Mass spectrometry compatibility of two-dimensional gel protein stains

As proteomic technology evolves, protein staining sensitivity is constantly being improved, enabling researchers to better visualize the proteome of t heir system. The current challenge is to balance the limits of detection of protein visualization with those of the mass spectrometric methods. In thi s report, mass spectra generated from human serum or rat liver proteins sta ined with either colloidal Coomassie blue, Daiichi silver, SYPRO Orange, SY PRO Red, SYPRO Ruby, or SYPRO Tangerine are compared. it has been concluded that the newest generation of fluorescent protein stains, compared with tr aditional staining methods, are more compatible to matrix-assisted laser de sorption/ionization (MALDI) and liquid chromatography-tandem mass spectrome try (LC-MS/MS) methods. The number of database matches obtained using each mass spectrometry method and the percent sequence coverage obtained from tr ypsin digested proteins stained using these six methods is provided.