Benchmarking Spectral Library and Database Search Approaches for Metaproteomics Using a Ground-Truth Microbiome Dataset.

ABSTRACT: Mass spectrometry-based metaproteomics, the identification and quantification of thousands of proteins expressed by complex microbial communities, has become pivotal for unraveling functional interactions within microbiomes. However, metaproteomics data analysis encounters many challenges, including the search of tandem mass spectra against a protein sequence database using proteomics database search algorithms. We used a ground-truth dataset to assess a spectral library searching method against established database searching approaches. Mass spectrometry data collected by data-dependent acquisition (DDA-MS) was analyzed using database searching approaches (MaxQuant and FragPipe), as well as using Scribe with Prosit predicted spectral libraries. We used FASTA databases that included protei

SUBMITTER: Rajczewski AT 

PROVIDER: S-EPMC12139738 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature