Proteomics multi-dimensional protein identification

More importantly insoluble proteins, such as membrane-bound and nuclear proteins, are under-represented within 2DE analysis. However, membrane proteins can be identified by MS following a IDE separation. Unfortunately, hydrophobicity is the most common reason for poor representation of abundant proteins and seems set to be with us for quite some time (Santoni et al., 2000 Rabilloud, 2002). Emerging proteomic methods without the use of 2DE are being developed, such as isotope-coded affinity tagging (ICAT) and multi-dimensional protein identification technology (MuDPIT). 

Washburn, M. R, Worters, D., Yates, J. R. (2001). Large-scale analysis of the yeast proteome by multi-dimensional protein identification technology. Nature Biotechnology, 19, 242-247. 

---