Table S1. Table showing various significant QDs in proteomic applications QD CdSe-ZnS QDs. Protein analytes Application Methods Ref. histidine, cysteine, methionine, and tryptophan [1] oligohistidine fused proteins [2] thrombin Flourescence [3-5] recombinant proteins [6] InGaP/ZnS bovine serum albumin (BSA) [7] CdSe QDs (Telomere associated proteins telomeric repeat binding factor (TRF1, a 56 kDa protein) and TRF1interacting nuclear protein 2 (Tin2,40 kDa protein) directly in cell lysate [8] QDs western blot CdTe QDs protein A [9] CdSe/ZnS QDs carcinoembryonic antigen CEA [10] CdSe/ZnS QDs TNF-α, IL-8, IL-6, MIP-1β, IL-13 and IL-1β CdSe/ZnS prostate specific antigens (PSAs) Protein chip [11] Cancer protein chip [13] Insulin CdS QDs Protein and peptides [12] Mass spectrometry Cytochrome, HSA, BSA. [14] [15] References 1. Peelle, B. R.; Krauland, E. M.; Wittrup, K. D.; Belcher, A. M. Design Criteria for Engineering Inorganic Material- Specific Peptides. Langmuir 2005, 21, 6929–6933. 2. Sapsford, K. E.; Pons, T.; Medintz, I. L.; Higashiya, S.; Brunel, F. M.; Dawson, P. E.; Mattoussi, H. Kinetics of Metal-Affinity Driven Self-Assembly between Proteins or Peptides and CdSe−ZnS Quantum Dots. J. Phys.Chem. C 2007, 111, 11528–11538. 3. Levy, M., Cater, S.F., Ellington, A.D., Quantum dot aptamer beacons for the detection of proteins. Chembiochem 2005, 6, 2163–2166. 4. Swain, M.D., Octain, J., Benson, D.E., Unimolecular, Soluble Semiconductor Nanoparticle-Based Biosensors for Thrombin Using Charge/Electron Transfer. Bioconjugate Chem 2008, 19, 2520–2526. 5. Chi, C.W., Lao, Y.H., Li, Y.S., Chen,L.-C., A quantum dot-aptamer beacon using a DNA intercalating dye as the FRET reporter: Application to label-free thrombin detection, Biosens. Bioelectron. 2011, 26, 3346–3352. 6. Mattoussi, H., Mauro, J.M., Goldman, E.R., Anderson, G.P., Sundar, V.C, Mikulec, F .V., Bawendi,M.G., Self-Assembly of CdSe-ZnS Quantum Dot Bioconjugates Using an Engineered Recombinant Protein. J. Am. Chem. Soc 2000, 122, 12142-12150. 7. Kumar, P., Deep, A., Sharma, S.C., Bharadwaj, L.M., Bioconjugation of InGaP quantum dots for molecular sensing. Anal Biochem 2012, 421, 285–290. 8. Ornberg, R.L., Harper, T.F., Liu, H., Western blot analysis with quantum dot fluorescence technology: a sensitive and quantitative method for multiplexed proteomics. Nat Methods. 2005, 2,79-81. 9. Bakalova, R., Zhelev, Z., Ohba, H., Baba, Y., Quantum Dot-Based Western Blot Technology for Ultrasensitive Detection of Tracer Proteins. J. Am. Chem. Soc 2005,127, 9328-9329. 10. Xu, Y., Gang, Bao, B., A Filtration-Based Protein Microarray Technique. Anal. Chem 2003, 75, 5345-5351. 11. Hu, M., Yan, J., He, Y., Lu, H., Weng, L., Song, S., Fan, C., Wang, L., Ultrasensitive, Multiplexed Detection of Cancer Biomarkers Directly in Serum by Using a Quantum Dot-Based Microfluidic Protein Chip. ACS Nano 2010, 4,488–494. 12. Jin, L.H., Li, S.M., Cho, Y.H., Enhanced detection sensitivity of pegylated CdSe/ZnS quantum dots-based prostate cancer biomarkers by surface plasmon-coupled emission. Biosens. Bioelectron. 2012, 33, 284– 287. 13. Shrivas, K., Kailasa, S.K, Wu, H.F., Quantum dots laser desorption/ionization MS: Multifunctional CdSe quantum dots as the matrix, concentrating probes and acceleration for microwave enzymatic digestion for peptide analysis and high resolution detection of proteins in a linear MALDI-TOF MS, Proteomics 2009, 9, 2656–2667. 14. Wu, H. F., Chung, F.T., 3-Mercaptopropionic acid modified ZnSe quantum dots as the matrix for direct surface assisted laser desorption/ionization mass spectrometric analysis of peptides/proteins from sodium salt solution. Rapid Commun. Mass Spectrom. 2011, 25, 1779–1786. 15. Ke, Y., Kailasa, S. K., Wu, H. F.,Chen, Z. Y., High resolution detection of high mass proteins up to 80,000 Da via multifunctional CdS quantum dots in laser desorption/ionization mass spectrometry. Talanta, 2010, 83, 178–184.