Protein separate techniques, such as 2D PAGE, are limited in that they cannot handle very high or low molecular weight protein species.  Alternative methods have been developed to deal with such cases.  These include liquid chromatography mass spectrometry along with sodium dodecyl sulfate polyacrylamide gel electrophoresis, or liquid chromatography mass spectrometry run in multiple dimensions.  Compared to simple 2D page, liquid chromatography mass spectrometry can handle a larger range of protein species size, but it is limited in the amount of protein sample it handle at once.  Liquid chromatography mass spectrometry is also limited in its lack of a reference map from which to work with.  Complex algorithms are usually used to analyze the fringe results that occur after a procedure is run.  The unknown portions of the protein species are usually not analyzed in favor of familiar proteomes, however.  This fact reveals a fault with current technology; new techniques are needed to increase both the specificity and scope of proteome mapping.