The detection of quantum-dot labeled proteins is demonstrated within lead silicate soft glass microstructured optical fibers using near infrared light. The protein concentration is measured using a new fluorescence capture approach. Light guided within the fiber is used both to excite and collect fluorescent photons, and the detection limit achieved without optimization of the fiber geometry is 1 nM, using just 3% of the guided mode of the fiber. Issues that currently restrict the detection of lower protein concentrations are discussed.