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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Description</p> <p>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.</p> <p>Conclusion</p> <p>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.</p

Redundant functions but temporal and regional regulation of two alternatively spliced isoforms of semaphorin 3F in the nervous system.

SEMA3F is a secreted semaphorin that affects axon and cell guidance in the developing nervous system, and is also thought to have anti-tumor activity. Two spliced forms of SEMA3F have been identified that differ by the insertion of 31 amino acids in the sema domain. Here, we investigated the bioactivity of these isoforms and show, using coculture and binding assays, that they share common axonal chemorepulsive properties and binding to neuropilin receptors. SEMA3F isoforms were also found to regulate endothelial cell morphology by remodeling lamellipodial protrusions. Although Sema3F expression globally decreased during mouse development, we noted an enrichment of the longest isoform at postnatal stages in some territories such as the brainstem and spinal cord. These results indicate that although functionally redundant in cell culture assays, Sema3F spliced forms are characterized in vivo by a temporal and regional specific regulation during maturation of the nervous system

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system-1

) 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.<p><b>Copyright information:</b></p><p>Taken from "PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system"</p><p>http://www.biomedcentral.com/1471-2105/8/483</p><p>BMC Bioinformatics 2007;8():483-483.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2266781.</p><p></p

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system-2

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.<p><b>Copyright information:</b></p><p>Taken from "PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system"</p><p>http://www.biomedcentral.com/1471-2105/8/483</p><p>BMC Bioinformatics 2007;8():483-483.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2266781.</p><p></p

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system-0

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.<p><b>Copyright information:</b></p><p>Taken from "PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system"</p><p>http://www.biomedcentral.com/1471-2105/8/483</p><p>BMC Bioinformatics 2007;8():483-483.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2266781.</p><p></p