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Remarks combined_data_mFAO_processed combined_data_mFAO dataset1 dataset2 SCAD_peaks ETF_peaks CPT2_peaks
 
 
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Remarks:
1. Data from two experiments were used: one from 2017-09-06 and one from 2019-04-16. The data from those are presented in two separate sheets named "dataset1" and "dataset2", respectively.
2. We try to optimize the ratios between the endogenous protein and the standards for each individual experiment, since we know that there might be a slight bias in the total protein determinations and mitochondrial content of each sample preparation. This choice is always a balance between the high and low abundant protein targets. Therefore the concentrations might be slightly different between the individual experiments but in this way we did try to choose the most optimal conditions for each experiment. We do not expect that these differences will have a significant effect on the quantification as we have shown previously with the assay development of the targeted proteomics panels that the amount of standard can vary much wider than the differences described within this manuscript, without affecting the quantification of the endogenous proteins significantly (this has been shown previous in supplementary Figure S2 from PMID: 27447838).
3. A colour code is used to indicate whether the sample could be quantified or not:
endogenously below limit of detection
endogenously near limit of detection (LOD)
endogenously detected
4. For measurements indicated as "endogenous near limit of detection", comments are given in the final column of the sheet.
5. The data in "combined_data_mFAO_processed" were the values used to make the personalised models. These pertained to the enzymes of the mitochondrial fatty acid oxidation (mFAO).
6. Two peptides of both ETFb and HADHb were quantified. Their concentrations were assumed equal to the average of the two peptides.
7. The concentration of the ETFb subunit - being the only ETF subunit that was quantifiable - was assumed for the whole ETF protein
8. The concentration of MTP was assumed equal to the subunit (HADHa and HADHb) with the lowest concentration, since both are necessary for a functional enzyme
9. A representative selection of peaks from the mass spectrometry is included in the sheets titled "SCAD_peaks", "ETF_peaks", and "CPT2_peaks"


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