Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

Abstract

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.

The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment

“…The analysis of functional protein abundances was performed attending to the area under the curve (AUC) of unique peptides. The amino acid sequences of these peptides were searched at the NCBI database (Blastp tool) and the relative phylogenetic contribution for each protein was calculated by the sum of AUCs of singles peptides after phylogenetic analysis in Unipept (http://unipept.ugent.be/) [34].…”

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

“…SwissProt accession numbers of annotated biofilm proteins were submitted for analysis (www.uniprot.org) to retrieve taxonomic hierarchy, gene ontology (GO) annotations, GO term numbers and protein families. An independent analysis of the identified peptide sequences was also performed using Unipept 2.3 multipeptide analysis (Mesuere et al 2012) which used the UniProt database (www.uniprot.org) and NCBI taxonomy. Briefly, the sequences of all identified peptides were submitted to the Unipept web application (http:// unipept.ugent.be/) using the following settings to calculate the lowest common ancestors: multi-peptide analysis, peptides were deduplicated, isoleucine and leucine residues were equated, and advanced missed cleavage handling was applied.…”

An Alignment-Free “Metapeptide” Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing

“…We used Unipept 19,20 to infer the lowest common ancestor taxon for peptides detected in each search. Comparison of the results revealed a much richer taxonomic characterization of the proteins present in the samples from the metapeptide search than from either of the other methods.…”