Advanced liquid chromatography-mass spectrometry enables merging widely targeted metabolomics and proteomics

Either widely targeted metabolomics or quantitative proteomics usually requires unique analytical platform. However, cross-platform omics studies entail higher levels of complexity and uncertainty, and result in a significant obstacle for high throughput assay as well. It is thereby urgent to pursue an integrative approach being capable of merging these two omics terms, namely widely targeted bi-omics. As an eligible analytical tool for large-scale targeted metabolomics, reversed phase liquid chromatography-hydrophilic interaction liquid chromatography–tailored selected reaction monitoring (RPLC-HILIC–tailored SRM) was deployed here to further receive the tryptic peptides as the analytes. Comparative evaluation of metabolites and tryptic peptides, 101 ones in total, between HepG2 and SK-Hep1 cells was conducted as a proof-of-concept. All analytes, regardless of metabolites or peptides, exhibited satisfactory chromatographic behaviors on RPLC-HILIC. Quantitative MS parameters, such as SRM transitions and collision energies (CEs), of either tryptic peptides or metabolites were online optimized in a standard compound-independent manner. It was worthwhile to mention that the signal responses of the peptides-of-choice generated by the optimized CEs were significantly superior to those values suggested by Skyline software. Calibration curves of both metabolites and peptides were constructed by serially diluting a so-called universal metabolome standard (UMS) sample. The quasi-content of each peptide or metabolite was gained according to applying those regressive calibration curves. After subjecting the quasi-content dataset into SIMCA-P software, significant differences took place between the two hepatic cell lines, and not only metabolites but tryptic peptides contributed to the discrimination. Above all, RPLC-HILIC–tailored SRM offered a promising choice towards widely targeted bi-omics attributing to the advantage of simultaneous monitoring metabolites and tryptic peptides.