Fig. 2.

Integral membrane protein detection is enabled by in vivo crosslinking and denaturing extraction. A, The fractional intensity of each protein detected (intensity of each protein/sum of all intensity in data set) in either a native protein complex extraction (6), or the in vivo crosslinked and denatured extract from this study, are plotted. Proteins detected in either only the native extracts (dashed yellow box), or only the crosslinked and denatured extracts (dashed blue box), are also shown. Proteins without predicted transmembrane (TM) helices are shown as green dots. Proteins with one or more TM helices are shown as red circles, with the size of each circle being proportional to the number of TM helices in each protein. The diagonal line indicates equal fractional intensity between data sets. A representative experiment is shown (n = 3). B, Analysis of enriched GO terms (cellular component) within the proteins detected only from crosslinked and denatured extracts. The y axis indicates the EASE score (-log₁₀ transformed) for each GO cellular component term enriched data set versus the whole human proteome, all terms have a p < 0.001. The x axis shows the number of proteins detected only from crosslinked and denatured extracts associated with each GO term. The size of the circle representing each GO term increases with higher proportional contribution to the subset of proteins detected only from crosslinked and denatured extracts. Colors are randomly chosen. A representative experiment is shown (n = 3). C, Stacked histogram showing the distribution of proteins with various numbers of TM helices from none up to 12 (indicated in colored legend) across the fractional intensity range from native protein complex extraction (6). Data from proteins only detected in the crosslinked and denatured extracts (dashed blue box) are also shown. A representative experiment is shown (n = 3).