Peptidome Analysis
The (tryptic) peptidome is the complete set of (tryptic) peptides encoded in the proteome of an organism. Unipept provides fast and flexible analysis tools for identifying the unique peptidome of a given taxon and peptidome-based clustering.
Proteome library
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Analyzed proteomes
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The order of the proteomes in this table currently doesn't correspond with the order in the similarity matrix Use clustered order Undo clustering |
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Find unique peptides for a species of your choice, based on proteome data. Unique tryptic peptides are found in all selected proteomes and in none of the Uniprot records belonging to taxa outside those of the selected proteomes. These taxon-specific peptides can be downloaded and used for targeted proteomics experiments.
Incremental unions and intersections are computed for the peptidomes of all selected proteomes. The size of the incremental unions (pan peptidome) is shown in blue and the size of the incremental intersections (core peptidome) in orange. The size of the unique peptidome — the subset of the core peptidome that is unique to the lowest common ancestor (LCA) of the taxa of the selected proteomes — is shown in green. The size of the individual peptidomes — expressed as the total number of tryptic peptides — is shown in grey. Individual data sets can be shown/hidden by clicking their name in the graph legend.
1. Add proteomes
You can add proteomes to the analysis by selecting them from the filterable table on the bottom right.
2. Reorder
You can easily reorder the proteomes by dragging them to the desired position on the graph or table. Alternatively, you can use one of the automatic sort options.
3. Download unique peptides
You can download a list of peptides present in all of the selected proteomes but nowhere outside of this taxonomic group, by clicking on the rightmost datapoint in de graph. Next, use the 'Download peptides' button and select 'Unique peptides'.
Find similarities between a selection of proteomes and view the results in a similarity matrix or a phylogenetic tree. UPGMA is used to cluster the proteomes based on their peptidome content. You can choose between five similarity measures to calculate the pairwise similarities.
1. Add proteomes
You can add proteomes to the analysis by selecting them from the filterable table on the bottom right.
2. Cluster
You can easily cluster the proteomes by clicking the blurred phylogenetic tree next to the similarity matrix. A phylogenetic tree will be draw by using UPGMA on the pairwise similarities.
3. Download results
You can download the similarity matrix by clicking the 'Download data' button in the top-right corner. The pairwise similarities between the proteomes are offered as a Microsoft Excel-compatible CSV file, the UPGMA tree in the newick format.