The spectral networks approach enables the detection of pairs of spectra from related peptides and thus allows for the propagation of annotations from identified peptides to unidentified spectra of related peptides. Beyond allowing for unbiased discovery of unexpected post-translational modifications, spectral networks are also applicable to multi-species comparative proteomics or metaproteomics to identify numerous orthologous versions of a protein. With recent algorithmic and statistical advances, spectral networks identified peptides with highly divergent sequences with up to dozens of variants per peptide in multi-species analysis, including many novel peptides in species with unknown protein sequences. Furthermore, ～70% of unidentified multi-species networks included at least two polymorphic peptide variants, strongly suggesting the presence of many novel peptides even in known species.
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