Proteins are important substances in living organisms and characterization of proteins is an indispensible part for protein study. Analysis of proteins using electrospray ionization-mass spectrometry (ESI-MS) with porous substrates was investigated in this study. The results revealed that the ionization process had two stages. At the first stage, mobility and resulting spectra of proteins were similar to those obtained with conventional capillary-based ESI-MS. At the second stage, hydrophobic-hydrophobic interactions between proteins and the tip surfaces played an important role in mobility and detectability of protein ions, which were size and shape dependent, and a linear relationship could be found between the peak area of selected ion chromatogram and the cross section of protein ions. Preparative separation of proteins could be achieved by collecting the proteins remained on the porous substrates. These results led us to propose that electrospray ionization from porous substrates offer a potential approach for analysis of proteins and investigation of protein structures and conformations.