Metaproteomics

13 workflows · 2007–2026

Metaproteomics: Mixed microbial communities, where which organisms are present is part of the question. 13 catalogued workflows and 17 papers.

Mixed microbial communities, where which organisms are present is part of the question.

Workflows 13
Papers 17
Authors 108
Active 2007-03-01 to 2026-10-11

Workflows (13)

  • Cadmium-exposed bacterial community metaproteomics (2007): 2DE, MALDI-TOF/TOF and de novo sequencing identified proteins of a bacterial community responding to cadmium over time.
  • Thermophilic biogas reactor metaproteome (2012): Metaproteomics of a thermophilic biogas community fed agricultural biomass, identifying housekeeping and methanogenesis enzymes through Mascot search plus de novo sequencing.
  • Resistant-starch CKD rat gut metaproteomics (2019): Rat cecum metaproteomics in which PEAKS de novo peptides gave the taxonomic profile through Unipept and seeded the custom search database.
  • NovoBridge (2020): A database-independent metaproteomics pipeline that maps de novo peptide sequences to taxonomy and function, giving quantitative community profiles without a sample-specific database.
  • CKD mouse cecal metaproteome with resistant starch (2020): Cecal metaproteomics of 5/6 nephrectomy mice fed resistant starch, where PEAKS de novo peptides above 80% ALC were submitted to Unipept to profile the bacterial taxa, alongside database identification.
  • Oxygen-deficient zone de novo peptidomics (2022): De novo peptides from sinking and suspended particles in the eastern tropical North Pacific revealed fungal proteins and tracked modified cyanobacterial peptides with depth.
  • Kaiko (2022): Deep-learning (CNN + RNN) de novo peptide sequencer trained on 5 M peptide-spectrum matches from 55 phylogenetically diverse bacteria. Identifies microbial community members directly from metaproteomic MS/MS, then builds sample-specific protein databases without requiring matched metagenomes: validated on native soil microbiome samples.
  • NovoLign (2024): Aligns de novo sequences from whole metaproteomics experiments to give rapid taxonomic profiles and to check the coverage of database search results.
  • uMetaP / novoMP (2024): Ultra-sensitive gut metaproteomics workflow with an FDR-validated de novo strategy (novoMP) that expands the dark metaproteome and maps host-microbiome interactions in intestinal injury.
  • Orthrus (2024): Open-source metaproteomics pipeline combining Casanovo transformer-based de novo sequencing with Sage database search and Mokapot rescoring.
  • De novo peptide databases for Protein-SIP (2024): Builds peptide databases from de novo sequencing of the raw data and uses them for protein-based stable isotope probing of microbial communities, reaching species-level resolution.
  • NovoTax (2026): Open-source pipeline that identifies prokaryotic species and strain directly from bottom-up proteomics data by searching de novo peptide sequences against an extensive proteome database; also finds contaminants and abundant community members.
  • FastaLake (2026): 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.

Papers (17)

Sequencing tools these papers used

Casanovo, PEAKS, SPIDER

Authors (108)

Alan Tackett, Allison M. Barry, André Mateus, Angelika Hanreich, Anitra E. Ingalls, Ankit Sinha, Ben Abbas, Bin Ma, Boris Zybailov, Carla M. R. Lacerda, Carrie D. Nicora, Chang Ding, Christian White, Christoph Krisp, Christophe Junot, Clara A. Fuchsman, Claudia G. Tugui, Dari Shalon, David Gómez-Varela, Dennis Svedberg, Dirk Benndorf, Dirk Haller, Dmitri S. Andreyev, Doriane Aguanno, Dorothy A. Kieffer, Edwin H. Rodriguez, Elisabeth Urbauer, Erdmann Rapp, Eric D. Merkley, Ernesto S. Nakayasu, Feng Xian, Florian A. Rosenberger, Gabrielle Rocap, Galina Glazko, Georg Wallmann, Hugh D. Mitchell, Hugo B.C. Kleikamp, Jacquelyn A. Neibauer, Jamee Adams, Janet K. Jansson, Jessica A. Grembi, Jinqiu Xiao, Jitske M van Ede, Johannes B. Mueller-Reif, John Arthur, Jonathan R. Krieger, Jonel Trebicka, Joon-Yong Lee, Karsten Borgwardt, Kathrin Korff, Kenneth F. Reardon, Kerwyn Casey Huang, Kristin E. Burnum-Johnson, Laxmi Yeruva, Leila H. Choe, Leonor Guedes da Silva, Lisa Alvarez-Cohen, Lisa Orr, Lorenz Adrian, Malena Brenek, Mani Arumugam, Manuela Schmidt, Mario Pronk, Marisa I. Keller, Mark C. M. van Loosdrecht, Markus Pioch, Martin Pabst, Matthew James Collins, Matthias Mann, Maximilian T. Strauss, Maximilian Zwiebel, Maximilienne T Allaart, Meagan C. Burnet, Megan E. Duffy, Michael Klocke, Michael Kuhn, Mikhail Lebedev, Nosratola D. Vaziri, Oleg Karaduta, Peter V. Treit, Philip Hartout, Philipp E. Geyer, Pim Schaasberg, Qixin Liu, R. J. Martin, Rachel A. Lundeen, Ramon van Valderen, Ramon van der Zwaan, Ranjith Kumar Ravi Kumar, Richard G. Keil, Ricky D. Edmondson, Robert Heyer, Ruonan Wu, Samuel H. Payne, Samuel Mackintosh, Sarah C. Jenson, Sean H. Adams, Simon Klaes, Stephanie D. Byrum, Taylor McElroy, Tharan Srikumar, Udo Reichl, Vincenth Brennsteiner, Wen-Feng Zeng, Yasir Rahmatallah, Yue Mei Lin, Yun Chiang, Zeljko Dvanajscak

Where the work happened

Austria, Belgium, Canada, China, Denmark, France, Germany, Netherlands, Sweden, UK, USA

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