| Introduction:
CPXS 0.1(Comparative Proteomics XML Schema) is a draft of comparative proteomic minimum data standard. The most distinct feature of CPXS is taking comprehensive context as a crucial component of data mode, because data generated by proteomics experiments are only meaningful set in the correct biological, environmental and methodological context.
Purpose of the CPXS :
CPXS is a data exchange format for differential expressed protein profile comparison. It was designed to standardize minimum reporting requirement for comparative proteomics experiments, analogous to the MIAME guidelines for transcriptomics, is required to facilitate the analysis, exchange and dissemination of comparative proteomics data.
Structure of a CPXS record :
The root element of a CPXS XML file is the ComparisonList. An ComparisonList contains one or more Comparisons. Each ComparisonList is a self-contained unit. This allows to concatenate the contents of multiple files into a single file by simply adding all the Comparisons into the ComparisonList.
Figure1: The comparison top level element.
Basic elements of CPXS are shown in Figure 1 and their function will be described as follow.
1). The EntryInfor element includes the information about importer and the entry time.
2) The source element describes the source of the data, usually paper's title, PMID, author and journal.
3).The SamplePair provides statements on the biological context of sample and control. It contains detail information about specimen's species, organ, suborgan, tissue, cell type, cell name and EnviromentFactorID. The last one connect biological context with environmental contexts.
4).The EnvironmentalFactorList element contains a set of EnvironmentalFactor elements which describes environmental factors' type, name, during-time and additional information.
5).The MethodologicalContext includes three method types as follow: PSMethod, PIMethod and DCMethod which contains type, machine name, method type, software name and so on. As elements mentioned above may be not enough to describe complex experiment protocol comprehensively, additional information can be stored in the reference element. In this case PS, PI and DC means protein separation, protein identification and difference confirmation respectively.
6).The DEP element describes some key attributes of differentially expressed protein in this comparison. Detail structure was shown in figure 2.
 Figure2: The child elements of DEP.
Definition of Differential_Type, Spot_Name and Folds can be found in definition page. The Concentration element describes value of concentration of the protein in specimen and is an preparative element for quantitative proteomics in the future. MW_Theo, MW_Nature, PI_Theo and PI_Nature reprenst the DEP's molecular weight and pI value in theory and nature.
3. Future work
We are interested in knowing what the items should be included in the next version and need your suggestions.
Some modification will be made in the next version.
• Provide a better framework for methodological context
to describe methods more accurately.
• Optimize the structure of EnvironmentalFactor type.
If you would like to comment on this schema, please send a mail to: hqyone@hotmail.com .
4. Download
The schema can be downloaded from download page after you logging in the system.
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