Project Details:

JCAMP-DX-CD: Standardization of Data and Meta-data formats for Circular Dichroism and Synchrotron Radiation Circular Dichroism Spectroscopy, and interface with the Protein Circular Dichroism Data Bank

This project will extend the JCAMP-DX initiative for use in Circular Dichroism (CD) and Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy. It is aimed at interfacing with the Protein Circular Dichroism Data Bank, a new online facility for data sharing and access to CD and SRCD spectra with their associated metadata.

Circular Dichroism (CD) spectroscopy is a technique employed in numerous chemical and biochemical labs around the world sometimes as support for verifying data from another method, sometimes as the key approach to gaining a result of significant impact in its own right. In the past 3 years, more than 5000 papers have included CD studies. Today there are a number of CD spectrophotometer manufacturers and all employ their own data output formats when creating output files. Extra meta-data that can be recorded in addition to the raw spectroscopic data often get left out of these files even though this information is of vital importance for establishing and reproducing how the experiments were set up. In addition, the related technique of Synchrotron Radiation Circular Dichroism (SRCD) has been developed at synchrotron site around the work. Recognising that this is a propitious time to enable the access to, and data sharing of, CD data we have developed a new online resource, the Protein Circular Dichroism Data Bank (PCDDB). The PCDDB is a repository of CD spectral data together with its associated meta-data, and we believe the establishment of a JCAMP-DX format for CD would be a project that would provide the field with an agreed format approved by the IUPAC, and an appropriate one for users of the PCDDB data to download the data.

July 2011 update - We have completed the creation of the JCAMP format for Circular Dichroism spectroscopy, coordinating the fields with those included in the Protein Circular Dichroism Data Bank (PCDDB). It includes both raw and processed data and all the necessary metadata needed for interpretation. We have tested it with JSpecView plotting software and it is works well. We are now in the process of writing parsers to convert all outputs of all instrument manufacturers to this JCAMP format. The PhD student who has been involved in this is writing up the work for his thesis (due date Sept 2011). Once that is completed, we will write it up for the JCAMP consultation website and then publication in Pure and Applied Chemistry. To enable us to complete this work, the co-director, Dr. Robert Janes, has just obtained a short term grant from the U.K. Biotechnology and Biological Science Research Council (BBSRC) to pay for a salary for the student to complete the work on the parsers and papers once his thesis is submitted, so we can ensure the project is fully completed. Having IUPAC support for the project was critical obtaining this grant.

Prof. Wallace will present this project at the CD2011 meeting in Oxford in July 2011, which is the major international meeting for the CD community this year. We also confirm that our International Technical Advisory Board (consisting of representatives of all CD instrument manufacturers and all SRCD beamline scientists) and our International Scientific Advisory Board (consisting of senior members of the user community) for the Protein Circular Dichroism Data Bank have both approved and were highly supportive of this concept at their most recent meetings.

Oct 2012 - JCAMP-DX for circular dichroism spectra and metadata (IUPAC Recommendations 2012) published in Pure Appl. Chem., 2012, Vol. 84, No. 10, pp. 2171-2182; http://dx.doi.org/10.1351/PAC-REC-12-02-03

 

Last updated 7 June 2013

• Wallace, Bonnie

• Cammack, Richard
• Gekko, Kunihiko
• Janes, Robert
• Kelly, Sharon
• Rodger, Alison
• Sutherland, John