What are the advantages and disadvantages of in-gel versus in-solution digestion?
Carrying out in-gel digestion allows for low cost high throughput processing of samples and the generation of peptide solutions devoid of salts and detergents that are detrimental to the subsequent mass spec analysis. It allows for a certain degree of sample fractionation and separation after 1-dimensional or 2-dimensional electrophoresis and provides information regarding the observed molecular weight of the protein that is identified. The disadvantages are the potential loss of material incurred by the additional sample manipulation steps introduced by loading samples onto gels and the sometimes inefficient extraction of peptides from gels after tryptic digestion. The advantage of doing an in-solution digestion is the potential for improving protein detection and sequence coverage since little or no protein or peptide fragment losses are incurred. However, depending on the constitution of the solution it may be essential to carry out additional sample clean-up steps before proceeding
