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. 2020 Feb 25;36(10):3148–3155. doi: 10.1093/bioinformatics/btaa118

Fig. 3.

Fig. 3.

Estimated versus expected ratios for UPS1 proteins. The abundances of the 48 UPS1 proteins were extracted by Proline (left panel) and MaxQuant (right panel) in each sample from the standard dataset, using either a sum aggregation (upper panels) or ratio-fitting algorithms (bottom panels). The ratios determined, calculated relative to the 50 fmol/µg concentration, were plotted against the expected ratios for the UPS1 proteins across the 10 different concentration points. Both Proline and MaxQuant accurately estimated the ratios calculated for concentration spikes down to 1 fmol/µg (expected ratio 5:6) for most UPS1 proteins. For lower concentration points, when some peptides fell below their limit of detection, the two software behaved differently, with a trend for overestimation of the ratio for MaxQuant, while Proline ratios were still well-fitted down to 250 amol/µg (expected ratio 7:6). When the ratios were calculated using MRF in Proline (bottom left), ratio variability around expected values was reduced compared with the sum method; variability was increased when MaxQuant MaxLFQ was applied (bottom right)