Several methods have been employed in order to identify the array of proteins that comprise the T3SS. Isolated needle complexes can be separated with SDS-PAGE. The bands that appear after staining can be individually excised from the gel and analyzed using protein sequencing and mass spectrometry. The structural components of the NC can be separated from each other (the needle part from the base part, for instance), and by analyzing those fractions the proteins participating in each one can be deduced. Alternatively, isolated NCs can be directly analyzed by mass spectrometry, without prior electrophoresis, in order to obtain a complete picture of the NC proteome.
