Mass spectrometry data formats

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.cite journal |author=Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R |title=A common open representation of mass spectrometry data and its application to proteomics research |journal=Nat. Biotechnol. |volume=22 |issue=11 |pages=1459–66 |year=2004 |pmid=15529173 |doi=10.1038/nbt1031] cite journal |author=Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA |title=What is mzXML good for? |journal=Expert review of proteomics |volume=2 |issue=6 |pages=839–45 |year=2005 |pmid=17342793 |doi=] 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 [ cite web|url=http://sashimi.sourceforge.net |title=Sashimi |accessdate=2007-10-11 ] offers a collection of converter programs for some common mass spectrometric file formats. Currently there are converters available at Sashimi for ThermoFinnigan (Xcalibur format using ReAdW), Micromass (MassLynx format using MassWolf) and SCIEX/ABI (SCIEX/ABI Analyst using mzStar). 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.cite journal |author=Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H |title=Five years of progress in the Standardization of Proteomics Data 4(th) Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France |journal=Proteomics |volume=7 |issue=19 |pages=3436–40 |year=2007 |pmid=17907277 |doi=10.1002/pmic.200700658]

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. [ cite web|url=http://www.psidev.info/index.php?q=node/257 |title=mzML |accessdate=2007-10-11 ] As of 2008-06-01, mzML 1.0.0 is ready. This format was officially released at the 2008 American Society for Mass Spectrometry Meeting [cite web|url=http://www.psidev.info/index.php?q=node/257 |title=mzML |accessdate=2008-06-30] . For details of the current status of mzML support see the [http://www.psidev.info/index.php?q=node/257 HUPO-PSI ] Project page.

Viewers

Known viewers for mzXML and mzData: :Insilicos ( [http://www.insilicos.com Insilicos website] ):MS-Spectre ( [http://ms-spectre.sourceforge.net MS-Spectre website] ):TOPPView ( [http://open-ms.sourceforge.net OpenMS and TOPP website] ):Spectra Viewer ( [http://staff.icar.cnr.it/cannataro/projects/SpectraViewer/ An open source viewer developed under academic projects ] ):SeeMS ( [http://proteowizard.sourceforge.net An open source viewer developed by Matt Chambers at Vanderbilt ] ):msInspect ( [http://proteomics.fhcrc.org/CPL/msinspect.html An open source viewer developed by at the Fred Hutchinson Cancer Center ] )

Converters

Known converters for mzData to mzXML: : [http://blogs.ethz.ch/andreas/2008/05/09/mzdata-to-mzxml-converter/ Hermes] : Java based application that runs with a graphical user interface, Institute of Molecular Systems Biology, ETH Zurich: [http://open-ms.sourceforge.net FileConverter] : A command line tool that converts to/from various mass spectrometry formats, part of [http://open-ms.sourceforge.net/TOPP.php TOPP] Known converters for mzXML: : The Institute for Systems Biology maintains a [http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML list] of converters [cite web|url=http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML |title=mzXML |accessdate=2008-06-30] Known converters for mzML: : [http://proteowizard.sourceforge.net msConvert] : A command line tool that converts to/from various mass spectrometry formats; The reference implementation of mzML has been provided by the ProteoWizard project [cite web|url=http://proteowizard.sourceforge.net |title=ProteoWizard |accessdate=2008-06-30] . : [http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW ReAdW] : The Institute for Systems Biology command line converter for Thermo RAW files, part of the [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP TransProteomicPipeline]

ee also

*Mass spectrometry software

References


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