Disseminating metaproteomic informatics capabilities and knowledge using the galaxy-P framework

Clemens Blank; Caleb Easterly; Bjoern Gruening; James Johnson; Carolin A. Kolmeder; Praveen Kumar; Damon May; Subina Mehta; Bart Mesuere; Zachary Brown; Joshua E. Elias; W. Judson Hervey; Thomas McGowan; Thilo Muth; Brook L. Nunn; Joel Rudney; Alessandro Tanca; Timothy J. Griffin; Pratik D. Jagtap

doi:10.3390/proteomes6010007

Disseminating metaproteomic informatics capabilities and knowledge using the galaxy-P framework

Clemens Blank, Caleb Easterly, Bjoern Gruening, James Johnson, Carolin A. Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E. Elias, W. Judson Hervey, Thomas McGowan, Thilo Muth, Brook L. Nunn, Joel Rudney, Alessandro Tanca, Timothy J. Griffin, Pratik D. Jagtap

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

Abstract

The impact ofmicrobial communities, also known as themicrobiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.

Original language	English (US)
Article number	7
Journal	Proteomes
Volume	6
Issue number	1
DOIs	https://doi.org/10.3390/proteomes6010007
State	Published - Mar 1 2018

Bibliographical note

Funding Information:
This work is supported by grants from the NSF award 1458524 and NIH award U24CA199347 to T.J. Griffin and the core Galaxy-P research team. BLN and DM were supported by NSF grant OCE-1633939. The authors would also like to thank Intergalactic Utilities Commission (https://galaxyproject.org/iuc/) for encouraging and supporting the contribution fest. We would also like to thank the organizers of Association of Biomolecular Research Facilities (ABRF), American Society of Mass Spectrometry (ASMS), Galaxy Community Conference (GCC), and International Metaproteomics Symposium (IMS) for providing us a platform for conducting workshops and facilitating interesting discussions during the conferences.

Publisher Copyright:
© 2018 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

Bioinformatics
Community development
Functional microbiome
Galaxy platform
Mass spectrometry
Software workflow development
metaproteomics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Publisher link

10.3390/proteomes6010007

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5874766

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Blank, C., Easterly, C., Gruening, B., Johnson, J., Kolmeder, C. A., Kumar, P., May, D., Mehta, S., Mesuere, B., Brown, Z., Elias, J. E., Hervey, W. J., McGowan, T., Muth, T., Nunn, B. L., Rudney, J., Tanca, A., Griffin, T. J., & Jagtap, P. D. (2018). Disseminating metaproteomic informatics capabilities and knowledge using the galaxy-P framework. Proteomes, 6(1), [7]. https://doi.org/10.3390/proteomes6010007

Blank, C, Easterly, C, Gruening, B, Johnson, J, Kolmeder, CA, Kumar, P, May, D, Mehta, S, Mesuere, B, Brown, Z, Elias, JE, Hervey, WJ, McGowan, T, Muth, T, Nunn, BL, Rudney, J, Tanca, A, Griffin, TJ & Jagtap, PD 2018, 'Disseminating metaproteomic informatics capabilities and knowledge using the galaxy-P framework', Proteomes, vol. 6, no. 1, 7. https://doi.org/10.3390/proteomes6010007

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abstract = "The impact ofmicrobial communities, also known as themicrobiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics {"}Contribution Fest{"} undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.",

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author = "Clemens Blank and Caleb Easterly and Bjoern Gruening and James Johnson and Kolmeder, {Carolin A.} and Praveen Kumar and Damon May and Subina Mehta and Bart Mesuere and Zachary Brown and Elias, {Joshua E.} and Hervey, {W. Judson} and Thomas McGowan and Thilo Muth and Nunn, {Brook L.} and Joel Rudney and Alessandro Tanca and Griffin, {Timothy J.} and Jagtap, {Pratik D.}",

note = "Funding Information: This work is supported by grants from the NSF award 1458524 and NIH award U24CA199347 to T.J. Griffin and the core Galaxy-P research team. BLN and DM were supported by NSF grant OCE-1633939. The authors would also like to thank Intergalactic Utilities Commission (https://galaxyproject.org/iuc/) for encouraging and supporting the contribution fest. We would also like to thank the organizers of Association of Biomolecular Research Facilities (ABRF), American Society of Mass Spectrometry (ASMS), Galaxy Community Conference (GCC), and International Metaproteomics Symposium (IMS) for providing us a platform for conducting workshops and facilitating interesting discussions during the conferences. Publisher Copyright: {\textcopyright} 2018 by the authors. Licensee MDPI, Basel, Switzerland.",

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T1 - Disseminating metaproteomic informatics capabilities and knowledge using the galaxy-P framework

AU - Blank, Clemens

AU - Easterly, Caleb

AU - Gruening, Bjoern

AU - Johnson, James

AU - Kolmeder, Carolin A.

AU - Kumar, Praveen

AU - May, Damon

AU - Mehta, Subina

AU - Mesuere, Bart

AU - Brown, Zachary

AU - Elias, Joshua E.

AU - Hervey, W. Judson

AU - McGowan, Thomas

AU - Muth, Thilo

AU - Nunn, Brook L.

AU - Rudney, Joel

AU - Tanca, Alessandro

AU - Griffin, Timothy J.

AU - Jagtap, Pratik D.

N1 - Funding Information: This work is supported by grants from the NSF award 1458524 and NIH award U24CA199347 to T.J. Griffin and the core Galaxy-P research team. BLN and DM were supported by NSF grant OCE-1633939. The authors would also like to thank Intergalactic Utilities Commission (https://galaxyproject.org/iuc/) for encouraging and supporting the contribution fest. We would also like to thank the organizers of Association of Biomolecular Research Facilities (ABRF), American Society of Mass Spectrometry (ASMS), Galaxy Community Conference (GCC), and International Metaproteomics Symposium (IMS) for providing us a platform for conducting workshops and facilitating interesting discussions during the conferences. Publisher Copyright: © 2018 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2018/3/1

Y1 - 2018/3/1

N2 - The impact ofmicrobial communities, also known as themicrobiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.

AB - The impact ofmicrobial communities, also known as themicrobiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research. The Galaxy for proteomics platform (Galaxy-P) offers an open source, web-based bioinformatics platform for disseminating metaproteomics software and workflows. Within this platform, we have developed easily-accessible and documented metaproteomic software tools and workflows aimed at training researchers in their operation and disseminating the tools for more widespread use. The modular workflows encompass the core requirements of metaproteomic informatics: (a) database generation; (b) peptide spectral matching; (c) taxonomic analysis and (d) functional analysis. Much of the software available via the Galaxy-P platform was selected, packaged and deployed through an online metaproteomics "Contribution Fest" undertaken by a unique consortium of expert software developers and users from the metaproteomics research community, who have co-authored this manuscript. These resources are documented on GitHub and freely available through the Galaxy Toolshed, as well as a publicly accessible metaproteomics gateway Galaxy instance. These documented workflows are well suited for the training of novice metaproteomics researchers, through online resources such as the Galaxy Training Network, as well as hands-on training workshops. Here, we describe the metaproteomics tools available within these Galaxy-based resources, as well as the process by which they were selected and implemented in our community-based work. We hope this description will increase access to and utilization of metaproteomics tools, as well as offer a framework for continued community-based development and dissemination of cutting edge metaproteomics software.

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KW - Community development

KW - Functional microbiome

KW - Galaxy platform

KW - Mass spectrometry

KW - Software workflow development

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Disseminating metaproteomic informatics capabilities and knowledge using the galaxy-P framework

Abstract

Bibliographical note

Keywords

UN SDGs

Publisher link

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