The iMPAQT method (Nat Methods, vol. 14, no. 3, pp. 251-258, Feb. 2017, doi: 10.1038/nmeth.4116.), a targeted proteomics method, was performed on skeletal muscle from TFAM transgenic mice. This data is its skyline processing data.

The iMPAQT (isotopic mass spectrometry for Protein Absolute Quantification Technique) method is a comprehensive approach in proteomics for precise protein quantification. It begins with the preparation of internal standards. For each of the 1,123 metabolic enzymes, at least one proteotypic peptide is selected, and these peptides are combined to create QconCAT sequences. These sequences are integrated into expression vectors and introduced into E. coli, where stable isotopes are incorporated into arginine and lysine residues for optimal labeling efficiency. Inclusion bodies are purified, and an internal standard solution is produced by mixing 24 different QconCAT solutions. The method involves the analysis of skeletal muscle tissue. Tissue is frozen, crushed, and then lysed using a specific buffer. Protein concentrations are determined, and the samples are treated to reduce and alkylate cysteine residues. After precipitation and washing, protein pellets are obtained. These pellets are resuspended and subjected to digestion using lysyl endopeptidase and trypsin. The resulting material is analyzed through liquid chromatography with tandem mass spectrometry (LC-MS/MS). The iMPAQT method employs various mass spectrometry parameters to optimize analysis and quantifies protein levels by comparing endogenous peptides to labeled internal standards, providing accurate and reliable protein quantification in proteomic studies.

The sample data in skyline "Tg-Mouse_peakpicked_2023-10-25_15-15-15-33.sky" is categorized into the following three types of samples (Wildtype, TFAM Tg , TFAM TgTg). # Wild type "human-TFAM heterozygous (TFAM Tg)" "human-TFAM homozygous (TFAM Tg/Tg)" 1 WT-1 Tg-2 TgTg-2 2 WT-2 Tg-12 TgTg-5 3 WT-4 Tg-6 TgTg-6 4 WT-5 Tg 15608TFAM 5 15544TFAM 15543TFAM 15542TFAM