imzML: Imaging Mass Spectrometry Markup Language: A Common Data Format for Mass Spectrometry Imaging

Abstract

Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

Novel mass spectrometry imaging software assisting labeled normalization and quantitation of drugs and neuropeptides directly in tissue sections

“…The peak intensity of the drug of an ROI in a dosed tissue section is subsequently converted to drug concentration. The software in the present version is only able to read MALDI MSI raw data from Bruker Daltonics MS instruments, but is being prepared to read other data formats as well such as imzML [19].…”

Inclusive sharing of mass spectrometry imaging data requires a converter for all

“…Currently, MSI data are collected and stored in proprietary vendor formats which limit the ease of exchange and the data analysis software that can be used. The imzML standard [1] was developed as part of the COMPUTIS project to provide a unified format for data storage of mass spectrometry imaging experiments, by extending the open mass spectrometry format mzML [2,3]. mzML was designed for storing MS experiments consisting of small numbers of spectra, and because of this it is not appropriate for large imaging experiments.…”

Myc Expression Drives Aberrant Lipid Metabolism in Lung Cancer

“…Data from MALDI-MSI were converted to imzML format for processing (22). Using an in-house R script ions were retained above a threshold intensity and the m/z ratio of ions detected were summed across integral regions of 10 ppm to allow for alterations in m/z mass accuracy across the experiment ("binning").…”