Figure 4. Pulsed-SILAC experiment performed on human iPSCs.

A human iPS cell line was exposed to a pulse of heavy amino acids and sampled at four time points in duplicates (see Panel b). (a) The RT difference between the light and heavy signal as a function of the intensity. Aligned values reported by TRIC (in red) have lower intensity and higher RT error (distribution on top only displays values below 10⁴ in intensity) (c) Standard deviation of the RT difference between heavy and light pairs with and without TRIC alignment. For the analysis without alignment, a simple FDR cutoff was applied (naïve approach). Alignment increases the number of quantified SILAC pairs at the cost of slightly higher variance. Pairs from both replicates are aggregated. No heavy-light pairs are expected at t=0 as heavy amino acids were added afterwards. (d) The number of isotopic SILAC pairs quantified per sample increases through the TRIC alignment, especially for the earlier time points with little heavy isotope signal. For each timepoint, average values across two replicates are shown with standard deviation.