Assessment of filter plates for multi-well in-gel digestion of proteins separated by polyacrylamide gel electrophoresis to identify them with LC-ESI/MSMS

In-gel digestion is an important technique for proteome analysis using polyacrylamide gel electrophoresis. Although the identification by MSMS ion search is much reliable than PMF, MSMS analysis of peptides separated by nanoLC directly coupled to MS is time consuming and clogging with particles from in-gel digest interrupts separation of peptide by nanoLC. Removal of particles from the digest with filtration is essential for nanoLC analysis, but it is laborious process, when a large number of samples should be processed. Simple and high-throughput method is necessary for in-gel digestion and the sample preparation of nanoLC. The characteristics of filter plates are investigated and a method of in-gel digestion for nanoLC-MSMS systems using inexpensive 96-well filter plate is presented.