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 patientderived xenografts and its speed and scalability enable a novel de novo proteomic workflow for complex microbiota samples.

Original languageEnglish
Article numbere1007741
JournalPLoS computational biology
Issue number3
StatePublished - 2020


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