MzXML

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mzXML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data. Most mass spectrometers do not directly produce mzXML data, but there are several tools available that generate mzXML files from native acquisition files. An open source project known as Sashimi offers a collection of converter programs for some common mass spectrometric file formats. Currently there are converters available at Sashimi for ThermoFinnigan (Xcalibur), MassWolf (Micromass MassLynx) and mzStar (SCIEX/ABI Analyst). Bruker's free CompassXport tool will nicely generate mzXML (and now mzData) files for many of their native file formats. Recently Human Proteome Organisation (HUPO) has developed a common file format called mzData which offers similar functionality to mzXML.

Known viewers for mzXML and mzData:

Complex Tracker (CovalX web site)
Insilicos (Insilicos web site)


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