Molecular phylogeny is a well-established method for inferring evolutionary relationships from DNA and RNA sequences. Here, we extend this concept beyond genetic information by applying phylogeny-like analysis to proteomic and metabolomic mass spectrometry data, capturing relationships based on the realized molecular phenotype. The resulting phenotype-derived trees can be directly compared with conventional genetic-based trees to identify where molecular phenotypes reflect evolutionary history and where they diverge due to functional adaptation, regulation, or environmental influence. To enable this analysis, we introduce TreeMS2, a computational tool that constructs similarity matrices by directly comparing tandem mass spectra between samples. By bypassing spectrum annotation, TreeMS2 enables rapid, unbiased comparisons to reconstruct biologically meaningful relationships across diverse datasets. In proteomics, phenotype-derived trees recapitulate established taxonomy, with deviations pinpointing sample handling errors. In single-cell proteomics our method distinguishes cell types despite sparse and noisy measurements, and in metabolomics it resolves major biochemical divisions and fine-scale compositional structure. Together, these results establish TreeMS2 as a scalable, annotation-independent framework for deriving molecular relationships from raw mass spectral data. To validate some of our observations, we reprocessed some files that are saved here. Pseudomonas psychrotolerans, Pseudomonas orientalis, and Pseudomonas mandelii were reprocessed because a missampling was expected. These files were searched against the reference proteome of the annotated species and against the proteome of its closest neighbor in the proteomics-based tree, respectively, Ligilactobacillus murinus, Geobacillus stearothermophilus, and Bacillus mojavensis. The Dictyostelium discoideum (D. discoideum) was reprocessed to see whether we would be able to find Escherichia coli (E. coli) in the sample, which was expected as the two were clustered together in the proteomics-based tree and E. coli was the food source on the agar plate D. discoideum was growing on (Carolina item #155996). To investigate whether E. coli was sampled together with Dictyostelium discoideum, a database search was performed on eight D. discoideum fractions against a combined FASTA database containing E. coli and D. discoideum protein sequences.