Proteomics Data Formats
Proteomics data formats are standardized file formats defined by the Human Proteomics Standards Initiative (PSI 2011) and based on XML Schema (XML 2011). The standards are part of larger-scale standardization efforts which aim to facilitate data exchange and mediate between various types of software, databases, and file systems (BioSharing 2011; MIBBI 2011; OBO 2011; ISA-TAB 2011). The standards evolve in response to new technological developments. In most cases, a standard is associated with a document type definition which software can use to check if a file conforms to the standard, and tools for conversion into other formats. The reference to the XML schema of the data format used is found at the top of each XML file.
mzML: The data measured by MS is normally stored as a collection of spectra or ion chromatograms in a format called mzML. Each spectrum has some metadata associated with...
- BioSharing (2011) http://biosharing.org. Accessed 24 May 2011
- ISA (2011) Investigation/Study/Assay Infrastructure. http://isatab.sourceforge.net. Accessed 24 May 2011
- MIBBI (2011) Minimum Information for biological and biomedical investigations. http://mibbi.org. Accessed 24 May 2011
- OBO (2011) Open biomedical ontologies. http://www.obofoundry.org. Accessed 24 May 2011
- PSI (2011) Human Proteomics Standards Initiative. http://www.psidev.info. Accessed 24 May 2011
- XML (2011) XML Schema. http://www.w3.org/2001/XMLSchema-instance. Accessed 24 May 2011