Identification of Proteins from SDS-PAGE Gels by Mass Spectrometryæ

The mass spectrometry tools described on this web site have provided us with the very useful capability of identifying proteins from one- and two-dimensional SDS-PAGE gels. In these experiments proteolytic digestion of the excised gel slice containing the protein of interest is followed by mass spectrometric analysis of the resulting peptides. This can be done in two ways. In the case of peptide mass mapping, the masses all of the peptides resulting from the proteolytic digestion are determined simultaneously by MALDI-TOF Mass Spectrometry. The masses of the peptides are used to search public genomic databases to identify the proteins. As a rule of thumb the protein can be identified if sufficient material to be visualized by Coomassie Blue staining is present, and the sequence is present in the database. If the protein cannot be identified in this way, the sequence of one or more of these peptides can be determined by Q-TOF Mass Spectrometry, and the resulting sequence can be used to search genomic databases for an exact match. Normally 100 fmol of a protein in a gel slice, which manifests as a faint silver band using our mass spec-compatible silver staining protocols, is needed to identify a protein in this way. If the protein still cannot be identified, the peptide sequence can be used for a  BLAST search to identify a similar protein,  perhaps from another species, which sequence can be found in a database. Alternatively the peptide sequence(s) can be used to design primers for cloning of the gene encoding the protein. Because we use nanoflow LC-MS/MS for our Q-TOF identifications, up to 50 or more proteins can be identified from a single gel band. Please follow these guidelines for Gel Staining for preparing your protein for identification in this way.