imzML — A common data format for the flexible exchange and processing of mass spectrometry imaging data

• Published in: Journal of proteomics Vol. 75; no. 16; pp. 5106 - 5110
• Main Authors: Schramm, Thorsten, Hester, Zoë, Klinkert, Ivo, Both, Jean-Pierre, Heeren, Ron M.A., Brunelle, Alain, Laprévote, Olivier, Desbenoit, Nicolas, Robbe, Marie-France, Stoeckli, Markus, Spengler, Bernhard, Römpp, Andreas
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.08.2012; Elsevier
• Subjects: biomedical research; Chemical Sciences; Computer Science; computer software; Data format; Data Interpretation, Statistical; Data processing; Databases, Protein; Diagnostic Imaging; Diagnostic Imaging - instrumentation; Diagnostic Imaging - methods; Electronic Data Processing; Electronic Data Processing - methods; image analysis; Information Dissemination; Information Dissemination - methods; Information Storage and Retrieval; Information Storage and Retrieval - methods; instrumentation; mass spectrometry; Mass Spectrometry - instrumentation; Mass Spectrometry - methods; Mass spectrometry imaging; methods; Models, Biological; new methods; Organic chemistry; Signal and Image Processing; Software; spectral analysis; Standardization; User-Computer Interface; Data processing; Data format; Mass spectrometry imaging; Standardization; mass spectrometry imaging; spectrum analysis; signal processing; XML; data processing; data format; data format imzML; standardization; Mass spectral data; mzML format
• ISSN: 1874-3919; 1876-7737; 1876-7737
• DOI: 10.1016/j.jprot.2012.07.026

The application of mass spectrometry imaging (MS imaging) is rapidly growing with a constantly increasing number of different instrumental systems and software tools. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software. imzML data is divided in two files which are linked by a universally unique identifier (UUID). Experimental details are stored in an XML file which is based on the HUPO-PSI format mzML. Information is provided in the form of a ‘controlled vocabulary’ (CV) in order to unequivocally describe the parameters and to avoid redundancy in nomenclature. Mass spectral data are stored in a binary file in order to allow efficient storage. imzML is supported by a growing number of software tools. Users will be no longer limited to proprietary software, but are able to use the processing software best suited for a specific question or application. MS imaging data from different instruments can be converted to imzML and displayed with identical parameters in one software package for easier comparison. All technical details necessary to implement imzML and additional background information is available at www.imzml.org. This article is part of a Special Issue entitled: Imaging Mass Spectrometry: A User’s Guide to a New Technique for Biological and Biomedical Research. [Display omitted] ► Common format for exchange of mass spectrometry imaging data ► Comprehensive and efficient description of MS imaging experiments ► Converters and data analysis tools are available. ► Flexible structure allows adaption to new methods and instruments.