High MS‐compatibility of silver nitrate‐stained protein spots from 2‐DE gels using ZipPlates and AnchorChips for successful protein identification

The availability of easy‐to‐handle, sensitive, and cost‐effective protein staining protocols for 2‐DE, in conjunction with a high compatibility for subsequent MS analysis, is still a prerequisite for successful proteome research. In this article we describe a quick and easy‐to‐use methodological protocol based on sensitive, homogeneous, and MS‐compatible silver nitrate protein staining, in combination with an in‐gel digestion, employing the Millipore 96‐well ZipPlate system for peptide preparation. The improved quality and MS compatibility of the generated protein digests, as compared to the otherwise weakly MS‐compatible silver nitrate staining, were evaluated on real tissue samples by analyzing 192 Coomassie‐stained protein spots against their counterparts from a silver‐stained 2‐DE gel. Furthermore, the applicability of the experimental setup was evaluated and demonstrated by the analysis of a large‐scale MALDI‐TOF MS experiment, in which we analyzed an additional ˜1000 protein spots from 2‐DE gels from mouse liver and mouse brain tissue.

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