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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.

Show MeSH
PARPs database user interfaces. (A) In the Sample Origin section the user can enter experimental parameters and visualize the experimental protocol; (B) In the Mass Spectrometry section the user defines the parameters of the mass spectrometer; IPxxx is the identification of immunoprecipitation experience. (C) The Protein Identification section summarizes protein identifications, including protein accession number, entrez gene accession, number of peptides identified and a protein summary function; (D) The Protein Card Layout contains links to a variety of external public sources; (E) The Protein-Protein Interaction Viewer allows the user to display protein-protein interactions from internal and external (publicly available) data sources. The full-scale schema is available on-line as supplemental Figure.
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Figure 3: PARPs database user interfaces. (A) In the Sample Origin section the user can enter experimental parameters and visualize the experimental protocol; (B) In the Mass Spectrometry section the user defines the parameters of the mass spectrometer; IPxxx is the identification of immunoprecipitation experience. (C) The Protein Identification section summarizes protein identifications, including protein accession number, entrez gene accession, number of peptides identified and a protein summary function; (D) The Protein Card Layout contains links to a variety of external public sources; (E) The Protein-Protein Interaction Viewer allows the user to display protein-protein interactions from internal and external (publicly available) data sources. The full-scale schema is available on-line as supplemental Figure.

Mentions: To facilitate data analysis, a graphical user interface (GUI) was developed. The GUI guides the user through all steps of the experiment to enter information such as immunoprecipitation methods, gel images, mass spectra, search engine results, etc. (Figure 3), which ensure a complete documentation of the experimental setting. After all necessary data have been stored in the system, the user can select data sets for visualization.


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)

PARPs database user interfaces. (A) In the Sample Origin section the user can enter experimental parameters and visualize the experimental protocol; (B) In the Mass Spectrometry section the user defines the parameters of the mass spectrometer; IPxxx is the identification of immunoprecipitation experience. (C) The Protein Identification section summarizes protein identifications, including protein accession number, entrez gene accession, number of peptides identified and a protein summary function; (D) The Protein Card Layout contains links to a variety of external public sources; (E) The Protein-Protein Interaction Viewer allows the user to display protein-protein interactions from internal and external (publicly available) data sources. The full-scale schema is available on-line as supplemental Figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: PARPs database user interfaces. (A) In the Sample Origin section the user can enter experimental parameters and visualize the experimental protocol; (B) In the Mass Spectrometry section the user defines the parameters of the mass spectrometer; IPxxx is the identification of immunoprecipitation experience. (C) The Protein Identification section summarizes protein identifications, including protein accession number, entrez gene accession, number of peptides identified and a protein summary function; (D) The Protein Card Layout contains links to a variety of external public sources; (E) The Protein-Protein Interaction Viewer allows the user to display protein-protein interactions from internal and external (publicly available) data sources. The full-scale schema is available on-line as supplemental Figure.
Mentions: To facilitate data analysis, a graphical user interface (GUI) was developed. The GUI guides the user through all steps of the experiment to enter information such as immunoprecipitation methods, gel images, mass spectra, search engine results, etc. (Figure 3), which ensure a complete documentation of the experimental setting. After all necessary data have been stored in the system, the user can select data sets for visualization.

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