Proteomic profiling of over 13,000 proteins across ten mouse tissues using multi-dimensional peptide pre-fractionation.

Proteome-wide abundance profiling across tissues can provide insight into the biological mechanisms underlying tissue-specific function, as well as potential related dysfunction and amelioration thereof. Here, we use sample multiplexing to profile the proteomes of ten diverse mouse tissues using quantitative mass spectrometry-based sample multiplexing. Our optimized workflow, incorporating two-dimensional peptide pre-fractionation (which included both basic pH reversed-phase and strong ion exchange chromatography) enabled the quantification of over 13,000 proteins across brain, brown fat, heart, kidney, liver, lung, skeletal muscle, spleen, ovaries, and testes. Global analysis revealed distinct proteome profiles for each tissue, with clear clustering patterns reflecting functional similarities and differences. We highlighted the abundance of numerous tissue-specific proteins, exemplified by Synapsin-1 in brain, Uncoupling protein 1 in brown fat, and Zona pellucida proteins in reproductive tissues. Gene ontologies and pathway analyses of the most relatively abundant proteins in each tissue revealed enrichment patterns consistent with known physiological functions. For instance, brain tissue showed enrichment for synaptic components and neurotransmission processes, while liver tissue was enriched for metabolic pathways. This dataset serves as a valuable resource for mapping tissue-specific protein landscapes in mammals, offering potential insights into the molecular mechanisms of tissue function. SIGNIFICANCE: We present a proteome-wide analysis of ten diverse mouse tissues using an optimized TMTpro-based quantitative mass spectrometry workflow. This workflow is enhanced by two-dimensional peptide pre-fractionation with strong anion exchange partitioning followed by basic pH reversed-phase chromatography. By quantifying over 13,000 proteins, we provide an unprecedented dataset revealing distinct tissue-specific protein abundance profiles and their alignment with known physiological functions. This dataset as a resource offers valuable insights into the molecular underpinnings of tissue-specific biology and establishes a foundation for future research into physiological processes, disease mechanisms, and therapeutic development in mammals.