Mass spectrometry is a scientific technique for measuring the mass 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 spectromters 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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Open formats
mzXML
mzXML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data.[1][2] Most mass spectrometers do not directly produce mzXML data, but there are several tools available that generate mzXML files from native acquisition files.
mzData
The Human Proteome Organization (HUPO) has developed a common file format called mzData which offers similar functionality to mzXML.[3]
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.[3][4] 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.[5]
Proprietary formats
Here is a list of different file format extensions :
- .BAF : Bruker instrument data format
- .D : Agilent QTOF instrument data format
- .FID : Bruker instrument data format
- .PKL : MassLynx associated format
- .RAW :
- Thermo Xcalibur file format
- Micromass MassLynx file format
- .WIFF : ABI/Sciex (QSTAR and QTRAP instrument) file format
- .YEP : Bruker instrument data format
Softwares
Viewers
There are several viewers for mzXML and mzData: PEAKS,[6] Insilicos,[7] MS-Spectre,[8] TOPPView,[9] Spectra Viewer,[10] SeeMS,[11] msInspect,[12] and Mascot Distiller.[13] There is one viewer for mzML: jmzML.[14]
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[15][16]
- FileConverter: A command line tool that converts to/from various mass spectrometry formats,[17] part of TOPP[18]
Known converters for mzXML:
- The Institute for Systems Biology maintains a list of converters[19]
Known converters for mzML:
- 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[20].
- ReAdW:[21] The Institute for Systems Biology command line converter for Thermo RAW files, part of the TransProteomicPipeline.[22]
- FileConverter: A command line tool that converts to/from various mass spectrometry formats,[23] part of TOPP[24]
Converters for proprietary formats:
- CompassXport, Bruker's free tool generating mzXML (and now mzData)[citation needed] 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[25]
- Sashimi, an open source project[26] offering a collection of converter programs for some common mass spectrometric file formats. Currently available converters are :
- MassWolf, for Micromass MassLynx .Raw format
- mzStar, for SCIEX/ABI SCIEX/ABI Analyst format
- ReAdW, for ThermoFinnigan Xcalibur format
Compressors
- mzSquash: Command line utilities and Java API to compress and uncompress mzML files.[27]
See also
References
- ^ 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 (2004). "A common open representation of mass spectrometry data and its application to proteomics research". Nat. Biotechnol. 22 (11): 1459–66. doi:. PMID 15529173.
- ^ Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA (2005). "What is mzXML good for?". Expert review of proteomics 2 (6): 839–45. doi:. PMID 17342793.
- ^ a b Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H (2007). "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". Proteomics 7 (19): 3436–40. doi:. PMID 17907277.
- ^ "mzML". http://www.psidev.info/index.php?q=node/257. Retrieved 2007-10-11.
- ^ HUPO-PSI
- ^ BSI: PEAKS website
- ^ Insilicos website
- ^ MS-Spectre website
- ^ OpenMS and TOPP website
- ^ An open source viewer developed under academic projects
- ^ An open source viewer developed by Matt Chambers at Vanderbilt
- ^ An open source viewer developed by at the Fred Hutchinson Cancer Center
- ^ Commercial software with free viewer mode for mzXML and many proprietary formats
- ^ jmzML
- ^ Hermes
- ^ Hermes website
- ^ FileConverter
- ^ TOPP
- ^ "mzXML". http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML. Retrieved 2008-06-30.
- ^ "ProteoWizard". http://proteowizard.sourceforge.net. Retrieved 2008-06-30.
- ^ ReAdW
- ^ TransProteomicPipeline
- ^ FileConverter
- ^ TOPP
- ^ http://www.sisweb.com/software/masstransit.htm
- ^ "Sashimi". http://sashimi.sourceforge.net. Retrieved 2007-10-11.
- ^ mzSquash
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