Fractionation efficiency and protein characterization of neural soluble and insoluble proteins by sequential extraction was scrutinized by gel-based proteomic analysis. Spinal cord proteins of adult rats were first extracted with aqueous buffer (fraction A), followed by standard (fraction B) or modified (fraction C) enhanced solutions. Of the top 30 most abundant proteins in fractions A, B and C, the percentage of cytoplasmic proteins was 74% (28/38) , 37% (14/38) and 42% (15/36), respectively; membrane organellar proteins accounted for 8% (3/38), 45% (17/38), and 44% (16/36); membrane proteins accounted for 13% (5/38), 18% (7/38) and 14% (5/36). The number of hydrophobic domains was 5, 15 and 9. Shared proteins in three fractions were only 13%. When additional less abundant 30 spots enriched the insoluble fraction C were characterized, membrane proteins accounted for 31%, among which 83% were peripheral membrane proteins and 17% were integral membrane proteins. Functional analysis also revealed some difference between different fractions although all fractionated proteins are involved in energy metabolism, redox regulation, signal transduction and cellular architecture.