Supplementary material 1 for Thesis Chapter 2 - An obligate aerobe hybridises hydrogen fermentation and carbon storage to adapt to hypoxia

Abstract

Supplementary material for paired comparative metabolomics and proteomics on Mycobacterium smegmatis mc2155 during hypoxia, as part of chapter 2 for the thesis "Biochemistry and physiology of mycobacterial adaptations to energy starvation". Description below is identical to that provided in 'Summary.docx'. Proteomics_analysis.xlsx Includes raw and annotated data for comparative proteomics experiments for chapter 2. The tab ‘Annotated comparisons’ contains fold change and p values for the comparisons for each protein from Mycobacterium smegmatis mc2155 derived from LFQ-Analyst. Functional annotations are derived from KEGG pathways and modules, which utilise the spreadsheets in ‘MSMEG gene annotation’ ‘Protein ids to KEGG pathway’ and ‘KEGG Pathway and Modules’ to link KEGG annotations to MSMEG_XXXX gene identifiers and MSMEG_XXXX to Uniprot ID. Output from LFQ-Analyst is provided in the ‘Full_dataset’, ‘Imputed_matrix’ and ‘Original_matrix’ tabs. Data provided by the Monash Proteomics and Metabolomics Facility for upload into LFQ-analyst are provided as the ‘combined_protein.tsv’ and ‘LFQ-Analyst_experimental_design.txt’. Metabolism_analysis.xlsx Includes annotated data for comparative metabolomics experiments for chapter 2. Within the spreadsheet, TR refers to transition, ST refers to stationary phase and EXP refers to exponential phase. The tabs ‘TRvsEXP’, ‘STvsTR’ and ‘STvsEXP’ contain fold change and p values for each metabolite detected for each comparison. The remaining tabs categorise the metabolites based on KEGG database and IDEOM annotations. For broader categories (‘Lipid metabolism’,’ Carbohydrate metabolism’, ‘Cofactor metabolism’, ‘Nucleotide metabolism’, ‘Amino acid metabolism’ and ‘Peptides’ tabs), annotations were derived directly from filtering the ‘Map’ column of ‘Comparisons’ tab of the IDEOM worksheet (IDEOM_analysis.xlsb). Screenshots are pasted into each tab to show the filtering settings. The remaining tabs comprise narrower categories which were manually annotated with reference to KEGG pathways and maps, and also include rows corresponding to the proteomics data for these categories, so the proteomics and metabolomics data can be interpreted together. The ‘Proteomics’ tab contains the proteomics data referenced by these tabs, which is a copy of the ‘Annotated comparisons’ tab from the ‘Proteomics_analysis.xlsx’ file. A value of ‘N’ indicates the metabolite or protein (at least according to the name in the same row) was not found in these datasets. The IDEOM worksheet (IDEOM_analysis.xlsb) was provided by the Monash Proteomics and Metabolomics Facility and was used for further analysis and for annotations. ‘Data_for_MA_no_normalization.csv’ was also provided by the Monash Proteomics and Metabolomics Facility for upload into Metaboanalyst (https://www.metaboanalyst.ca/)

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Last time updated on 08/08/2023

This paper was published in ZENODO.

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