I want to be informed about the procedures available to analyse 2D PAGE spots after silver or copper staining? I know MALDI-MS is a option. But I want some information about other procedures.
LCMS after a trypsin digestion works. One problem with silver stained 2D PAGE spots is the amount of protein is very low - may be 10ng or less. With so little protein, typically only keratin from dust collecting on the surface of the gel will be identified. Comassie visible spots from a 2D gel will give adequate protein identifications after trypsin digestion. But Comassie is visible for 100ng or more.
There are a swisssprot 2D PAGE data base where you will get analyzed 2D gels. You can match your spot with those reference gel and can have an idea about the spot.