Should I use 1D or 2D SDS PAGE?
I’m interested in isolating and identifying cell surface receptor proteins.
They typically have high MW, are glycosylated, and have transmembrane domains.
I’m considering 2D electrophoresis, but do you have any recommendations?
2D PAGE is the classical approach to separate and visualize many proteins from complex proteomics samples. However, 2D PAGE has some known disadvantages. As an example, hydrophobic membrane proteins precipitate during IEF and are almost never observed. So most likely, you will only observe proteins within the pI range of the gel, typically pH 4-7, or 3-10, and the MW range of proteins in the gel is approximately 10-130 kDa [1-3].
For large and hydrophobic proteins it is therefore better to use 1D SDS PAGE. Mainly because the proteins can be dissolved in the 1D SDS PAGE buffer containing 0.1% SDS. In addition, the gels have no pI limits, and the MW range can go up as high as 1.000 kDa .
Another possibility is to use in-solution digestion of the protein mixture. You would typically then perform protein identification by LC-MS/MS [1-3].
 Sickmann et al: “The proteome of Saccharomyces cerevisiae mitochondria“, Proceedings of the National Academy of Sciences of the United States of America (PNAS), 2003
 Andersen et al: “Directed Proteomic Analysis of the Human Nucleolus“, Current Biology, 2002
 Wiśniewski et al: “Universal sample preparation method for proteome analysis“, Nature Methods, 2009