Problems arising from using commercial staining kits:
Scientists use silver staining for sensitive detection of proteins separated by 1D and 2D SDS PAGE. The detection limits should be 0.5-5 ng [1, 2].
Many silver staining protocols and commercial staining kits are not compatible with mass spectrometry. This is because they use cross-linking reagents. Therefore, it is important with a silver stain protocol compatible with mass spec if one wishes to identify proteins (protein identification) from bands and spots isolated from SDS PAGE gels [1, 2].
For low protein amounts, we recommend that you use a silver staining method optimized for compatibility and sensitivity with trypsin digestion and MS analysis. Many silver staining protocols are not compatible and thus do not work with protein identification using mass spec (mass spectroscopy) [1, 2].
In the protocol (follow the link below), we describe our Alphalyse SDS Page gel silver staining protocol which we optimized for mass spectrometric analysis.
Get a confident protein identifications and high sequence coverage:
The protocol results in confident protein identifications. In addition, it provides a high sequence coverage by MALDI MS and ESI MS. This is due to a high recovery of peptides from the stained gel. The protocol has been tested and documented in many publications .
 Chevallet et al: “Silver staining of proteins in polyacrylamide gels“, Nature Protocols, 2006
 Rabilloud, T.: “Mechanisms of protein silver staining in polyacrylamide gels: a 10-year synthesis“, Electrophoresis, 1990