2-D differential membrane proteome analysis of scarce protein samples

Proteome studies with small sample amounts are difficult to perform, especially when membrane proteins are the focus of interest. In our study a new method for the analysis of scarce membrane protein samples combining large gel 2‐D‐CTAB/SDS‐PAGE with fluorescence dye saturation labelling (satDIGE) was developed, allowing a highly sensitive differential analysis of different cell states. After Triton X‐114 phase partitioning, enriched membrane protein samples of T cells were labelled at cysteine residues using fluorescence dyes and separated by large gel 2D‐CTAB/SDS‐PAGE. For a differential analysis 3 μg protein was found to be sufficient to detect proteins in a widespread well‐separated diagonal spot pattern.