Fig. 1

Workflow for assessing species biomass contributions using metaproteomics. The presented workflow can be adapted to different LC-MS/MS systems and computational tools. The critical considerations for achievement of high accuracy and sensitivity are as follows: (1) use of a protein sequence database derived from a metagenome of a sample matching to the metaproteomic samples; (2) selection and optimization of protein inference parameters with test datasets to achieve sufficient specificity; and (3) quantification of taxa using the sum of PSM counts or peptide intensities based on inferred proteins and not based on peptide inference