Kaiko

downstream-application · CNN + RNN

Kaiko: downstream-application · CNN + RNN. Deep-learning (CNN + RNN) de novo peptide sequencer trained on 5 M peptide-spectrum matches from 55 phylogenetically diverse bacteria. Identifies microbial community…

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.

Kind	downstream-application
Family	CNN + RNN
Deep learning	yes
Acquisition	DDA
Application area	metaproteomics

Code

• https://github.com/PNNL-Comp-Mass-Spec/Kaiko

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Papers

• Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics (2022, Journal of Proteome Research, peer-reviewed)

Authors (11)

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

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