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.
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.
| Original language | English |
|---|---|
| Pages (from-to) | 1758-1769 |
| Number of pages | 12 |
| Journal | Proteomics |
| Volume | 6 |
| Issue number | 6 |
| Early online date | 3 Feb 2006 |
| DOIs | |
| Publication status | Published - Mar 2006 |