2D DIGE vs LC-MS/MS

What are the differences between 2D DIGE and LC-MS/MS?

It is important to understand that 2D DIGE separates proteins by both MW and isoelectric point (pI), thus offering very high resolutions of all proteins within a sample and any modified forms (such as those featuring post translation modifications (PTMs) or degraded forms of proteins) with a wide dynamic range. On the other hand, liquid chromatography mass spectrometry (LC-MS/MS) separates samples into individual peptides, which exceeds the number of proteins by several magnitudes.

The separation of proteins by both MW and pI produces data of a higher resolution than that of a large number of small peptides separated by hydrophobicity only, as is the case in LC-MS/MS. Of course, the resolution of both platforms can be increased if coupled with a prior sample purification step to remove abundant proteins. In addition, protein fractionation in combination with hydrophobicity separation can increase the peptide resolution in LC-MS/MS however, all of these extra steps will increase the cost and may compromise the reproducibility of data. One of the benefits of 2D DIGE is that it allows direct visualization of total protein profiles natively between all the samples.