Metaproteomics is used to explore the composition, dynamics and function of microbial communities. However, acquiring data by tandem mass spectrometry is time consuming and resource intensive. To mediate this challenge, we present MetaProClust-MS1, a computational framework for microbiome screening developed to reduce the time required for data acquisition by mass spectrometry. In this proof-of-concept study, we tested MetaProClust-MS1 on data acquired using short 15 minute MS1-only mass spectrometry gradients and compared the results to those produced using data acquired by a traditional tandem mass spectrometry approach. MetaProClust-MS1 identified robust microbiome shifts caused by xenobiotics in both datasets. Cluster topologies were also significantly correlated. We demonstrate that MetaProClust-MS1 is able to rapidly screen microbiomes using only short MS1 profiles. This approach can be used to prioritize samples for deep metaproteomic analysis and will be especially useful in large-scale metaproteomic screens or in clinical settings where rapid results are required.
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