A robust and universal metaproteomics workflow for research studies and routine diagnostics within 24 hours

A new workflow for metaproteomics is presented in this study and is shown to enable the analysis of a broad range of different samples in only 24 h. The standardized sample preparation includes the combined cell lysis and phenol extraction in a ball mill followed by FASP digestion. The bioinformatic workflow using the MetaProteomeAnalyzer software was expanded with new functionalities such as annotation of metaproteins via protein BLAST or an integrated compare tool. The new workflow was shown to produce at least two times the protein identifications than previous iterations. Through many individual improvements combined into a single standardized workflow, a drastic increase in the quantity and quality of generated results was achieved.