Award details

JCAMP-DX-CD: A Universal Format for CD and SRCD Spectroscopy Enabling Data Standardisation and Data Sharing

Reference	BB/I023887/1
Principal Investigator / Supervisor	Dr Robert Janes
Co-Investigators / Co-Supervisors
Institution	Queen Mary University of London
Department	Sch of Biological and Chemical Sciences
Funding type	Research
Value (£)	118,022
Status	Completed
Type	Research Grant
Start date	03/10/2011
End date	02/04/2013
Duration	18 months

Abstract

Circular dichroism (CD) spectroscopy is a major technique used in structural biology by both academic and industrial labs. All manufacturers of CD spectrophotometers generate their own data formats, and record meta-data associated with instrument and sample parameters. Often only limited meta-data are recorded and crucial parameters may be lost, making it difficult for either the originator or others to repeat an experiment or to assess the validity of a published experiment. Synchrotron radiation CD (SRCD) is a newer version of this technique. There are currently 14 SRCD beamlines worldwide, including ones at the UK Diamond Light Source. Some beamlines have coordinated their efforts to create similar (but not identical and not sharable) data formats, but there is no common data format used by CD instruments and beamlines. To enhance public data sharing and creation of 'good practice' standards and interoperability/cross-comparisons between instruments and experiments, a standardised format is required which includes full documentation of the experimental conditions. To date, instrument manufacturers and beamlines have been unwilling to adopt the formats of others. This project will generate an independent format for CD/SRCD data based on the long established International Union of Pure and Applied Chemistry (IUPAC) Joint Committee on Atomic and Molecular Physical Data Exchange (JCAMP-DX). In preparation for this, we have contacted senior representatives of all CD instrument manufacturers and beamlines, and they have agreed to accept that as 'impartial' users we are in an excellent position to create this format/standard and the associated software. Since it will be comparable to the JCAMP-DX protocols currently in use by nine other spectroscopic techniques it should promote and enhance cross-disciplinary studies. In addition, it will provide an enhancement to the DICHROWEB server and Protein Circular Dichroism Data Bank resources.

Summary

Circular dichroism (CD) spectroscopy is a structural biology method that is widely used in academia and industry for the characterisation of proteins, nucleic acids, and sugars. At present there are four different types of lab-based commercial CD instruments and 14 different synchrotron radiation circular dichroism (SRCD) beamline instruments that are used to collect CD data. All of them produce output data in different formats and therefore these data are 'machine-dependent'; parameters used by one instrument from one manufacturer are not readable by instruments from another manufacturer, or by beamlines. The aims of this project are to create a common format that will contain all the relevant spectral data and machine (and sample) parameters (the 'meta-data') produced by these instruments, and to create the software to enable the interconversion between it and the existing formats of manufacturers and beamlines. We have obtained the imprimatur of the International Union of Pure and Applied Chemistry to create a (Joint Committee on Atomic and Molecular Physical Data Exchange) JCAMP-DX_CD format that will fulfill this remit. Although none of the individual instrument manufacturers or beamline scientists wishes to use the format of another company or beamline, all of them have agreed that they are willing to have us create this common format for universal usage. This will enable data sharing and standardisation and interoperability between instruments as well as cross-disciplinary usage with other spectroscopic methods, of which there are currently nine, that have JCAMP-DX formats.

Impact Summary

Circular dichroism is a method that is widely used in academia and industry (both biopharm and SME companies) for characterisation and analysis of biomacromolecules. In addition, CD is a method that has been approved for use for the characterisation of proteins for the registration of pharmaceuticals for human use and so also has a role in quality control in industry. This proposal to create a common JCAMP-DX-CD data format and standards which will enable data sharing, traceability, documentation and standards establishment. In addition, the manufacturers of CD instruments and SRCD beamlines will benefit by enabling their users to readily share data and facilitate online analyses, as well as providing interoperability between data collected on different types of CD instruments and between CD and other spectroscopic techniques currently supported by JCAMP-DX format protocols.

Committee	Research Committee C (Genes, development and STEM approaches to biology)
Research Topics	Structural Biology, Technology and Methods Development
Research Priority	Technology Development for the Biosciences
Research Initiative	Tools and Resources Development Fund (TRDF) [2006-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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