Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses.
Pieter VerschaffeltAlessandro TancaMarcello AbbondioTim Van Den BosscheTibo Vande MoortelePeter DawyndtLennart MartensBart MesuerePublished in: Journal of proteome research (2023)
Unipept Desktop 2.0 is the most recent iteration of the Unipept Desktop tool that adds support for the analysis of metaproteogenomics datasets. Unipept Desktop now supports the automatic construction of targeted protein reference databases that only contain proteins (originating from the UniProtKB resource) associated with a predetermined list of taxa. This improves both the taxonomic and functional resolution of a metaproteomic analysis and yields several technical advantages. By limiting the proteins present in a reference database, it is also possible to perform (meta)proteogenomics analyses. Since the protein reference database resides on the user's local machine, they have complete control over the database used during an analysis. Data no longer need to be transmitted over the Internet, decreasing the time required for an analysis and better safeguarding privacy-sensitive data. As a proof of concept, we present a case study in which a human gut metaproteome dataset is analyzed with Unipept Desktop 2.0 using different targeted databases based on matched 16S rRNA gene sequencing data.
Keyphrases
- big data
- electronic health record
- cancer therapy
- machine learning
- artificial intelligence
- protein protein
- deep learning
- adverse drug
- endothelial cells
- amino acid
- health information
- binding protein
- healthcare
- genome wide
- copy number
- dna methylation
- social media
- single molecule
- transcription factor
- rna seq
- high throughput sequencing