Recently, TDP-43 negative, FUS-positive FTLD inclusions were found to contain EWS and TAF15. We note that these 3 related proteins FUS, EWS, and TAF15 were among the 585 reliably quantified proteins in this study, but our results pose the interesting implication that overexpressed TDP-43 preferentially could co-aggregate in HEK-293 cells with EWS rather than FUS or TAF15, consistent with cell type specific interactions, which may not occur in the neurons affected in either FTLD or ALS. An equally plausible alternative to the interpretation of protein-protein interaction is that TDP-43 overexpression may indirectly and differentially affect transcription, translation, or post-translational stability of these intrinsically detergent-resistant proteins that have potential overlapping function with TDP-43. The quantitative approach employed for this study following qualitative detergent insoluble protein enrichment has two important caveats that must be addressed. First, qualitatively, the aggregate proteome is not the entire detergent insoluble proteome. In fact, the makeup of the mock-transfected detergent insoluble proteome provides insight into a (+)-JQ1 Epigenetic Reader Domain inhibitor background level of proteins that copurify with aggregate proteins. These proteins fall into categories of possibly ordered protein complexes with nucleic acid chains, cytoskeletal proteins, or mitochondrial organelle contaminants, where categories for localization, domain content, or nucleic acid association were determined using the Database for Annotation, Visualization, and Integrated Discovery. The target aggregate proteome is best defined as the proteins which change quantitatively from the background under conditions that are expected to alter intermolecular interactions. Under such conditions, distinct protein species significantly shift into or from the detergent insoluble fraction, as when TDP-43 intracellular concentration is increased by overexpression. After cell lysis, solvent makeup, including salts and a number of additional stabilizers. The stringent RIPA buffer used here and an absence of freezing the transfected cell pellets before fractionation would be expected to maintain the biochemical segregation of proteins that already occurred in the live cells, by keeping folded proteins in the detergent-extracted fraction. In fact, the control detergent soluble and insoluble fractions were derived from cells which had been frozen before fractionation. Freeze-thaw induced aggregation of distinct species is one explanation for differences in the relative abundance of some detergent-insoluble proteins between the SILAC internal standard and mock-transfected group; increased passage number to accommodate complete labeling is another possible source of differences. Regardless, the mock transfected/control distribution of relative protein abundances in the insoluble fraction remains a normal distribution with the population mean centered at zero, representing no gross change.