Formats:mzXML

A data format for storage and exchange of mass spectroscopy data, developed at the ISB originally by Patrick Pedrioli.

Several versions of this format exist. Currently these are 1.0 (also called "msXML"), 2.0, 2.1 and 3.0. 2.1 is the version most commonly in use.

raw data to mzXML converters

Converters exist for several instrument/software vendors:

ReAdW: Thermo/XCalibur raw data (.RAW files) to mzXML converter
mzStar: Analyst (ABI/MDS Sciex) software's raw data (.wiff files) to mzXML converter
massWolf: MassLynx (Waters) raw data (.raw directories) to mzXML converter
CompassXport is the recommended converter for Bruker (.baf) files-- please see the page on our retired Bruker converter, mzBruker. Also see "additional resources" below.
T2DExtractor - SCIEX/ABI 4700/4800 MALDI TOFTOF Data to mzXML: Java application to convert data from a SCIEX/ABI 4000 series MALDI TOFTOF instruments into mzXML format. This application is provided courtesy of Phil Andrews lab at the University of Michigan. Please see this link: [1]

out2linux.pl: working with Bioworks Sequest output. See Software:Out2XML page.
working with Bruker ion trap and DataAnalysis software: Software:da2tpp page coming soon!

Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti R, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK Jr, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. (2004) "A Common Open Representation of Mass Spectrometry Data and its Application in a Proteomics Research Environment." Nature Biotechnology 22(11):1459-1466. Download PDF
Learn more at the Sashimi project website, the original website for the mzXML format.