The Unipept web application (http://unipept.ugent.be) supports biodiversity 
analysis of large and complex metaproteome samples using tryptic peptide 
information obtained from shotgun MS/MS experiments. Its underlying index 
structure is designed to quickly retrieve all occurrences of a tryptic peptide 
in UniProtKB records. Taxon-specificity of the tryptic peptide is successively 
derived from these occurrences using a novel lowest common ancestor approach 
that is robust against taxonomic misarrangements, misidentifications, and 
inaccuracies. Not taking into account this identification noise would otherwise 
result in drastic loss of information. Dynamic treemaps visualize the 
biodiversity of metaproteome samples, which eases the exploration of samples 
with highly complex compositions. The potential of Unipept to gain novel 
insights into the biodiversity of a sample is evaluated by reanalyzing publicly 
available metaproteome data sets taken from the bacterial phyllosphere and the 
human gut.