2-DE is the other method of choice for the separation of proteins
in complex biological samples (Miller, Crawford, & Gianazza, 2006).
Protein spots of interest are excised, digested with proteases and
the resulting peptides identified by MS. 2-DE remains the most
widely applied separation method in proteome analysis due to the
high protein resolution. In addition, this method is the most powerful
option for non-completely sequenced organisms (i.e. fish species), in
which the identification of proteins is based on comparing peptides
from the proteins of interest with orthologous proteins from other
species or by means of de novo mass spectrometry sequencing strategies.
However, gel-based methods still have some limitations, such as
the separation of hydrophobic and poorly soluble proteins and the
limited sensitivity of the available detection methods. Nevertheless,
we believe as do other authors, that both the gel-based and gel-free
methods will continue to prove useful in the long term.