Our paper on Rapid Profiling of Protein Complex Reorganization in Perturbed Systems. The message: co-fractionation methods are very informative but not much used because the resources needed are large - we speed this up with short gradient DIA analysis and new differential assessent tools. Relies heavily on Evosep chromatography, a great match for DIA-MS. We implemented approaches to assess differential complex changes (CCProfiler) including a complex-centric hypothesis driven approach, and more flexible hypothesis-free approaches that look at protein SEC features or at the distribution of a protein across the SEC/MW range. We benchmark the method versus more standard long gradient analysis, and demonstrate its utility in a model of THP1 monocyte to macrophage differentation by phorbol ester, followed by stimluation of the macrophage cells by lipopolysaccharide. The hope is that this will enable larger studies with more experimental groups and replication to push this type of approach to look at protein complex (re-)organization in perturbed biological systems. This study was started quite a while back at ETH and finished in a distributed manner as the Zurich crew went their separate ways so it took a while to get finalized. The DIA method/instrument are a little out of date but combining with the latest DIA methods should be powerful.