%0 Journal Article
%T ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
%A Arshag D. Mooradian
%A Jason M. Held
%A Kristen M. Naegle
%A Sjoerd van der Post
%J -
%D 2020
%R 10.1371/journal.pcbi.1007741
%X We present ProteoClade, a Python toolkit that performs taxa-specific peptide assignment, protein inference, and quantitation for multi-species proteomics experiments. ProteoClade scales to hundreds of millions of protein sequences, requires minimal computational resources, and is open source, multi-platform, and accessible to non-programmers. We demonstrate its utility for processing quantitative proteomic data derived from patient-derived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples
%K Sequence databases
%K Proteomic databases
%K Database searching
%K Taxonomy
%K Proteomes
%K Data processing
%K Microbiome
%K Information retrieval
%U https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007741