Limits...
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: 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.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
Schematic overview of the approach for PARPs protein interaction research. The steps are (A) PARPs co-immunoprecipitation and with interactors; (B) generation of mass spectral data; (C) peptide sequence assignments using different search engines and protein identifications using different methods of inference; (D) the annotations and results are loaded automatically into PARPs database for viewing, annotation and analyses.
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Figure 2: Schematic overview of the approach for PARPs protein interaction research. The steps are (A) PARPs co-immunoprecipitation and with interactors; (B) generation of mass spectral data; (C) peptide sequence assignments using different search engines and protein identifications using different methods of inference; (D) the annotations and results are loaded automatically into PARPs database for viewing, annotation and analyses.

Mentions: The workflow of the PARPs protein interaction research is illustrated in Figure 2. In our LIMS, the data processing is divided into sections corresponding to the four main steps: sample preparation, MS Data acquisition, protein identification, and PARPs-DB.


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)

Schematic overview of the approach for PARPs protein interaction research. The steps are (A) PARPs co-immunoprecipitation and with interactors; (B) generation of mass spectral data; (C) peptide sequence assignments using different search engines and protein identifications using different methods of inference; (D) the annotations and results are loaded automatically into PARPs database for viewing, annotation and analyses.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Schematic overview of the approach for PARPs protein interaction research. The steps are (A) PARPs co-immunoprecipitation and with interactors; (B) generation of mass spectral data; (C) peptide sequence assignments using different search engines and protein identifications using different methods of inference; (D) the annotations and results are loaded automatically into PARPs database for viewing, annotation and analyses.
Mentions: The workflow of the PARPs protein interaction research is illustrated in Figure 2. In our LIMS, the data processing is divided into sections corresponding to the four main steps: sample preparation, MS Data acquisition, protein identification, and PARPs-DB.

Bottom Line: 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.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