Chromatography　and　mass　spectrometry　(MS)　techniques　have　greatly　improved　the　power　of　proteomic　analyses.　However,　sample　processing　methods　used　prior　to　MS,　including　protein　extraction　and　digestion,　remain　bottlenecks　in　the　large-scale　clinical　application　of　proteomics.　Ionic　liquids,　composed　entirely　of　ions,　have　high　solubility　in　various　solvents.　In　this　study,　the　effects　of　the　cationic　surfactant　1-dodecyl-3-methylimidazolium　chloride　(C12Im-Cl)　on　protein　digestion　were　evaluated　for　clinical　proteomic　applications.　C12Im-Cl　was　compatible　with　trypsin　and　reduced　the　protein　digestion　time　from　16　h　to　1　h.　Residual　C12Im-Cl　was　easily　removed　with　a　strong　anion　exchange　membrane　before　MS.　We　evaluated　the　performance　of　C12Im-Cl　extraction　and　rapid　protein　digestion　using　formalin-fixed　paraffin-embedded　liver　cancer　tissues.　The　number　of　proteins　and　peptides　identified　was　nearly　equal　to　that　identified　by　the　traditional　filter-aided　sample　preparation　method　(2705　vs.　2739　and　16　682　vs.　17　214).　In　general,　the　C12Im-Cl-aided　rapid　sample　preparation　method　is　promising　for　proteomic　applications.