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Updated: Dec 26, 2025

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis
Published on: September 15, 2015
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
Arshag D Mooradian1, Sjoerd van der Post1, Kristen M Naegle2
1Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, United States of America.
Abstract:
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.
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