MetaLab Platform Enables Comprehensive DDA and DIA Metaproteomics Analysis

Abstract Metaproteomics studies the collective protein composition of complex microbial communities, providing insights into microbial roles in various environments. Despite its importance, metaproteomic data analysis is challenging due to the data’s large and heterogeneous nature. While Data-Independent Acquisition (DIA) mode enhances proteomics sensitivity, it traditionally requires Data-Dependent Acquisition (DDA) results to build the library for peptide identification. This paper introduces an updated version of MetaLab, a software solution that streamlines metaproteomic analysis by supporting both DDA and DIA modes across various mass spectrometry (MS) platforms, including Orbitrap and timsTOF. MetaLab’s key feature is its ability to perform DIA analysis without DDA results, allowing more experimental flexibility. It incorporates a deep learning strategy to train a neural network model, enhancing the accuracy and coverage of DIA results. Evaluations using diverse datasets demonstrate MetaLab’s robust performance in accuracy and sensitivity. Benchmarks from large-scale human gut microbiome studies show that MetaLab increases peptide identification by 2.7 times compared to conventional methods. MetaLab is a versatile tool that facilitates comprehensive and flexible metaproteomic data analysis, aiding researchers in exploring microbial communities’ functionality and dynamics.