Quantitative proteome profiling of parental cell lines used in the RESOLUTE project (https://re-solute.eu).

ABSTRACT: To enable successful SLC function deorphanization we aimed to select a minimal number of cell lines covering expression of as many SLCs as possible. Based on a publicly available RNA-Seq dataset of 675 cell lines (Klijn C. et al, Nat. Biotechnol. 2015) we selected a set of 6 adherent human cell lines (HCT 116, Huh 7, LS180, MDA MB 468, SK MEL 28, 1321N1) cumulatively covering expression (TPM>1) of about 80% of all human SLCs. These cell lines will be used to generate SLC-knockout and SLC-overexpressing single cell clones. Additionally, Jump-In T-REx HEK293 cells will be used for generating SLC-overexpression cell lines. In order to characterize the expressed proteome of these parental cell lines, we performed extensive proteomic profiling using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Mass spectra were acquired on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific) in data-dependent acquisition (DDA) mode. Instrument performance was monitored by a quality control routine using BSA- and HeLa digest standards. Data was analyzed using Thermo Proteome Discoverer 2.3 software. This data release consist of (1) RAW mass spectrometry data files generated by the instrument per fraction, (2) ProteomeDiscoverer result files containing all Peptide-Spectrum-Matches (PSMs), peptide and protein grouping, scoring and confidence values, as well as abundance values from label-free-quantitation (LFQ). As RESOLUTE will generate a significant number of protein-protein interaction data sets (AP-MS and BioID), the presented whole proteome profiling data set can serve as a reference core proteome data set, providing I) technical information on detected and expressed tryptic peptides and proteins; and II) provide valuable information on quantitative distribution of i.e. bait and prey proteins in the different cell lines. In conjunction with the other Omics data sets, like the previously published transcriptomics data, the characterization of the proteome will complement and enable valuable insight into the biological state of the investigated cell lines under default culturing conditions. Furthermore, members of the research community might apply advanced analyses with a focus out of the scope of the RESOLUTE project (e.g. PTM analysis).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Sk-mel-28 Cell, Ls-180 Cell, Huh-7 Cell, Mda-mb-468 Cell, 1321-n1 Cell, Hct-116 Cell, T-rex 293 Cell

SUBMITTER: Ulrich Goldmann  

LAB HEAD: Giulio Superti-Furga

PROVIDER: PXD051747 | Pride | 2024-04-29

REPOSITORIES: Pride