ghent university multidisciplinary research partnership  bioinformatics : from nucleotides to networks ; fund for scientific research ( fwo)flanders ( belgium ) ( postdoctoral research fellowship to f.i . ) ; institute for the promotion of innovation through science and technology in flanders ( iwt - vlaanderen ) ( phd to k.p . ) ; proteomexchange project , funded by the european union 7th framework program under grant agreement number [ 260558 to n.h . ] ; prime - xs project , funded by the european union 7th framework program under grant agreement number [ 262067 to k.g . and l.m . ] .
we here present the online protein processing resource ( toppr ; http://iomics.ugent.be/toppr/ ) , an online database that contains thousands of published proteolytically processed sites in human and mouse proteins . 
 these cleavage events were identified with combinded fractional diagonal chromatography proteomics technologies , and the resulting database is provided with full data provenance . 
 indeed , toppr provides an interactive visual display of the actual fragmentation mass spectrum that led to each identification of a reported processed site , complete with fragment ion annotations and search engine scores . 
 apart from warehousing and disseminating these data in an intuitive manner , toppr also provides an online analysis platform , including methods to analyze protease specificity and substrate - centric analyses . 
 concretely , toppr supports three ways to retrieve data : ( i ) the retrieval of all substrates for one or more cellular stimuli or assays ; ( ii ) a substrate search by uniprotkb / swiss - prot accession number , entry name or description ; and ( iii ) a motif search that retrieves substrates matching a user - defined protease specificity profile . 
 the analysis of the substrates is supported through the presence of a variety of annotations , including predicted secondary structure , known domains and experimentally obtained 3d structure where available . across substrates , substrate orthologs and conserved sequence stretches can also be shown , with icelogo visualization provided for the latter .