The peptides digested from two biological replicates of iPSC cells at time zero (cells in light medium) were both measured on an AB SCIEX 5600 plus TripleTOF mass spectrometer operated in DDA mode. The mass spectrometer was interfaced with an Eksigent NanoLC Ultra 2D Plus HPLC system as previously described [48 (link), 49 (link)]. Peptides were directly injected onto a 20-cm PicoFrit emitter (New Objective, self-packed to 20 cm with Magic C18 AQ 3-µm 200-Å material), and then separated using a 120-min linear gradient of 2 % buffer B to 35 % buffer B (buffer A 0.1 % (v/v) formic acid, 2 % (v/v) acetonitrile, buffer B 0.1 % (v/v) formic acid, 90 % (v/v) acetonitrile) at a flow rate of 300 nL/min. MS1 spectra were collected in the range 360–1,460 m/z. The 20 most intense precursors with charge state 2–5 which exceeded 250 counts per second were selected for fragmentation, and MS2 spectra were collected in the range 50–2,000 m/z for 100 ms. The precursor ions were dynamically excluded from reselection for 20 s.