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PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system.

Droit A, Hunter JM, Rouleau M, Ethier C, Picard-Cloutier A, Bourgais D, Poirier GG - BMC Bioinformatics (2007)

Bottom Line: This data must be archived and analysed using specialized bioinformatics tools.PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified.Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5.

View Article: PubMed Central - HTML - PubMed

Affiliation: Health and Environment Unit, Laval University Medical research Center, CHUQ, Québec, Canada. arnaud.droit@gmail.com

ABSTRACT

Background: In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools.

Description: We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified.

Conclusion: Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5.

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The biochemical and physical protein interaction network for PARP-1. This figure is a summary of the results of the protein-protein interaction databases and literature searches for PARP-1 substrates and cooperators. This figure is a hand-drawn representation from the interaction viewer.
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Figure 4: The biochemical and physical protein interaction network for PARP-1. This figure is a summary of the results of the protein-protein interaction databases and literature searches for PARP-1 substrates and cooperators. This figure is a hand-drawn representation from the interaction viewer.

Mentions: The first step in the generation of PARP-1 interaction model is an extensive search of the literature in order to collect published experimental data on PARP-1 interactions. The keyword used in the PARPs-DB search for literature was PARP-1. However, a functional network is not only limited to physical protein-protein interactions but also includes genetic and biochemical interactions (Figure 4).


PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system.

Droit A, Hunter JM, Rouleau M, Ethier C, Picard-Cloutier A, Bourgais D, Poirier GG - BMC Bioinformatics (2007)

The biochemical and physical protein interaction network for PARP-1. This figure is a summary of the results of the protein-protein interaction databases and literature searches for PARP-1 substrates and cooperators. This figure is a hand-drawn representation from the interaction viewer.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2266781&req=5

Figure 4: The biochemical and physical protein interaction network for PARP-1. This figure is a summary of the results of the protein-protein interaction databases and literature searches for PARP-1 substrates and cooperators. This figure is a hand-drawn representation from the interaction viewer.
Mentions: The first step in the generation of PARP-1 interaction model is an extensive search of the literature in order to collect published experimental data on PARP-1 interactions. The keyword used in the PARPs-DB search for literature was PARP-1. However, a functional network is not only limited to physical protein-protein interactions but also includes genetic and biochemical interactions (Figure 4).

Bottom Line: This data must be archived and analysed using specialized bioinformatics tools.PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified.Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5.

View Article: PubMed Central - HTML - PubMed

Affiliation: Health and Environment Unit, Laval University Medical research Center, CHUQ, Québec, Canada. arnaud.droit@gmail.com

ABSTRACT

Background: In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools.

Description: We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified.

Conclusion: Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5.

Show MeSH