This document discusses challenges in analyzing protein aggregates using analytical methods. It provides examples of unusual aggregation phenomena observed:
1) An "aggregate" peak seen by SEC in a stressed sample was shown to be a partially denatured monomer using SEC-MALLS and sedimentation velocity.
2) Freeze/thaw stress generated transient, metastable oligomers in a protein that were difficult to detect by SEC due to their stickiness. Sedimentation velocity detected a much higher level of aggregates.
3) Different analytical methods can perturb aggregate distributions in different ways by dissociating or creating new aggregates. Method selection depends on the aggregate properties and no single method is optimal in all cases.