Mass spectrometry data formats

Here the main mass spectrometry data formats are listed.

mzXML
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.

mzData
The Human Proteome Organization (HUPO) has developed a common file format called mzData which offers similar functionality to mzXML.

mzML
The existence of the two above standard formats for proteomics data is an undesirable state. Thus, mzData and mzXML developers are currently developing the joint format called mzML.

Viewers
Known viewers for mzXML and mzData:
 * Complex Tracker (CovalX website)
 * Insilicos (Insilicos website)
 * MS-Spectre (MS-Spectre website)
 * TOPPView (OpenMS and TOPP website)