Analysis of primary animal and human tissues is key in biological and biomedical research. Comparative proteomic analysis of primary biological material would benefit from uncomplicated experimental workflows capable of evaluating an unlimited number of samples. In this report we describe the application of label-free proteomics to the quantitative analysis of five mouse core proteomes. We developed a computer program and normalization procedures that allow to exploit the quantitative data inherent in LC-MS/MS experiments for relative and absolute quantification of proteins in complex mixtures. Important features of this approach include (i) its ability to compare an unlimited number of samples, (ii) its applicability to primary tissues and cultured cells, (iii) its straightforward workflow without chemical reaction steps, and (iv) its usefulness not only for relative quantification but also for estimation of absolute protein abundance. We applied this approach to quantitatively characterize the most abundant proteins in murine brain, heart, kidney, liver and lung. We matched 8,800 MS/MS peptide spectra to 1,500 proteins and generated 44,000 independent data points to profile the ~1,000 most abundant proteins in mouse tissues. This dataset provides a quantitative profile of the fundamental proteome of a mouse, identifies the major similarities and differences between organ-specific proteomes, and serves as a paradigm of how label-free quantitative MS can be used to characterize the phenotype of mammalian primary tissues at the molecular level.