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Metaproteomics boosted up by untargeted data-independent acquisition data analysis framework

Sami Pietilä, Tomi Suomi, Laura L. Elo
doi: https://doi.org/10.1101/2020.12.21.423800
Sami Pietilä
1Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
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Tomi Suomi
1Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
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Laura L. Elo
1Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
2Institute of Biomedicine, University of Turku, FI-20520 Turku, Finland
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  • For correspondence: laura.elo@utu.fi
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Abstract

Mass spectrometry based metaproteomics is a relatively new field of research that provides the ability to characterize the functionality of microbiota. Recently, we were the first to demonstrate the applicability of data-independent acquisition (DIA) mass spectrometry to the analysis of complex metaproteomic samples. This allowed us to circumvent many of the drawbacks of the conventionally used data-dependent acquisition (DDA) mass spectrometry, mainly the limited reproducibility when analyzing samples with complex microbial composition. However, the previous method still required additional DDA data on the samples to assist the DIA analysis. Here, we introduce, for the first time, a DIA metaproteomics approach that does not require any DDA data, but instead replaces a spectral library generated from DDA data with a pseudospectral library generated directly from the metaproteomics DIA samples. We demonstrate that using the new DIA-only approach, we can achieve higher peptide yields than with the DDA-assisted approach, while the amount of required mass spectrometry data is reduced to a single DIA run per sample. The new DIA-only metaproteomics approach is implemented as open-source software package DIAtools 2.0, which is freely available from DockerHub.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* Shared first author

  • https://github.com/elolab/diatools

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted December 22, 2020.
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Metaproteomics boosted up by untargeted data-independent acquisition data analysis framework
Sami Pietilä, Tomi Suomi, Laura L. Elo
bioRxiv 2020.12.21.423800; doi: https://doi.org/10.1101/2020.12.21.423800
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Metaproteomics boosted up by untargeted data-independent acquisition data analysis framework
Sami Pietilä, Tomi Suomi, Laura L. Elo
bioRxiv 2020.12.21.423800; doi: https://doi.org/10.1101/2020.12.21.423800

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