High-throughput MS/MS Datasets from Diverse Cell Lines

An MS/MS dataset from 11 human cell lines (A549, GAMG, HEK293, HeLa, HepG2, Jurkat, K562, LnCap, MCF7, RKO, and U2OS, each with three replicates) was obtained using an LTQ-Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) [9 (link)]. The HEK293 24-fraction MS/MS dataset was obtained with a Q-Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) [10 (link)]. The S. cerevisiae Elite MS/MS dataset was obtained with an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) [11 (link)]. The S. cerevisiae 2DLC MS/MS dataset was obtained using a LTQ-Orbitrap hybrid mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) [12 (link)]. Peptide fragmentation was performed using the higher-energy collisional dissociation (HCD) method. Supplementary Table 1 shows the number of spectrum in the human cell lines, the HEK293 24 fraction, in the S. cerevisiae Elite and 2DLC datasets.