High-Throughput Stool Metaproteome Extraction v1

The gut microbiome is strongly associated various disease related periods. In order to better understand how the host and microbiome interact during these periods, it is necessary to survey the proteomic response of both the host and microbes in a large portion of a population. However to date, techniques used to isolate stool proteins have been low-throughput and due to their lack of purity can foul columns and increase mass spectrometer downtime. To address these shortcomings, this protocol was developed. It allows for the processing of 96 samples in parallel and is compatible with common multiplexing labeling technology. It has thus far been used to process anywhere between 10 and 400 samples, with very reproducible results.