What is mzXML good for?

mzXML (extensible markup language) is one of the pioneering data formats for mass spectrometry-based proteomics data collection. It is an open data format that has benefited and evolved as a result of the input of many groups, and it continues to evolve. Due to its dynamic history, its structure, purpose and applicability have all changed with time, meaning that groups that have looked at the standard at different points during its evolution have differing impressions of the usefulness of mzXML. In discussing mzXML, it is important to understand what mzXML is not. First, mzXML does not capture the raw data. Second, mzXML is not sufficient for regulatory submission. Third, mzXML is not optimized for computation and, finally, mzXML does not capture the experiment design. In general, it is the authors' opinion that XML is not a panacea for bioinformatics or a substitute for good data representation, and groups that want to use mzXML (or other XML-based representations) directly for data storage or computation will encounter performance and scalability problems. With these limitations in mind, the authors conclude that mzXML is, nonetheless, an indispensable data exchange format for proteomics.