MBZ lysate normalized raw LC/MS data
Description
Metabolomics for MBZ treated VM-M3 cell line
Files
Steps to reproduce
Supernatant extracts were split, and analyses were performed using gas chromatography-mass spectrometry (GC-MS), reversed-phase liquid chromatography-mass spectrometry (RP-LC-MS), and HILIC-LC-MS/MS with applied multiple reaction monitoring. RP-LC-MS separation was performed using a NEXERA XR UPLC system (Shimadzu, Columbia, MD, USA), coupled with a Triple TOF 6600 System (AB Sciex, Framingham, MA, USA). GC-MS aliquots separation was performed using an Agilent 7890B gas chromatograph (Agilent, Palo Alto, CA, USA) interfaced to a Time-of-Flight Pegasus HT Mass Spectrometer (Leco, St. Joseph, MI, USA). The GC system was fitted with a Gerstel temperature- programmed injector, cooled injection system (model CIS 4). An automated liner exchange (ALEX) (Gerstel, Muhlheim an der Ruhr, Germany) was used to eliminate cross-contamination from the sample matrix occurring between runs. A standard quality control sample containing a mixture of amino and organic acids was injected daily to monitor mass spectrometer response. A pooled quality control sample was obtained by taking an aliquot of the same volume of all samples from the study and injected daily with a batch of analyzed samples to determine the optimal dilution of the batch samples and validate metabolite identification and peak integration. Collected raw data were manually inspected, merged, imputed, and normalized by the sample median. Global metabolomic data was analyzed as previously described (Chi et al. 2022, Tolstikov et al. 2014). Identified metabolites were subjected to pathway analysis with MetaboAnalyst 4.0, using MSEA module which consists of an enrichment analysis relying on measured levels of metabolites and pathway topology, and provides visualization of the identified metabolic pathways. Accession numbers of detected metabolites (HMDB, PubChem, and KEGG Identifiers) were generated, manually inspected, and utilized to map the canonical pathways.
Institutions
- Boston CollegeMassachusetts, Boston