Data files

Batch sample publishing

BC7 NLM-Chem-track data and materials

Excel template for metadata required by ENA to submit sequence data

The file contains the GC-MS raw data as cdf files, a sample list and an excel sheet with the results of metabolome analysis.

Volumes in fL, time in hours.

The first sheet in this excel file is a Table that collects the standard Gibbs energies of formation (from the elements) of a large number of chemical species that are relevant for metabolism. It obtained these from a substantial number of sources, including Thauer et al and Alberty, as indicated at the bottom of the first sheet of the Table. Following Alberty, (2006) the Table also computes the further transformed Gibbs energies of formation, under the standard conditions also used by Alberty, ...

Protein measurement used to normalised the oxygen consumption flux measured on an Oroboros oxygraph.

Measured in an Oroboros oxygraph.

Proteomics from MCADD and control individuals' fibroblasts.

Content:

• Compiled 15 columns annotation of P. cordatum (Dougan et al. 2022)
• Summary of predicted unknown proteins of P. cordatum
• Calculations of predicted unknown proteins of P. cordatum

Tab color: annotation, purple; unknowns, green

• Calculations of predictions of all identified proteins of P. cordatum
• Calculations of fold-changes of all identified proteins (cell vs. nuclei fraction) of P. cordatum
• Calculations of predictions of proteins of unknown function of_ P. cordatum_
• Calculations of fold-changes of unknowns (cell vs. nuclei fraction) of P. cordatum

Tab color: all identified proteins, purple; unkowns, green

Content:

• Nuclear protein fractions: NSP, NMP and NTP R1-R3 (Peptide counts)
• Summary nuclear proteins geLC
• Cellular protein fractions: CSP, CMP R1-R3 (Peptide counts)
• Summary cellular proteins geLC
• Summary nuclear protein fractions NSP R1-R3 (iBAQs)
• Summary cellular protein fractions CSP R1-R3 (iBAQs)
• 15 columns annotation
• Final summary of protein data
• Prediction results
• Annotation (biological processes and categories)

Tab color: raw data, green; summarized data, orange; final ...

• Summary of functional categorization of all identified proteins of P. cordatum
• Calculations of general functions (Fig. 5, left panel)
• Calculations of nuclear functions (Fig. 5, right panel)
• Categories in separate sheets

Tab color: Summarized data, purple; calculations, organge; functional categories, green

• Summary of nuclear proteins
• Separate sheets of nuclear processes (MBNP_Histones, DNA replication, DNA repair, RNA processing (rRNA and mRNA processing), transcription, import and export, ubiquitylation, proteasome, biogenesis ribosomes)
• Ribosomes (category translation)

Tab color: Summary, purple; nuclear processes, green; ribosomes, orange

Prepared (sub-)cellular fractions were separated by gradient SDS-PAGE and entire sample lanes cut into pieces prior to in-gel digest and nanoLC separation coulpled to iontrap MS/MS detection.