The importance of recognizing and reporting sequence database contamination for proteomics

Olivier Pible; Erica M. Hartmann; Gilles Imbert; Jean Armengaud

doi:10.1016/j.euprot.2014.04.001

The importance of recognizing and reporting sequence database contamination for proteomics

Olivier Pible, Erica M. Hartmann, Gilles Imbert, Jean Armengaud^*

^*Corresponding author for this work

Civil and Environmental Engineering

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

14 Scopus citations

Abstract

Advances in genome sequencing have made proteomic experiments more successful than ever. However, not all entries in a sequence database are of equal quality. Genome sequences are contaminated more frequently than is admitted. Contamination impacts homology-based proteomic, proteogenomic, and metaproteomic results. We highlight two examples in the National Center for Biotechnology Information non-redundant database (NCBInr) that are likely contaminated: the bacterium Enterococcus gallinarum EGD-AAK12 and the insect Ceratitis capitata. We hope to incite users of this and other databases to critically evaluate submitted sequences and to contribute to the overall quality of the database by signaling potential errors when possible.

Original language	English (US)
Pages (from-to)	246-249
Number of pages	4
Journal	EuPA Open Proteomics
Volume	3
DOIs	https://doi.org/10.1016/j.euprot.2014.04.001
State	Published - Jun 2014

Keywords

Blast analysis
Contamination
Curation
Database
Metaproteomics
Proteomics

ASJC Scopus subject areas

Biochemistry

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10.1016/j.euprot.2014.04.001

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@article{5e10d0cd68a44fdf82eeb99e0f45410c,

title = "The importance of recognizing and reporting sequence database contamination for proteomics",

abstract = "Advances in genome sequencing have made proteomic experiments more successful than ever. However, not all entries in a sequence database are of equal quality. Genome sequences are contaminated more frequently than is admitted. Contamination impacts homology-based proteomic, proteogenomic, and metaproteomic results. We highlight two examples in the National Center for Biotechnology Information non-redundant database (NCBInr) that are likely contaminated: the bacterium Enterococcus gallinarum EGD-AAK12 and the insect Ceratitis capitata. We hope to incite users of this and other databases to critically evaluate submitted sequences and to contribute to the overall quality of the database by signaling potential errors when possible.",

keywords = "Blast analysis, Contamination, Curation, Database, Metaproteomics, Proteomics",

author = "Olivier Pible and Hartmann, {Erica M.} and Gilles Imbert and Jean Armengaud",

note = "Funding Information: This work was supported by the Commissariat {\`a} l{\textquoteright}Energie Atomique et aux Energies Alternatives, and the Agence Nationale de la Recherche ( ANR-12-BSV6-0012-01 ). EMH would like to express her sincere gratitude to the Fulbright commission for initial support.",

year = "2014",

month = jun,

doi = "10.1016/j.euprot.2014.04.001",

language = "English (US)",

volume = "3",

pages = "246--249",

journal = "EuPA Open Proteomics",

issn = "2212-9685",

publisher = "Elsevier B.V.",

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TY - JOUR

T1 - The importance of recognizing and reporting sequence database contamination for proteomics

AU - Pible, Olivier

AU - Hartmann, Erica M.

AU - Imbert, Gilles

AU - Armengaud, Jean

N1 - Funding Information: This work was supported by the Commissariat à l’Energie Atomique et aux Energies Alternatives, and the Agence Nationale de la Recherche ( ANR-12-BSV6-0012-01 ). EMH would like to express her sincere gratitude to the Fulbright commission for initial support.

PY - 2014/6

Y1 - 2014/6

N2 - Advances in genome sequencing have made proteomic experiments more successful than ever. However, not all entries in a sequence database are of equal quality. Genome sequences are contaminated more frequently than is admitted. Contamination impacts homology-based proteomic, proteogenomic, and metaproteomic results. We highlight two examples in the National Center for Biotechnology Information non-redundant database (NCBInr) that are likely contaminated: the bacterium Enterococcus gallinarum EGD-AAK12 and the insect Ceratitis capitata. We hope to incite users of this and other databases to critically evaluate submitted sequences and to contribute to the overall quality of the database by signaling potential errors when possible.

AB - Advances in genome sequencing have made proteomic experiments more successful than ever. However, not all entries in a sequence database are of equal quality. Genome sequences are contaminated more frequently than is admitted. Contamination impacts homology-based proteomic, proteogenomic, and metaproteomic results. We highlight two examples in the National Center for Biotechnology Information non-redundant database (NCBInr) that are likely contaminated: the bacterium Enterococcus gallinarum EGD-AAK12 and the insect Ceratitis capitata. We hope to incite users of this and other databases to critically evaluate submitted sequences and to contribute to the overall quality of the database by signaling potential errors when possible.

KW - Blast analysis

KW - Contamination

KW - Curation

KW - Database

KW - Metaproteomics

KW - Proteomics

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U2 - 10.1016/j.euprot.2014.04.001

DO - 10.1016/j.euprot.2014.04.001

M3 - Article

AN - SCOPUS:84902440220

SN - 2212-9685

VL - 3

SP - 246

EP - 249

JO - EuPA Open Proteomics

JF - EuPA Open Proteomics

ER -

The importance of recognizing and reporting sequence database contamination for proteomics

Abstract

Keywords

ASJC Scopus subject areas

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