Abstract: In this work the identification method for protein mixture is reported, in which several proteins were varified by HPLC ESIMS/MSafter the whole complex proteins were directly digested in solution, instead of the routine 2-dimensional gel electrophoresis. The obtained data was then searched against NCBInr database by using MS/MS Ions Search(http://www.matrixscience.com), and a positive result was therefore obtained. With the simulated sequence spectra in database searching, a re identification method was developed for low-score matched protein by sequence-tag technique. As a typical example, Concanavalin A, a less-soluble protein with a low matching score, was also successfully identified, which indicated the great potential of complex digestion in proteomic study.

Key words: Identification of complex protein, Proteomics, Micro HPLC, Ion Trap tandem mass spectrometry, Sequence analysis