FastaLake

downstream-application · Hybrid de novo + database search

FastaLake: downstream-application · Hybrid de novo + database search. Metaproteomics workflow that uses full-length AlphaNovo de novo peptide predictions as exact queries to select compact search databases from large sequence reservoirs…

Metaproteomics workflow that uses full-length AlphaNovo de novo peptide predictions as exact queries to select compact search databases from large sequence reservoirs, then searches them with Sage. Matched metagenome-derived databases in two stool cohorts and found 20-35% more peptides in intestinal fluid, without matched metagenomic sequencing.

Kind	downstream-application
Deep learning	yes
Acquisition	DDA
Family	Hybrid de novo + database search
Application area	Metaproteomics

Code

• https://github.com/MannLabs/fasta-lake

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Paper describing it

• FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup (2026, bioRxiv, preprint)

Authors (25)

Peter V. Treit, Florian A. Rosenberger, Philip Hartout, Mikhail Lebedev, Jinqiu Xiao, Maximilian Zwiebel, Philipp E. Geyer, Ankit Sinha, Georg Wallmann, Vincenth Brennsteiner, Kathrin Korff, Edwin H. Rodriguez, Wen-Feng Zeng, Maximilian T. Strauss, Marisa I. Keller, Michael Kuhn, Jonel Trebicka, Christophe Junot, Mani Arumugam, Jessica A. Grembi, Dari Shalon, Kerwyn Casey Huang, Karsten Borgwardt, Johannes B. Mueller-Reif, Matthias Mann

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