Mitochondrial proteomics on human fibroblasts for identification of metabolic imbalance and cellular stress

Additional file 1:

Experimental protein identification data from the first experiment of fibroblast NHDF-1. Mass spectrometry data including peptide list.

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Additional file 2:

Experimental protein identification data from the second experiment of fibroblast NHDF-1. Mass spectrometry data including peptide list.

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Additional file 3:

Experimental protein identification data from the third experiment of fibroblast NHDF-1. Mass spectrometry data including peptide list.

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Additional file 4:

Experimental protein identification data from the experiment of fibroblast NHDF-2. Mass spectrometry data including peptide list.

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Additional file 5:

Enrichment factors of 39 mitochondrial proteins. Enrichment factors of 39 mitochondrial proteins detected in an iTRAQ experiment, where a mitochondrial sample is compared with a cell sample, for human fibroblasts cultivated in glucose and galactose, respectively. The enrichment factor is calculated, for each protein, as the iTRAQ signal ratio: Mitochondrial sample/Total cell sample.

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Additional file 6:

Mitochondrial proteins sorted into functional categories. The protein descriptions and isoform data are from the curated human IPI database http://www.ebi.ac.uk/IPI/IPIhelp.html webcite version 3.45 with 71,983 sequences, released 6/10/2008. All the sorted proteins have been predicted to be mitochondrial according to Pagliarini et al [11], and the total list of those mitochondrial proteins is below the sorted categories (starting at row 978). The categories are: Fatty acid metabolism, Citric acid cycle, Amino acid metabolism, Respiratory chain, Protein quality control systems, Antioxidant systems, Mitochondrial morphology, Mitochondrial translation and Apoptosis.

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Additional file 7:

Protein profiles of mitochondrial amino acid metabolism (AA), mitochondrial translation (TRANS) and miscellaneous mitochondrial proteins (MISC). The galactose to glucose ratio, derived from the protein levels of the cells cultivated in galactose and glucose, respectively, is depicted on the x-axis. Black bars indicate ratios calculated from the average of three independent cultivation studies of a control fibroblast (NHDF-1). The grey bar indicates the ratio from one cultivation study of a second control fibroblast (NHDF-2). A ratio of a protein was reported as significantly different from 1.0 if it passed two tests 1) a threshold test of two times the global standard error (2 × 0.055 = 0.11) and 2) a two-tailed student's T-test for equal variance data. The error bar is the standard error of the three values and "*" and "**" indicate statistically significant deviation from 1.0 with t-test probability value below 0.05 and 0.01, respectively.

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Additional file 8:

Gene products detected in the present study which have known disease association according to the OMIM database. Abbreviations: amino acid metabolism (AA), apoptosis and mitochondrial morphology (APOP), citric acid cycle (TCA), fatty acid oxidation (FAO), miscellaneous (MISC), protein quality control (PQC), respiratory chain (RESP) and translation (TRANS).

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