What do you want to learn from your samples?
We can quantitate aggregation and measure interaction constants (Kd's),
in addition to determining molar mass and frictional coefficients of monodisperse macromolecules.
FIRST LOOK AT A NEW SAMPLE:
Concentration dependence
The basic "run" that is usually performed on a new sample is to run three or four dilutions to determine whether
or not it exhibits concentration dependence either due to non-ideality or self-association.
Mono-disperse
Depending on the result of that initial run, if the sample is mono-disperse,
we can measure both molar mass and frictional coefficient.
Poly-disperse
or if it is poly-disperse, we can fit for the several components and either quantitate aggregates or measure self-association free energies.
If the sample exhibits both non-ideality and self-association,
analysis becomes a little more difficult and would require multiple runs to tease out both association constants and
non-ideality coefficients. This is not uncommon behavior; there are standard approaches to the experimental design and methods of analysis.
COMPLEX FORMATION: (hetero-association)
After the initial characterization of the individual proteins, they can be mixed together to check for complex formation.
Rapidly reversible interaction results in the formation of a reaction_boundary whose properties are
dependent on the absolute concentrations, ratios of loading concentrations,
magnitude of association constants, and relative values of sedimentation coefficients. Global fitting to multiple runs is genreally required to get good estimates of the interesting parameters.