Updated publication reference for PubMed record(s): 32175694. We employed an optimized, sensitive DIA-MS method on a high-resolution Orbitrap platform and re-measured the proteomic samples used in a previous study, in which the heterogeneity of HeLa cells across different research labs was analyzed by a multi-omic approach. Using the same MS sample sets of all HeLa strains we achieved higher sensitivity compared to our previous SWATH-MS results that were acquired on a TripleTOF instrument (5600 model). To benefit from the significantly improved sensitivity of this single-shot DIA-MS for both proteomic and protein turnover analysis, we analyzed the samples originating from six HeLa Kyoto strains and six HeLa CCL2 strains to profile both total protein-level abundances and the proxy protein turnover rates (Kloss, by pulsed SILAC labeling) across cell lines. Our results emphasized the importance of relative mRNA-protein turnover rate correlation analysis. The dataset demonstrate that specific biological processes, cellular organelles, subunits of organelles, and individual protein isoforms may have distinctive degradation rate and the corresponding buffering or concerting protein turnover control across cancer cell lines.