Proteomics dataset of liver tissue from spinal muscular atrophy, heterozygous, and wild-type mice, enabling pathway identification

We present a label-free quantitative proteomics dataset from liver tissue of wild-type (WT), heterozygous (HET), and spinal muscular atrophy (SMA) mice at postnatal day 10 (P10). Proteins were extracted using urea lysis, digested with trypsin, and analyzed by LC-MS/MS on an Orbitrap Exploris 480 mass spectrometer. DIA-NN and Perseus software were used for data processing and statistical analysis, including principal component analysis (PCA) and differential expression analysis for comparisons between WT and SMA, and HET and SMA. One mis-genotyped SMA sample was identified and excluded based on Western blot validation of the survival motor neuron (SMN) protein levels. The dataset provides complete protein identification and quantification tables, lists of significantly altered proteins, and Western blot validation for ferrochelatase (FECH) and survival motor neuron (SMN) protein in RIPA-extracted proteins from whole liver organ homogenates. All raw and processed data, including metadata and statistical outputs, have been deposited to the ProteomeXchange Consortium with the identifier PXD070887. The dataset can be reused for comparative proteomic analyses, cross-study integration, and meta-analyses of murine liver proteome alterations in neuromuscular and metabolic disease models.