Local drug delivery of paclitaxel is becoming ever more prevalent. As complex drug/excipient combinations are being developed and tested, new high performance liquid chromatography-mass spectrometry (HPLC-MS) techniques capable of quantifying paclitaxel from such formulations are needed. Here a method for quantifying paclitaxel from aqueous, protein and oil containing samples was developed and validated. Keratin, derived from human hair, is the protein component/paclitaxel excipient in the development and validation of said method. The novelty of this method is described by its ability to overcome water solubility issues and address clean-up of residual solvents in clinical grade paclitaxel injection composition. The method evaluates tert-butyl methyl ether and ethanol as extraction solvents with an extraction efficiency of 31.9 ± 2.3% and 86.4 ± 4.5% respectively. Upon evaporation and rehydration, samples were evaluated by HPLC-MS and a method was developed for paclitaxel quantification. The method developed had an inter-day precision of 9.1% relative standard deviation and an intra-day precision of 4.3% relative standard deviation normalized to a docetaxel internal standard. The described method is applicable to any aqueous paclitaxel sample containing protein and/or oils.