Cross-reactivity in antibody microarrays and multiplexed sandwich assays: Shedding light on the dark side of multiplexing

Current Opinion in Chemical Biology

Volumn 18, Issue 1, 2014, Pages 29-37

  Juncker, David ^a   Bergeron, Sébastien ^a   Laforte, Veronique ^a   Li, Huiyan ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; DNA; REAGENT;

ACCURACY; ANTIBODY MICROARRAY; ANTIGEN BINDING; CORRELATION ANALYSIS; CROSS REACTION; DILUTION; DNA BARCODING; GENE AMPLIFICATION; IMMUNOASSAY; MASS SPECTROMETRY; MICROARRAY ANALYSIS; MULTIPLEXED SANDWICH ASSAY; MULTIPLEXED SINGLE ANTIBODY ASSAY; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVIEW; SIGNAL DETECTION; SINGLE AFFINITY BINDER ASSAY;

ANTIBODIES; CROSS REACTIONS; IMMUNOASSAY; MASS SPECTROMETRY; MICROARRAY ANALYSIS;

EID: 84891109918     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2013.11.012     Document Type: Review

References (47)

1. Holm A., Wu W., Lund-Johansen F. Antibody array analysis of labelled proteomes: how should we control specificity?. New Biotechnol 2012, 29:8-585.
2. Landegren U., Vänelid J., Hammond M., Nong R.Y., Wu D., Ullerås E., Kamali-Moghaddam M. Opportunities for sensitive plasma proteome analysis. Anal Chem 2012, 84:1824-1830.
3. Taussig M.J., Stoevesandt O., Borrebaeck C.A.K., Bradbury A.R., Cahill D., Cambillau C., de Daruvar A., Dubel S., Eichler J., Frank R., et al. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods 2007, 4:13-17.
4. Davies C. Introduction to immunoassay principles. The Immunoassay Handbook 2005, 3-40. Elsevier. edn 3. D. Wild (Ed.).
5. Halperin R.F., Stafford P., Johnston S.A. Exploring antibody recognition of sequence space through random-sequence peptide microarrays. Mol Cell Proteomics 2011, 10.
6. James L.C., Roversi P., Tawfik D.S. Antibody multispecificity mediated by conformational diversity. Science 2003, 299:1362-1367.
7. Schwenk J.M., Igel U., Neiman M., Langen H., Becker C., Bjartell A., Ponten F., Wiklund F., Grönberg H., Nilsson P., et al. Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays. Mol Cell Proteomics 2010, 9:2497-2507.
8. Anderson N.L., Anderson N.G. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 2002, 1:845-867.
9. O'Malley S. Recent advances in label-free biosensors applications in protein biosynthesis and HTS screening. Protein Biosynthesis 2008, 1-33. Nova Science Publishers, Inc. T.E. Esterhous, L.B. Petrinos (Eds.).
10. Davies C. Concepts. The Immunoassay Handbook 2005, 103-135. Elsevier. edn 3. D. Wild (Ed.).
11. Walt D.R. Optical methods for single molecule detection and analysis. Anal Chem 2012, 85:1258-1263.
12. Tekin H.C., Cornaglia M., Gijs M.A.M. Attomolar protein detection using a magnetic bead surface coverage assay. Lab Chip 2013, 13:1053-1059.
13. Rissin D.M., Kan C.W., Song L., Rivnak A.J., Fishburn M.W., Shao Q., Piech T., Ferrell E.P., Meyer R.E., Campbell T.G., et al. Multiplexed single molecule immunoassays. Lab Chip 2013, 13:2902-2911.
14. de la Rica R., Stevens M.M. Plasmonic ELISA for the ultrasensitive detection of disease biomarkers with the naked eye. Nat Nanotechnol 2012, 7:821-824.
15. Ekins R., Chu F., Biggart E. Development of microspot multi-analyte ratiometric immunoassay using dual fluorescent-labelled antibodies. Anal Chim Acta 1989, 227:73-96.
16. Ray S., Britschgi M., Herbert C., Takeda-Uchimura Y., Boxer A., Blennow K., Friedman L.F., Galasko D.R., Jutel M., Karydas A., et al. Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins. Nat Med 2007, 13:1359-1362.
17. Williams R. Biomarkers: warning signs. Nature 2011, 475:S5-S7.
18. Pla-Roca M., Leulmi R.F., Tourekhanova S., Bergeron S., Laforte V., Moreau E., Gosline S.J.C., Bertos N., Hallett M., Park M., et al. Antibody colocalization microarray: a scalable technology for multiplex protein analysis in complex samples. Mol Cell Proteomics 2012, 11.
19. Kingsmore S.F. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov 2006, 5:310-321.
20. Butterfield L., Potter D., Kirkwood J. Multiplex serum biomarker assessments: technical and biostatistical issues. J Transl Med 2011, 9:173.
21. Gonzalez R.M., Seurynck-Servoss S.L., Crowley S.A., Brown M., Omenn G.S., Hayes D.F., Zangar R.C. Development and validation of sandwich ELISA microarrays with minimal assay interference. J Proteome Res 2008, 7:2406-2414.
22. Khan S.S., Smith M.S., Reda D., Suffredini A.F., McCoy J.P. Multiplex bead array assays for detection of soluble cytokines: comparisons of sensitivity and quantitative values among kits from multiple manufacturers. Cytometry B Clin Cytom 2004, 61B:35-39.
23. Djoba Siawaya J.F., Roberts T., Babb C., Black G., Golakai H.J., Stanley K., Bapela N.B., Hoal E., Parida S., van Helden P., et al. An evaluation of commercial fluorescent bead-based Luminex cytokine assays. PLoS ONE 2008, 3:e2535.
24. Fu Q., Zhu J., Van Eyk J.E. Comparison of multiplex immunoassay platforms. Clin Chem 2010, 56:314-318.
25. Breen E.C., Reynolds S.M., Cox C., Jacobson L.P., Magpantay L., Mulder C.B., Dibben O., Margolick J.B., Bream J.H., Sambrano E., et al. Multisite comparison of high-sensitivity multiplex cytokine assays. Clin Vaccine Immunol 2011, 18:1229-1242.
26. Browne R.W., Kantarci A., LaMonte M.J., Andrews C.A., Hovey K.M., Falkner K.L., Cekici A., Stephens D., Genco R.J., Scannapieco F.A., et al. Performance of multiplex cytokine assays in serum and saliva among community-dwelling postmenopausal women. PLoS ONE 2013, 8:e59498.
27. de Koning L., Liptak C., Shkreta A., Bradwin G., Hu F.B., Pradhan A.D., Rifai N., Kellogg M.D. A multiplex immunoassay gives different results than singleplex immunoassays which may bias epidemiologic associations. Clin Biochem 2012, 45:848-851.
28. Ellington A.A., Kullo I.J., Bailey K.R., Klee G.G. Antibody-based protein multiplex platforms: technical and operational challenges. Clin Chem 2010, 56:186-193.
29. Carlsson A., Wingren C., Kristensson M., Rose C., Fernö M., Olsson H., Jernström H., Ek S., Gustavsson E., Ingvar C., et al. Molecular serum portraits in patients with primary breast cancer predict the development of distant metastases. Proc Natl Acad Sci U S A 2011, 108:14252-14257.
30. Schröder C., Jacob A., Tonack S., Radon T.P., Sill M., Zucknick M., Rüffer S., Costello E., Neoptolemos J.P., Crnogorac-Jurcevic T., et al. Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies. Mol Cell Proteomics 2010, 9:1271-1280.
31. Gold L., Ayers D., Bertino J., Bock C., Bock A., Brody E.N., Carter J., Dalby A.B., Eaton B.E., Fitzwater T., et al. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS ONE 2010, 5:e15004.
32. Davies D.R., Gelinas A.D., Zhang C., Rohloff J.C., Carter J.D., O'Connell D., Waugh S.M., Wolk S.K., Mayfield W.S., Burgin A.B., et al. Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets. Proc Natl Acad Sci U S A 2012, 109:19971-19976.
33. Wu W., Slåstad H., de la Rosa Carrillo D., Frey T., Tjønnfjord G., Boretti E., Aasheim H.-C., Horejsi V., Lund-Johansen F. Antibody array analysis with label-based detection and resolution of protein size. Mol Cell Proteomics 2009, 8:245-257.
34. Slaastad H., Wu W., Goullart L., Kanderova V., Tjønnfjord G., Stuchly J., Kalina T., Holm A., Lund-Johansen F. Multiplexed immuno-precipitation with 1725 commercially available antibodies to cellular proteins. Proteomics 2011, 11:4578-4582.
35. Lundberg M., Thorsen S.B., Assarsson E., Villablanca A., Tran B., Gee N., Knowles M., Nielsen B.S., González Couto E., Martin R., et al. Multiplexed homogeneous proximity ligation assays for high-throughput protein biomarker research in serological material. Mol Cell Proteomics 2011, 10.
36. Lundberg M., Eriksson A., Tran B., Assarsson E., Fredriksson S. Homogeneous antibody-based proximity extension assays provide sensitive and specific detection of low-abundant proteins in human blood. Nucleic Acids Res 2011, 39:e102.
37. Ke R., Nong R.Y., Fredriksson S., Landegren U., Nilsson M. Improving precision of proximity ligation assay by amplified single molecule detection. PLoS ONE 2013, 8:e69813.
38. Poetz O., Henzler T., Hartmann M., Kazmaier C., Templin M.F., Herget T., Joos T.O. Sequential multiplex analyte capturing for phosphoprotein profiling. Mol Cell Proteomics 2010, 9:2474-2481.
39. Bergsma D., Chen S., Buchweitz J., Gerszten R., Haab B.B. Antibody-array interaction mapping, a new method to detect protein complexes applied to the discovery and study of serum amyloid P interactions with kininogen in human plasma. Mol Cell Proteomics 2010, 9:446-456.
40. Chen S., LaRoche T., Hamelinck D., Bergsma D., Brenner D., Simeone D., Brand R.E., Haab B.B. Multiplexed analysis of glycan variation on native proteins captured by antibody microarrays. Nat Methods 2007, 4:437-444.
41. Li H., Bergeron S., Juncker D. Microarray-to-microarray transfer of reagents by snapping of two chips for cross-reactivity-free multiplex immunoassays. Anal Chem 2012, 84:4776-4783.
42. Whiteaker J.R., Zhao L., Abbatiello S.E., Burgess M., Kuhn E., Lin C., Pope M.E., Razavi M., Anderson N.L., Pearson T.W., et al. Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol Cell Proteomics 2011, 10.
43. Reid J.D., Holmes D.T., Mason D.R., Shah B., Borchers C.H. Towards the development of an immuno MALDI (iMALDI) mass spectrometry assay for the diagnosis of hypertension. J Am Soc Mass Spectrom 2010, 21:1680-1686.
44. Olsson N., James P., Borrebaeck C.A.K., Wingren C. Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry. Mol Cell Proteomics 2012, 11:342-354.
45. Blank K., Lankenau A., Mai T., Schiffmann S., Gilbert I., Hirler S., Albrecht C., Benoit M., Gaub H., Clausen-Schaumann H. Double-chip protein arrays: force-based multiplex sandwich immunoassays with increased specificity. Anal Bioanal Chem 2004, 379:974-981.
46. Severin P.M.D., Ho D., Gaub H.E. A high throughput molecular force assay for protein-DNA interactions. Lab Chip 2011, 11:856-862.
47. Brody E., Gold L., Mehan M., Ostroff R., Rohloff J., Walker J., Zichi D. Life's simple measures: unlocking the proteome. J Mol Biol 2012, 422:595-606.