Mass spectrometry is a scientific technique for measuring the mass to charge ratio of ions. It is often coupled to chromatographic techniques such as gas- or liquid chromatography and has found widespread adoption in the fields of analytical chemistry and biochemistry where it can be used to identify and characterize small molecules and proteins (proteomics). The large volume of data produced in a typical mass spectrometry experiment requires that computers be used for data storage and processing. Over the years, different manufacturers of mass spectrometers have developed various proprietary data formats for handling such data which makes it difficult for academic scientists to directly manipulate their data. To address this limitation, several open, XML-based data formats have recently been developed by the Trans-Proteomic Pipeline at the Institute for Systems Biology to facilitate data manipulation and innovation in the public sector. These data formats are described here.
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JCAMP-DX
This format was one of the earliest attempts to supply a standardized file format for data exchange in mass spectrometry. JCAMP-DX was initially developed for infrared spectrometry. JCAMP-DX is an ASCII based format and therefore not very compact even though it includes standards for file compression. JCAMP was officially released in 1988. JCAMP was found impractical for today's large MS data sets, but it is still used for exchanging moderate numbers of spectra. IUPAC is currently in charge and the latest protocol is from 2005.
ANDI-MS or netCDF
The ANalytical Data Interchange format for Mass Spectrometry is a format for exchanging data. Many mass spectrometry software packages can read or write ANDI files. ANDI is specified in the ASTM E1947 Standard. ANDI is based on netCDF which is a software tool library for writing and reading data files. ANDI was initially developed for chromatography-MS data and therefore was not used in the proteomics gold rush where new formats based on XML were developed.
mzData
mzData was the first attempt by the Proteomics Standards Initiative (PSI) from the Human Proteome Organization (HUPO) to create a standardized format for Mass Spectrometry data. This format is now deprecated, and replaced by mzML.
mzXML
mzXML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data. This format was developed at the Seattle Proteome Center/Institute for Systems Biology while the HUPO-PSI was trying to specify the standardized mzData format, and is still in use in the proteomics community.
mzML
As two formats (mzData and mzXML) for representing the same information is an undesirable state, a joint effort was set by HUPO-PSI, the SPC/ISB and instrument vendors to create a unified standard borrowing the best aspects of both mzData and mzXML, and intended to replace them. Originally called dataXML, it was officially announced as mzML. The first specification was published in June 2008. This format was officially released at the 2008 American Society for Mass Spectrometry Meeting, and is since then relatively stable with very few updates. On 1 June 2009, mzML 1.1.0 was released. There are no planned further changes as of 2013.
Proprietary formats
Below is a table of different file format extensions.
(*) Note that the RAW formats of each vendor are not interchangeable; software from one cannot handle the RAW files from another.
(**) Micromass was acquired by Waters in 1997
(***) Finnigan is a division of Thermo
Viewers
There are several viewers for mzXML, mzML and mzData: MZmine, PEAKS, Insilicos, MS-Spectre, TOPPView (mzXML, mzML and mzData), Spectra Viewer, SeeMS, msInspect, jmzML and Mascot Distiller.
Converters
Known converters for mzData to mzXML:
Hermes: A Java "mzData, mzXML, mzML" converter to all directions: publicly available, runs with a graphical user interface, by the Institute of Molecular Systems Biology, ETH Zurich FileConverter: A command line tool that converts to/from various mass spectrometry formats, part of TOPPKnown converters for mzXML:
The Institute for Systems Biology maintains a list of convertersKnown converters for mzML:
msConvert: A command line tool converting to/from various mass spectrometry formats. A GUI is also available for Windows users. ReAdW: The Institute for Systems Biology command line converter for Thermo RAW files, part of the TransProteomicPipeline. The latest update of this tool was made in September 2009. Users are now redirected by the TPP development team to use the msConvert software (see above). FileConverter: A command line tool that converts to/from various mass spectrometry formats, part of TOPPConverters for proprietary formats:
msConvert: A command line tool converting to/from various mass spectrometry formats including multiple proprietary formats. A GUI is also available for Windows users. CompassXport, Bruker's free tool generating mzXML (and now mzData) files for many of their native file formats (.baf). MASSTransit, a software to change data between proprietary formats, by Palisade Corporation and distributed by Scientific Instrument Services, Inc and PerkinElmer Aston, native support for several Agilent Chemstation, Agilent Masshunter and Thermo Isodat file formats unfinnigan, native support for Finnigan (*.RAW) file formats OpenChrom, an open source software with support to convert various native file formatsCurrently available converters are :