Computational protocol: Activity-Based Protein Profiling Reveals Mitochondrial Oxidative Enzyme Impairment and Restoration in Diet-Induced Obese Mice

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Protocol publication

[…] LTQ-MS raw data was extracted using Extract_MSn (version 3.0), and analyzed with the SEQUEST algorithm (V27, revision 12) searching the MS/MS data against the NCBI mouse protein database. Data filtering criteria based on the MS-GF score and precursor ion mass accuracy (+/−10 ppm) and were used to limit false positive identifications to <1% at the peptide level estimated employing a reverse database search . Relative protein abundance was estimated employing the accurate mass and time tag strategy . Analysis of quantification of the changes in protein abundance between SD and HFD mice was performed and visualized using DAnTE . Briefly, peptide intensities from the LC-MS analyses were log2 transformed, and peptides exhibiting significant differences (p<0.05) in abundance were identified applying an analysis of variance (ANOVA) test. Peptide abundances were then “rolled up” to the unique protein level employing the R-rollup method implemented in DAnTE. Functional enrichment and pathway analysis was performed with Ingenuity Pathways Analysis (Ingenuity® Systems). […]

Pipeline specifications

Software tools Comet, MS-GF
Application MS-based untargeted proteomics
Organisms Mus musculus
Diseases Diabetes Mellitus, Mitochondrial Diseases