Error-Free Data Visualization and Processing through imzML and mzML Validation

Open data formats are key to facilitating data processing, sharing, and integration. The imzML format (http://imzml.org/) has drastically improved these aspects of mass spectrometry imaging data. Efficient processing of data depends on data sets which are consistent and adhere to the specifications; however, this is not always the case. Here we present a validation tool for data stored in both imzML and the HUPO-PSI mass spectrometery counterpart, mzML, to identify any deviations from the published (i)mzML standard which could cause issues for the user when visualizing or processing data. The tool is released in two forms, a graphical user interface (GUI) for ease of use, and a command line version to fit into existing workflows and pipelines. When certain known issues are encountered, such as the presence of negative values for the location of the binary data, the validator resolves the issue automatically upon saving. The GUI version of the validator also allows editing of the metadata included within t...