Described herein are PEG-coated, core-shell nanoparticles, which display reduced aggregation and/or reduced non-specific or undesired attachment characteristics. These fluorescent nanoparticle include: a silica-based core having an organic functional group that includes a mercapto substituent, an organic fluorescent compound, a silica shell; and a silane-PEG compound. The silica shell of the nanoparticle encapsulates the silica-based core and the silane-PEG compound is conjugated to the silica shell.