Visualization of (phospho)peptide quantification (LC-SRM traces) and integrated peak area changes across the cell culture growth phases on the examples of two mTOR pathway proteins. Temporal dynamics of the log₂ normalized integrated peak area values (presented as average ± SD of three biological replicates, top panels) and representative peptide traces (three lower panels) are presented for (A) PRAS40 (AKT1S1) peptides, including the non-phosphorylated peptide FHPSGIEVEGQR used to determine the abundance level (yellow line) and the non-phosphorylated counterpart peptide (black line) along with  its corresponding phosphorylated peptide containing the regulatory phosphosite pSLPVSVPVWGYR (blue line), and (B) AMPK1 (PRKAa1) peptides, including the non-phosphorylated peptide HTLDELNPQK used to determine the abundance level (yellow line) and the non-phosphorylated counterpart peptide (black line) along with its corresponding phosphorylated peptide containing the regulatory phosphosite SGpSVGNYR (blue line). Phosphopeptides were measured in the bound fraction (Fe-NTA-enriched for phosphopeptides) and normalized using the respective spiked heavy-labelled phosphopeptide standard, while non-phosphorylated peptides were measured in the non-bound fraction and normalized to the average peak areas of housekeeping proteins (ACTB1 and RPS18) used to account for differences in total protein amount across samples. The representative extracted ion chromatograms (XICs) shown for each peptide display the actual LC-SRM traces from the last timepoint (day 28) of the first biological replicate; the retention time of the target peak is indicated with a black arrow on each graph and the transition used for quantitation is indicated in the top left corner (the two other transitions were used as qualifying to confirm the peptide identification).