AI Insight
FastaLake is a computational workflow that creates compact protein sequence databases for metaproteomics analysis by using AI-based de novo peptide sequencing (AlphaNovo) to retrieve relevant proteins from large sequence repositories, eliminating the need for sample-specific metagenomic sequencing. In tests using human intestinal samples, FastaLake identified similar or greater numbers of peptides compared to traditional metagenomic-derived databases while producing database files smaller than the human reference proteome. The method successfully revealed persistent personal functional profiles across different intestinal regions and enabled comprehensive proteomic analysis of 347 samples without requiring matched DNA sequencing.
Why it matters
This approach substantially reduces the cost and time required for metaproteomics studies of complex microbial communities by removing the requirement for metagenomic sequencing while maintaining or improving identification sensitivity. The compact databases also enable more comprehensive searches, including non-specific searches that can reveal unexpected protein modifications and biological patterns.
Understand the Science
⚠️ Preprint – Noch nicht peer-reviewed
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Metaproteomics analyses require protein sequence databases, yet the microbial proteins present in complex communities are not known in advance. Searching reference catalogs containing hundreds of millions of candidate sequences reduces identification sensitivity, while generating sample-specific databases through metagenomic sequencing adds time and cost. We introduce FastaLake, a computational workflow that uses full-length de novo peptide predictions by AlphaNovo to retrieve complete proteins from broad sequence resources and selects compact databases for conventional searching. In a defined eight-member community, FastaLake approached reference-search peptide yields without knowing its members. Using public sequence catalogs, FastaLake identified about as many peptides as matched metagenomic databases in two stool cohorts and 20-35% more in intestinal fluid at the same nominal 1% peptide false discovery rate. The resulting proteomes reveal personal functional profiles that persist across intestinal regions despite differences in leading species between intestinal fluid and stool. DNA, RNA and protein profiles agreed on broad differences between patients but only weakly on individual functions. All 726 acquisition-specific databases were smaller than the human reference proteome. Compact databases allowed non-specific searches of all 347 CapScan acquisitions, revealing histidine enrichment at peptide C termini in intestinal fluid. FastaLake enables metaproteomics analysis without matched metagenomic sequencing by constructing search databases from sequence resources and de novo peptide sequencing.