Table 2.

MS analysis of enriched aggregates: main features of the protein groups identified using Proteome Discoverer 1.4. Data are shown for the protein groups identified by ultracentrifugation only (UC), by Seprion Pads only (SEP), or “shared” by the two enrichment methods. The shared fraction included only the protein isoforms in common and not the parental proteins: coverage values are normally distributed and the mean was used for comparison.

fraction	total spectra	total PSMs	ID rat%	protein groups	Coverage%/ protein group (mean)	#Unique Peptides/ protein group (median)	#Peptides/ protein group (median)	#PSMs/ protein group (median)
UC	215,993	35,779	16.56	371	31.2%	5.0	6.0	12.0
SEP	210,875	34,865	16.53	609	25.6%	5.0	6.0	8.0
UC (shared)				209	34.7%	7.0	10.0	28.0
SEP (shared)				209	35.3%	8.0	10.0	21.0