DOI: 10.5281/zenodo.17613082
title: Supplementary datasets for the manuscript: Mapping unsolved lipidomes accelerates lipid discovery in major bacterial pathogens

description: Files Comprise:

Data S1. Replication R-Markdown

R markdown (lines 1 - 2333) and 6 supporting csv files, 10 phenotype objects, 12 xcms objects, and 1 table, required with formatted datasets S2–S13 to generate all R-based analysis and figures, including the feature credentialling pipeline. A second R markdown includes 4 custom functions to interface with R packages xcms and limms, and a new function mzrtMeta to align mass spectrometry experiments sourced by the replication markdown (available at: https://github.com/jamayfie/mzrtMatch). Users must modify path statements to their own data drive with downloaded data files below. Additionally all R packages, dependencies, and custom functions must be sourced and loaded. 

Data S2. MycoMassDB

Mycobacterial database of validated lipids and metabolites, including newly discovered lysine lipoamino acids, formatted for automated matching.

Data S3. MycoLOBSTAH

Mycobacterial database of theoretical lipids in the positive mode propagated from MycoMassDB using LOBSTAHs R-package.

Data S4. Credentialed map of known mycobacterial lipids and lysyldiacylglycerols

Map of Mtb H37Rv qualified features in two groups: known lipids with identities confirmed by collisional MS, and unknown features ranked by quality criteria.

Data S5. lysX/mprF domain ontology

M. tuberculosis genes with homology to firmicute mprF, including their subdomains and Interpro classifications.

Data S6. Lipids knocked down with lysX silencing in Mtb H37Rv

Lipids significantly enriched in the Mtb H37Rv lysX CRISPRi knockdown uninduced (-ATc) condition compared to the induced strain (+ATc). 

Data S7. Mtb H37Rv growth phase glycerolipids, 7H9

Acylform intensities of diacylglycerol, lysyldiacylglycerol and phosphatidylethanolamine detected across growth phases in Mtb H37Rv grown in 7H9 media. 

Data S8. Mtb H37Rv growth phase glycerolipids, Sauton’s

Acylform intensities of diacylglycerol, lysyldiacylglycerol and phosphatidylethanolamine detected across growth phases in Mtb H37Rv grown in Sauton’s media.

Data S9. Distribution of lysylDAG and other glycerolipids across mycobacteria

Aligned dataset of acylform intensities of diacylglycerol, lysyldiacylglycerol and phosphatidylethanolamine across 15 mycobacterial strains and species. 

Data S10. Lipids enriched in the Mm lysX mutant

Lipids meeting significance criteria as enriched in the Mm lysX mutant from a compound contrast against Mm WT and complement. 

Data S11. Lipids enriched in Mm WT and lysX complement 

Lipids meeting significance criteria as enriched in the Mm WT and lysX complement from a compound contrast against the Mm lysX mutant. 

Data S12. mprF-dependent lipids in S. aureus

Lipids meeting significance criteria as enriched in S. aureus WT compared to the ΔmprF mutant 

Data S13. S. aureus SA113 growth phase glycerolipids

Acylform intensities of diacylglycerol, lysyldiacylglycerol and lysyl phosphatidylglycerol detected across growth phases in S. aureus SA 113 and the ΔmprF mutant

Data S14. Spectra for chemical synthesis of lysyldiacylglycerol

NMR and mass spectrometry spectra supporting the synthesis of isomerically pure sn3-lysyldiacylglycerol

Data S15. Centroided raw peak data as .mzXML files

Zipped file containing 150 .mzXML raw data files comprising centroided mass spectrometry data pertaining to Figure 1 (8 files), Figure 2 (16 files), Figure 3 (18 files), Figure 4 (80 files), Figure S5 (20 files), Figure 5 (9 files), Figure 6 (6 files), Figure S7 (18 files). The structure of the experimensts that these files support is located in Data S1 Markdown.