118–1130.
  • Kuhn E, Whiteaker JR, Mani DR, et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol Cell Proteomics. 2012 Jun;11(6):M111 013854.
  • Oeckl P, Steinacker P, Otto M. Comparison of internal standard approaches for SRM analysis of alpha-synuclein in cerebrospinal fluid. J Proteome Res. 2018 Jan 5;17(1):516–523.
  • Carr SA, Abbatiello SE, Ackermann BL, et al. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics. 2014 Mar;13(3):907–917.
  • Abbatiello S, Ackermann BL, Borchers C, et al. New guidelines for publication of manuscripts describing development and application of targeted mass spectrometry measurements of peptides and proteins. Mol Cell Proteomics. 2017 Mar;16(3):327–328.
  • Whiteaker JR, Halusa GN, Hoofnagle AN, et al. CPTAC assay portal: a repository of targeted proteomic assays. Nat Methods. 2014 Jul;11(7):703–704.
  • Kemna EH, Tjalsma H, Podust VN, et al. Mass spectrometry-based hepcidin measurements in serum and urine: analytical aspects and clinical implications. Clin Chem. 2007 Apr;53(4):620–628.
  • Eigner U, Holfelder M, Oberdorfer K, et al. Performance of a matrix-assisted laser desorption ionization-time-of-flight mass spectrometry system for the identification of bacterial isolates in the clinical routine laboratory. Clin Lab. 2009;55(7–8):289–296.
  • Pasa-Tolic L, Masselon C, Barry RC, et al. Proteomic analyses using an accurate mass and time tag strategy. Biotechniques. 2004 Oct;37(4):621–4, 626–33, 636 passim.
  • Gillet LC, Navarro P, Tate S, et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics. 2012 Jun;11(6):O111 016717.
  • Sajic T, Liu Y, Aebersold R. Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications. Proteomics Clin Appl. 2015 Apr;9(3–4):307–321.
  • Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: from basic research to clinical applications. Proteomics. 2017 Feb;17(3–4):1600278.
  • Koopmans F, Ho JTC, Smit AB, et al. Comparative analyses of data independent acquisition mass spectrometric approaches: DIA, WiSIM-DIA, and untargeted DIA. Proteomics. 2018 Jan;18(1):1700304.
  • Souza GH, Guest PC, Martins-de-Souza D. LC-MS(E), multiplex MS/MS, ion mobility, and label-free quantitation in clinical proteomics. Methods Mol Biol. 2017;1546:57–73.
  • Helm S, Baginsky S. MSE for label-free absolute protein quantification in complex proteomes. Methods Mol Biol. 2018;1696:235–247.
  • Rosenberger G, Koh CC, Guo T, et al. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Sci Data. 2014;1(1):140031.
  • Schubert OT, Gillet LC, Collins BC, et al. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nat Protoc. 2015 Mar;10(3):426–441.
  • Wu JX, Song X, Pascovici D, et al. SWATH mass spectrometry performance using extended peptide MS/MS assay libraries. Mol Cell Proteomics. 2016 Jul;15(7):2501–2514.
  • Smith LM, Kelleher NL. Consortium for Top Down P. Proteoform: a single term describing protein complexity. Nat Methods. 2013 Mar;10(3):186–187.
  • Tiede C, Bedford R, Heseltine SJ, et al. Affimer proteins are versatile and renewable affinity reagents. Elife. 2017 Jun 27;6. DOI:10.7554/eLife.24903.
  • Lollo B, Steele F, Gold L. Beyond antibodies: new affinity reagents to unlock the proteome. Proteomics. 2014 Mar;14(6):638–644.
  • Gold L, Walker JJ, Wilcox SK, et al. Advances in human proteomics at high scale with the SOMAscan proteomics platform. N Biotechnol. 2012Jun15;29(5):543–549.
  • Katrlik J, Svitel J, Gemeiner P, et al. Glycan and lectin microarrays for glycomics and medicinal applications. Med Res Rev. 2010 Mar;30(2):394–418.
  • Latosinska A, Siwy J, Mischak H, et al. Peptidomics and proteomics based on CE-MS as a robust tool in clinical application: the past, the present, and the future. Electrophoresis. 2019 Sep;40(18–19):2294–2308.
  • Mischak H, Vlahou A, Ioannidis JP. Technical aspects and inter-laboratory variability in native peptide profiling: the CE-MS experience. Clin Biochem. 2013 Apr;46(6):432–443.
  • Sun L, Zhu G, Zhang Z, et al. Third-generation electrokinetically pumped sheath-flow nanospray interface with improved stability and sensitivity for automated capillary zone electrophoresis-mass spectrometry analysis of complex proteome digests. J Proteome Res. 2015 May 1;14(5):2312–2321.
  • Wuethrich A, Quirino JP. A decade of microchip electrophoresis for clinical diagnostics - A review of 2008-2017. Anal Chim Acta. 2019 Jan 3;1045:42–66.
  • Mascini M, Palchetti I, Tombelli S. Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects. Angew Chem Int Ed Engl. 2012 Feb 6;51(6):1316–1332.
  • Zakynthinos E, Pappa N. Inflammatory biomarkers in coronary artery disease. J Cardiol. 2009 Jun;53(3):317–333.
  • de Avila BE, Escamilla-Gomez V, Campuzano S, et al. Disposable amperometric magnetoimmunosensor for the sensitive detection of the cardiac biomarker amino-terminal pro-B-type natriuretic peptide in human serum. Anal Chim Acta. 2013 Jun 19;784:18–24.
  • Farzin L, Shamsipur M, Samandari L, et al. Recent advances in designing nanomaterial based biointerfaces for electrochemical biosensing cardiovascular biomarkers. J Pharm Biomed Anal. 2018 Nov 30;161:344–376.
  • Tsang HF, Xue VW, Koh SP, et al. NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics. Expert Rev Mol Diagn. 2017 Jan;17(1):95–103.
  • Bruzas I, Unser S, Yazdi S, et al. Ultrasensitive plasmonic platform for label-free detection of membrane-associated species [article]. Anal Chem. 2016 Aug;88(16):7968–7974.
  • Ciminelli C, Dell’Olio F, Conteduca D, et al. Integrated photonic and plasmonic resonant devices for label-free biosensing and trapping at the nanoscale. Phys Status Solidi A. 2019;216(3):1800561.
  • Acimovic SS, Sipova H, Emilsson G, et al. Superior LSPR substrates based on electromagnetic decoupling for on-a-chip high-throughput label-free biosensing [Article]. Light Sci Appl. 2017 Aug 6(8):e17042.
  • Yavas O, Acimovic SS, Garcia-Guirado J, et al. Self-calibrating on-chip localized surface plasmon resonance sensing for quantitative and multiplexed detection of cancer markers in human serum [article]. ACS Sens. 2018 Jul;3(7):1376–1384.
  • Wittenberg NJ, Im H, Johnson TW, et al. Facile assembly of micro- and nanoarrays for sensing with natural cell membranes [article]. Acs Nano. 2011 Sep;5(9):7555–7564.
  • Liu B, Li YL, Wan H, et al. High performance, multiplexed lung cancer biomarker detection on a plasmonic gold chip [article]. Adv Funct Mater. 2016 Nov;26(44):7994–8002.
  • Zhang R, Le BA, Xu W, et al. Magnetic “Squashing” of circulating tumor cells on plasmonic substrates for ultrasensitive NIR fluorescence detection [article]. Small Methods. 2019 Feb;3(2):7.
  • Fothergill SM, Joyce C, Xie F. Metal enhanced fluorescence biosensing: from ultra-violet towards second near-infrared window [Review]. Nanoscale. 2018 Dec;10(45):20914–20929.
  • Jawad ZAR, Theodorou IG, Jiao LR, et al. Highly sensitive plasmonic detection of the pancreatic cancer biomarker CA 19-9 [Article]. Sci Rep. 2017 Oct;7:7.
  • Tabakman SM, Lau L, Robinson JT, et al. Plasmonic substrates for multiplexed protein microarrays with femtomolar sensitivity and broad dynamic range [Article]. Nat Commun. 2011 Sep;2(1):9.
  • Ansari AA, Alhoshan M, Alsalhi MS, et al. Prospects of nanotechnology in clinical immunodiagnostics. Lect Notes Electr En. 2010 Jul;10(7):6535–6581.
  • Ramachandran R, Chen SM, Kumar GPG, et al. An overview of fabricating nanostructured electrode materials for biosensor applications. Int J Electrochem Sci. 2015;Oct;10(10):8607–8629.
  • Arris FA, Benoudjit AM, Sanober F, et al. Characterization of electrochemical transducers for biosensor applications. Multifaceted protocol in biotechnology.  Singapore: Springer; 2018:119–137.
  • Escamilla-Gómez V, Hernández-Santos D, González-García MB, et al. Simultaneous detection of free and total prostate specific antigen on a screen-printed electrochemical dual sensor. Biosens Bioelectron. 2009;24(8):2678–2683.
  • Rocha-Santos TA. Sensors and biosensors based on magnetic nanoparticles. Trends Analyt Chem. 2014;62:28–36.
  • Gill R, Zayats M, Willner I. Semiconductor quantum dots for bioanalysis. Angew Chem. 2008;47(40):7602–7625.
  • Li J, Wu N. Biosensors based on nanomaterials and nanodevices. CRC Press, Boca Raton; 2014.
  • Anker JN, Hall WP, Lyandres O, et al. Biosensing with plasmonic nanosensors. Nat Mater. 2008;7(6):442–453.
  • Pei X, Zhang B, Tang J, et al. Sandwich-type immunosensors and immunoassays exploiting nanostructure labels: A review. Anal Chim Acta. 2013;758:1–18.
  • Arntz Y, Seelig JD, Lang H, et al. Label-free protein assay based on a nanomechanical cantilever array. Nanotechnology. 2002;14(1):86.
  • Hong Y, Huh Y-M, Yoon DS, et al. Nanobiosensors based on localized surface plasmon resonance for biomarker detection. J Nanomater. 2012;2012:111.
  • Stern E, Klemic JF, Routenberg DA, et al. Label-free immunodetection with CMOS-compatible semiconducting nanowires. Nature. 2007;445(7127):519.
  • de Moraes A, Kubota L. Recent trends in field-effect transistors-based immunosensors. Chemosensors. 2016;4(4):20.
  • Syahir A, Usui K, Tomizaki K-Y, et al. Label and label-free detection techniques for protein microarrays. Microarrays. 2015;4(2):228–244.
  • Stekel D. Microarrays: making them and using them. Microarray Bioinf. 2003, Cambridge university press, chapter 1;1–18.
  • Bellassai N, D’Agata R, Jungbluth V, et al. Surface plasmon resonance for biomarker detection: advances in non-invasive cancer diagnosis. Front Chem. 2019;7:570.
  • Doucey M-A, Carrara S. Nanowire sensors in cancer. Trends Biotechnol. 2019;37(1):86–99.
  • Vashist S. Point-of-care diagnostics: recent advances and trends. Biosensors (Basel).2017 Dec 18;7(4). pii: E62.
  • Popowitch EB, O’Neill SS, Miller MB. Comparison of the biofire filmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J Clin Microbiol. 2013;51(5):1528–1533.
  • Cohen L, Walt DR. Single-molecule arrays for protein and nucleic acid analysis. Annu Rev Anal Chem (Palo Alto Calif). 2017 Jun 12;10(1):345–363.
  • Restrepo-Perez L, Joo C, Dekker C. Paving the way to single-molecule protein sequencing. Nat Nanotechnol. 2018 Sep;13(9):786–796.
  • Di Muccio G, Rossini AE, Di Marino D, et al. Insights into protein sequencing with an alpha-Hemolysin nanopore by atomistic simulations. Sci Rep. 2019 Apr 23;9(1):6440.
  • Swaminathan J, Boulgakov AA, Hernandez ET, et al. Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nat Biotechnol. 2018 Oct 22;36(11):1076–1082.
  • Bradbury A, Pluckthun A. Reproducibility: standardize antibodies used in research. Nature. 2015 Feb 5;518(7537):27–29.
  • Bradbury AM, Pluckthun A. Antibodies: validate recombinants once. Nature. 2015 Apr 16;520(7547):295.
  • Xu T, Fang Y, Rong A, et al. Flexible combination of multiple diagnostic biomarkers to improve diagnostic accuracy. BMC Med Res Methodol. 2015 Oct;31(15):94.
  • Captur G, Heywood WE, Coats C, et al. Identification of a multiplex biomarker panel for hypertrophic cardiomyopathy using quantitative proteomics and machine learning. Mol Cell Proteomics. 2020 Jan;19(1):114–127.
  • Van Eyk JE, Snyder MP. Precision medicine: role of proteomics in changing clinical management and care. J Proteome Res. 2019 Jan 4;18(1):1–6.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.