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Title: The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

Abstract

This dataset deposition announces the submission to public repositories of the PNNL Biodiversity Library, a large collection of global proteomics data for 112 bacterial and archaeal organisms. The data comprises 35,162 tandem mass spectrometry (MS/MS) datasets from ~10 years of research. All data has been searched, annotated and organized in a consistent manner to promote reuse by the community. Protein identifications were cross-referenced with KEGG functional annotations which allows for pathway oriented investigation. We present the data as a freely available community resource. A variety of data re-use options are described for computational modeling, proteomics assay design and bioengineering. Instrument data and analysis files are available at ProteomeXchange via the MassIVE partner repository under the identifiers PXD001860 and MSV000079053.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [1];  [1]
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  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Science Laboratory
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1213004
Report Number(s):
PNNL-SA-108944
48582; KP1601010
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Data, 2:Art. No. 150041
Additional Journal Information:
Journal Name: Scientific Data, 2:Art. No. 150041
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Environmental Molecular Sciences Laboratory

Citation Formats

Payne, Samuel H., Monroe, Matthew E., Overall, Christopher C., Kiebel, Gary R., Degan, Michael G., Gibbons, Bryson C., Fujimoto, Grant M., Purvine, Samuel O., Adkins, Joshua N., Lipton, Mary S., and Smith, Richard D. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. United States: N. p., 2015. Web. doi:10.1038/sdata.2015.41.
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Payne, Samuel H., Monroe, Matthew E., Overall, Christopher C., Kiebel, Gary R., Degan, Michael G., Gibbons, Bryson C., Fujimoto, Grant M., Purvine, Samuel O., Adkins, Joshua N., Lipton, Mary S., & Smith, Richard D. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. United States. https://doi.org/10.1038/sdata.2015.41
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Payne, Samuel H., Monroe, Matthew E., Overall, Christopher C., Kiebel, Gary R., Degan, Michael G., Gibbons, Bryson C., Fujimoto, Grant M., Purvine, Samuel O., Adkins, Joshua N., Lipton, Mary S., and Smith, Richard D. Tue . "The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity". United States. https://doi.org/10.1038/sdata.2015.41. https://www.osti.gov/servlets/purl/1213004.
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@article{osti_1213004,
title = {The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity},
author = {Payne, Samuel H. and Monroe, Matthew E. and Overall, Christopher C. and Kiebel, Gary R. and Degan, Michael G. and Gibbons, Bryson C. and Fujimoto, Grant M. and Purvine, Samuel O. and Adkins, Joshua N. and Lipton, Mary S. and Smith, Richard D.},
abstractNote = {This dataset deposition announces the submission to public repositories of the PNNL Biodiversity Library, a large collection of global proteomics data for 112 bacterial and archaeal organisms. The data comprises 35,162 tandem mass spectrometry (MS/MS) datasets from ~10 years of research. All data has been searched, annotated and organized in a consistent manner to promote reuse by the community. Protein identifications were cross-referenced with KEGG functional annotations which allows for pathway oriented investigation. We present the data as a freely available community resource. A variety of data re-use options are described for computational modeling, proteomics assay design and bioengineering. Instrument data and analysis files are available at ProteomeXchange via the MassIVE partner repository under the identifiers PXD001860 and MSV000079053.},
doi = {10.1038/sdata.2015.41},
journal = {Scientific Data, 2:Art. No. 150041},
number = ,
volume = ,
place = {United States},
year = {Tue Aug 18 00:00:00 EDT 2015},
month = {Tue Aug 18 00:00:00 EDT 2015}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1038/sdata.2015.41
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Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra
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Mapping protein post-translational modifications with mass spectrometry
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Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions
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A proteogenomic update to Yersinia: enhancing genome annotation
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journal, February 2008

Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study
journal, November 2011

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    • Molecular & Cellular Proteomics, Vol. 15, Issue 11
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