Proteome analysis by two-dimensional gel electrophoresis (2-DE) together with mass spectrometry was applied to screen acute phase response (APR)-related proteins with low molecular weight in loach skin following injury. Furthermore, Western blotting and function tests were applied to confirm the results obtained from the proteomic study. Fifteen APR-related proteins with sixteen spots (PLA with two spots) on a 2-DE map were identified in this study. Furthermore, six were known acute phase proteins including galactose-binding lectin (GBL), lysozyme, C3, CD59, double PLA and 50s ribosomal protein; while ATP kinase, zinc finger protein 183, alpha-neurotoxin homology, angiostatin, serine/threonine kinase, metalloproteinase inhibitor, regulator of G-protein 4, cryptdin-9 and disintegrin trigranin were found by our lab to be APR-related proteins. In addition, our results suggest that proteomes with low molecular weight can be characterized by 2-DE with a Tris-tricine system followed by mass spectrometry.