Article

SPLASH: systematic proteomics laboratory analysis and storage hub.

Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore.
PROTEOMICS (Impact Factor: 4.13). 04/2006; 6(6):1758-69. DOI: 10.1002/pmic.200500378
Source: PubMed

ABSTRACT In the field of proteomics, the increasing difficulty to unify the data format, due to the different platforms/instrumentation and laboratory documentation systems, greatly hinders experimental data verification, exchange, and comparison. Therefore, it is essential to establish standard formats for every necessary aspect of proteomics data. One of the recently published data models is the proteomics experiment data repository [Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D. et al., Nat. Biotechnol. 2003, 21, 247-254]. Compliant with this format, we developed the systematic proteomics laboratory analysis and storage hub (SPLASH) database system as an informatics infrastructure to support proteomics studies. It consists of three modules and provides proteomics researchers a common platform to store, manage, search, analyze, and exchange their data. (i) Data maintenance includes experimental data entry and update, uploading of experimental results in batch mode, and data exchange in the original PEDRo format. (ii) The data search module provides several means to search the database, to view either the protein information or the differential expression display by clicking on a gel image. (iii) The data mining module contains tools that perform biochemical pathway, statistics-associated gene ontology, and other comparative analyses for all the sample sets to interpret its biological meaning. These features make SPLASH a practical and powerful tool for the proteomics community.

0 Bookmarks
 · 
66 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: Biomedical research is evolving rapidly to address biological systems, such as molecular pathways integrated into complex networks. Tools for molecular discoveries are evolving to address old challenges and create new opportunities. Despite considerable financial and research effort combined with a variety of interventions, the rate of preterm birth has steadily increased to reach a high of 12.7%. Disappointingly, each year, 4.5 million premature infants are born in the USA alone. Although the etiology of most preterm births remains unknown, several distinct pathophysiological pathways are involved in triggering the syndrome, such as myometrial stretching, oxidative stress, decidual hemorrhage and infection. Novel research and diagnostic applications stemming from opportunities presented by the advances of genomics and proteomics begin to impact on clinical diagnosis, vaccine development, drug discovery and unique therapies in a modern diagnostic–therapeutic framework – part of the new scientific field of ‘theranostics.’ This review critically explores a number of newly discovered biomarkers that may potentially revolutionize the diagnosis and treatment of women at risk of preterm parturition.
    Expert Review of Obstetrics &amp Gynecology 01/2007; 2(5):743-753.
  • [Show abstract] [Hide abstract]
    ABSTRACT: The molecular mechanisms regulating myometrial contractility and preterm premature rupture of the membranes leading to preterm birth are poorly understood. The completion of the human genome sequence led to the development of functional genomics and gene array technology to simultaneously identify candidate genes potentially involved in regulation of human parturition. However, the study of living systems can now be expanded past genomics based on the rationale that it is the protein products of the genes, not simply gene expression, that have effects and cause disturbances at the cellular level. Therefore, identification of disease biomarkers, followed by a description of their functional networks, has the potential to significantly aid the development of new strategies for the prediction, diagnosis, and prevention of preterm birth. Interest in mass spectrometry and its use as a new clinical diagnostic tool has grown rapidly and is poised to become an important medical field for the next century.
    Obstetrical and Gynecological Survey 08/2006; 61(7):481-6. · 2.51 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Many "omics" techniques have been developed for one goal: biomarker discovery and early diagnosis of human cancers. A comprehensive review of mass spectrometry-based "omics" approaches performed on various biological samples for molecular diagnosis of human cancers is presented in this article. Furthermore, the existing and potential problems/solutions (both de facto experimental and bioinformatic challenges), and future prospects have been extensively discussed. Although the use of present omic methods as diagnostic tools are still in their infant stage and consequently not ready for immediate clinical use, it can be envisaged that the "omics"-based cancer diagnostics will gradually enter into the clinic in next 10 years as an important supplement to current clinical diagnostics.
    Mass Spectrometry Reviews 01/2007; 26(3):403-31. · 7.74 Impact Factor