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| Property | Fluoropores | Quantum Dots |
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| Absorption spectra | Variable/narrow generally a mirror of the emission spectra | Broad spectra, steadily increases towards the UV from the first absorption band edge |
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| Maturation time | Needed for fluorescent proteins | NA |
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| Molar extinction coefficients | Variable, Generally 200,000 | High, 10–100X that of fluorophores |
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| Fluorescent lifetime | Short 5 ns | Long 10–20 ns or greater |
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| Spectral range | Necessitates a different dye every 40–60 nm | UV-IR depending upon binary/ternary materialVis-CdSe |
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| Tunable emission | NA | Unique to QDs / can be size-tuned from the UV to IR |
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| Multiplexing capabilities | Rare | Excellent, largely unexplored |
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| Intermittency (blinking) | Negligible | Maybe problematic in isolated circumstances (single molecule tracking) |
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| Quantum yield | Variable, low to high | Generally high, 0.2 to 0.7 in buffer depending upon surface coating |
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| Photostability | Variable to poor | Excellent, strong resistance to photobleaching several orders of magnitude that of dyes multiple acceptor configurations possible |
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| Multiphoton cross section | Variable to poor | Excellent 2-3 orders of magnitude that of dyes |
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| Emission spectra Effective Stokes shifts | Broad, asymmetric red-tailed emission | Narrow-full width at half-maximum 25–40 nm for CdSe core materials |
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| Chemical resistance | variable | Excellent |
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| Reactivity | Multiple relativities commercially available | Limited conjugation chemistries available |
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| Mono-valent attachment | Easy | Difficult |
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| Multi-valent attachment | Rare-mostly bis-functional | Good possibilities, can attach several molecules to QDs depending upon size |
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| Physical size | 0.5 nm | 4–7 nm diameter for CdSe core material |
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| Cost effectiveness | Very good/multiple suppliers | Poor/2 commercial suppliers |
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| Electrochromicity | Rare | Largely untapped |
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