Proteomics

iMONdb

iMonDB (Instrument MONitoring DataBase) is a unique tool and resource for online, longitudinal quality control monitoring of mass spectrometry instruments and the data they produce. The advantage of instrument information at the lowest level is the high sensitivity to detect emerging defects in a timely fashion. To this end, iMonDB allows to automatically extract, store, and manage the instrument parameters from raw-data objects into a highly efficient database structure. iMONdb was developed at the University of Antwerp, the manuscript can be accessed here.

DynaMine

DynaMine is a fast predictor of protein backbone dynamics using only sequence information as input. DynaMine is able to accurately distinguish regions of different structural organization within proteins, such as folded domains and disordered linkers of different sizes. Additionally, it can identify disordered regions within proteins with an accuracy comparable to the most sophisticated existing disorder predictors. DynaMine achieves this high performance without depending on prior disorder knowledge or three-dimensional structural information, which makes it a unique approach on the field as well as providing independent proof of the relationship between dynamics and structural disorder in protein regions.

DynaMine was developed at the Interuniversity Institute of Bioinformatics in Brussels (IB)² and published in Nature Communications (the method) and Nucleic Acids Research (the web-server).

Tabloid Proteome

The online Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE. These associations represent a broad scala of biological associations between pairs of proteins that goes well beyond mere binary protein interactions. As such, the provided information is almost completely complementary to traditional direct protein interaction studies.

In addition to the collection of co-occurring protein pairs, Tabloid Proteome also links to their biological relation in existing knowledgebases. Moreover, pathway links from Reactome, protein-protein interactions from IntAct and BioGRID, protein complexes from CORUM, and paralog information from Ensembl are also superimposed. Functional annotation is provided by disease information from DisGeNET, and Gene Ontology annotations.

Tabloid Proteome was developed at the Ghent university in 2017 and published in Nucleid Acids Research (manuscript). In October 2018, the first training on Tabloid Proteome took place in Gent.

Unipept

Unipept is an open source web application developed at Ghent University that is designed for metaproteomics data analysis with a focus on interactive data visualizations. Unipept is powered by an index containing all UniProt entries, a tweaked version of the NCBI taxonomy and a custom lowest common ancestor algorithm. This combination enables a blazingly fast biodiversity analysis of large and complex metaproteome samples. Next to these core functions, Unipept also has a tool for selecting unique peptides for targeted proteomics and for comparing genomes based on peptide similarity.

Unipept 4.0 is the latest release of the Unipept framework and includes a completely new functional analysis tool and an updated database based on UniProt 2018.06. A tutorial on Unipept has been published in 2018. All Unipept journal articles can be found on this page.