A proteome quality index
A proteome quality index
We present the Proteome Quality Index (PQI; http://pqi-list.org), a much-needed resource for users of bacterial and eukaryotic proteomes. Completely sequenced genomes for which there is an available set of protein sequences (the proteome) are given a one- to five-star rating supported by 11 different metrics of quality. The database indexes over 3000 proteomes at the time of writing and is provided via a website for browsing, filtering and downloading. Previous to this work, there was no systematic way to account for the large variability in quality of the thousands of proteomes, and this is likely to have profoundly influenced the outcome of many published studies, in particular large-scale comparative analyses. The lack of a measure of proteome quality is likely due to the difficulty in producing one, a problem that we have approached by integrating multiple metrics. The continued development and improvement of the index will require the contribution of additional metrics by us and by others; the PQI provides a useful point of reference for the scientific community, but it is only the first step towards a 'standard' for the field.
Databases, Protein, Genome, Internet, Proteome/standards
4-9
Zaucha, Jan
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Stahlhacke, Jonathan
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Oates, Matt E
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Thurlby, Natalie
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Rackham, Owen J L
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Fang, Hai
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Smithers, Ben
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Gough, Julian
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29 January 2015
Zaucha, Jan
9a85596e-cec0-4366-85ea-b74bac4b4b4e
Stahlhacke, Jonathan
2e55897b-f50f-45e9-90cf-b538adf19d2f
Oates, Matt E
c90996e2-2ae0-4784-9633-a1db986b1831
Thurlby, Natalie
c74b438d-19f4-4b77-9c29-0efdf7797191
Rackham, Owen J L
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
Fang, Hai
58424580-2d92-4db2-934f-4c393989cea9
Smithers, Ben
d2cda838-0e6a-41ea-99ed-15ba2c4772ca
Gough, Julian
019ed039-9fd4-45d6-aa7a-12a8fcf7245c
Zaucha, Jan, Stahlhacke, Jonathan, Oates, Matt E, Thurlby, Natalie, Rackham, Owen J L, Fang, Hai, Smithers, Ben and Gough, Julian
(2015)
A proteome quality index.
Environmental Microbiology, 17 (1), .
(doi:10.1111/1462-2920.12622).
Abstract
We present the Proteome Quality Index (PQI; http://pqi-list.org), a much-needed resource for users of bacterial and eukaryotic proteomes. Completely sequenced genomes for which there is an available set of protein sequences (the proteome) are given a one- to five-star rating supported by 11 different metrics of quality. The database indexes over 3000 proteomes at the time of writing and is provided via a website for browsing, filtering and downloading. Previous to this work, there was no systematic way to account for the large variability in quality of the thousands of proteomes, and this is likely to have profoundly influenced the outcome of many published studies, in particular large-scale comparative analyses. The lack of a measure of proteome quality is likely due to the difficulty in producing one, a problem that we have approached by integrating multiple metrics. The continued development and improvement of the index will require the contribution of additional metrics by us and by others; the PQI provides a useful point of reference for the scientific community, but it is only the first step towards a 'standard' for the field.
Text
1462-2920.12622
- Version of Record
More information
e-pub ahead of print date: 22 October 2014
Published date: 29 January 2015
Additional Information:
© 2014 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
Keywords:
Databases, Protein, Genome, Internet, Proteome/standards
Identifiers
Local EPrints ID: 446670
URI: http://eprints.soton.ac.uk/id/eprint/446670
ISSN: 1462-2920
PURE UUID: 0afa43e6-e27f-4ec7-97c8-5bb8b408e57b
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Date deposited: 17 Feb 2021 17:33
Last modified: 17 Mar 2024 04:03
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Contributors
Author:
Jan Zaucha
Author:
Jonathan Stahlhacke
Author:
Matt E Oates
Author:
Natalie Thurlby
Author:
Hai Fang
Author:
Ben Smithers
Author:
Julian Gough
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