Extended Data Fig. 5: Downsampling analysis of published CF–MS experiments.

a, Recovery of proteins annotated to the same GO term after downsampling CF–MS chromatograms to a fixed number of fractions. b–c, Recovery of protein complexes, b, and GO terms, c, in downsampled CF–MS chromatograms, using mutual information as the measure of profile similarity. d–e, Recovery of protein complexes (AUC, d, and change in AUC, e), in downsampled CF–MS chromatograms, with experiments divided based on the separation method used (IEX, ion exchange chromatography; N-PAGE, native polyacrylamide gel electrophoresis; SEC, size exclusion chromatography). f, Recovery of protein complexes when downsampling windows of adjacent fractions of fixed length, rather than downsampling fractions randomly from the chromatogram matrix. g–h, Comparison of protein complex recovery (AUC, g, and change in AUC, h), in downsampled CF–MS chromatograms when drawing samples of random fractions or adjacent fractions from the chromatogram matrix. a–h, Shaded area shows the standard error.