Metaproteomics

2 workflows · 2022–2024

Metaproteomics: Mixed microbial communities, where which organisms are present is part of the question. 2 catalogued workflows and 2 papers.

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

Workflows 2
Papers 2
Authors 13
Active 2022-07-06 to 2024-11-15

Workflows (2)

  • 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.
  • Orthrus (2024): Open-source metaproteomics pipeline combining Casanovo transformer-based de novo sequencing with Sage database search and Mokapot rescoring.

Papers (2)

Authors (13)

Carrie D. Nicora, Eric D. Merkley, Ernesto S. Nakayasu, Hugh D. Mitchell, Janet K. Jansson, Joon-Yong Lee, Kristin E. Burnum-Johnson, Matthew James Collins, Meagan C. Burnet, Ruonan Wu, Samuel H. Payne, Sarah C. Jenson, Yun Chiang

Where the work happened

Denmark, France, UK, USA

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