Mass spectrometry data format

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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 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.

Contents

[edit] Open formats

[edit] 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 a ASCII based format and therefore not very compact even though it includes standards for file compression. JCAMP was officially released in 1988.[1] JCAMP was found impractical for today's large MS data sets, but it is still used for exchanging moderate numbers of spectra. IUPAC[2] is currently in charge and the latest protocol is from 2005.[3]

[edit] 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.[4] 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.

[edit] mzXML

mzXML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data.[5][6] Most mass spectrometers do not directly produce mzXML data, but there are several tools available that generate mzXML files from native acquisition files.

[edit] mzData

The Human Proteome Organization (HUPO) has developed a common file format called mzData which offers similar functionality to mzXML.[7]

[edit] 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.[7][8][9] As of 1 June 2008, mzML 1.0.0 is ready. This format was officially released at the 2008 American Society for Mass Spectrometry Meeting.[10]

On 1 June 2009, mzML 1.1.0 was released.[11] There are no planned further changes as of mid 2010.

[edit] 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 directory format
    • PerkinElmer TurboMass file format
  • .WIFF : ABI/Sciex (QSTAR and QTRAP instrument) file format
  • .YEP : Bruker instrument data format

[edit] Software

[edit] Viewers

There are several viewers for mzXML and mzData: PEAKS,[12] Insilicos,[13] MS-Spectre,[14] TOPPView,[15] Spectra Viewer,[16] SeeMS,[17] msInspect,[18] and Mascot Distiller.[19] There is one viewer for mzML: jmzML.[20]

[edit] 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[21][22]
FileConverter: A command line tool that converts to/from various mass spectrometry formats,[23] part of TOPP[24]

Known converters for mzXML:

The Institute for Systems Biology maintains a list of converters[25]

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.[26]
ReAdW:[27] The Institute for Systems Biology command line converter for Thermo RAW files, part of the TransProteomicPipeline.[28]
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[29] and PerkinElmer[30]
Sashimi, an open source project[31] 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
Wiff2dta for SCIEX/ABI SCIEX/ABI Analyst format to mzXML, DTA, MGF and PMF

[edit] Compressors

mzSquash: Command line utilities and Java API to compress and uncompress mzML files.[32]

[edit] Libraries

pymzML[33]: A free Python module to interface mzML data in Python based on cElementTree[34] with additional tools for MS-informatics. It offers easy access to mass spectrometry data that allows the rapid development of tools, a very fast parser for mzML data and a set of functions to compare or handle spectra.[35]

[edit] See also

[edit] References

  1. ^ R.S. McDonald and P.A. Wilks; "JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer-Readable Form"; Applied Spectroscopy, Vol. 42, No. 1, January 1988, pp 151-162.
  2. ^ IUPAC CPEP Subcommittee on Electronic Data Standards
  3. ^ JCAMP-DX V.6.00 for CHROMATOGRAPHY and MASS SPECTROMETRY HYPHENATED METHODS (IUPAC Technical Note 2005); J. Hau, P. Lampen, R.J. Lancashire, R.S. McDonald, P.S. McIntyre, D.N. Rutledge, W. Schrader, A.N. Davies
  4. ^ ASTM E1947 - 98(2009) Standard Specification for Analytical Data Interchange Protocol for Chromatographic Data
  5. ^ 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:10.1038/nbt1031. PMID 15529173. 
  6. ^ 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:10.1586/14789450.2.6.839. PMID 17342793. 
  7. ^ 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:10.1002/pmic.200700658. PMID 17907277. 
  8. ^ "mzML". http://www.psidev.info/index.php?q=node/257. Retrieved 2007-10-11. 
  9. ^ Deutsch EW (2008). "mzML: A single, unifying data format for mass spectrometer output". Proteomics 8 (14): 2776–7. doi:10.1002/pmic.200890049. PMID 18655045. 
  10. ^ HUPO Proteomics Standards Initiative. "Hupo-Psi". Psidev.info. http://www.psidev.info/index.php?q=node/257. Retrieved 29 November 2011. 
  11. ^ HUPO Proteomics Standards Initiative. "mzML 1.1.0 Specification | HUPO Proteomics Standards Initiative". Psidev.info. http://www.psidev.info/index.php?q=node/257. Retrieved 29 November 2011. 
  12. ^ "BSI: PEAKS website". Bioinfor.com. http://www.bioinfor.com/peaks. Retrieved 29 November 2011. 
  13. ^ Insilicos website
  14. ^ "MS-Spectre website". Ms-spectre.sourceforge.net. http://ms-spectre.sourceforge.net. Retrieved 29 November 2011. 
  15. ^ "OpenMS and TOPP website". Open-ms.sourceforge.net. http://open-ms.sourceforge.net. Retrieved 29 November 2011. 
  16. ^ "An open source viewer developed under academic projects". Staff.icar.cnr.it. http://staff.icar.cnr.it/cannataro/projects/SpectraViewer/. Retrieved 29 November 2011. 
  17. ^ "An open source viewer developed by Matt Chambers at Vanderbilt". Proteowizard.sourceforge.net. http://proteowizard.sourceforge.net. Retrieved 29 November 2011. 
  18. ^ "An open source viewer developed by at the Fred Hutchinson Cancer Center". Proteomics.fhcrc.org. http://proteomics.fhcrc.org/CPL/msinspect.html. Retrieved 29 November 2011. 
  19. ^ Matrix Science Limited. "Commercial software with free viewer mode for mzXML and many proprietary formats". Matrixscience.com. http://www.matrixscience.com/distiller.html. Retrieved 29 November 2011. 
  20. ^ "jmzML". Google. http://code.google.com/p/jmzml/. Retrieved 29 November 2011. 
  21. ^ Hermes[dead link]
  22. ^ "Hermes website". Icecoffee.ch. http://www.icecoffee.ch/hermes/converter.html. Retrieved 29 November 2011. 
  23. ^ a b "FileConverter". Open-ms.sourceforge.net. http://open-ms.sourceforge.net. Retrieved 29 November 2011. 
  24. ^ a b TOPP[dead link]
  25. ^ "mzXML". http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML. Retrieved 2008-06-30. 
  26. ^ "ProteoWizard". http://proteowizard.sourceforge.net. Retrieved 2008-06-30. 
  27. ^ "ReAdW". Tools.proteomecenter.org. http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW. Retrieved 29 November 2011. 
  28. ^ "TransProteomicPipeline". Tools.proteomecenter.org. 25 May 2011. http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP. Retrieved 29 November 2011. 
  29. ^ [1][dead link]
  30. ^ "Gas Chromatography (GC)". PerkinElmer. http://www.perkinelmer.com/gc. Retrieved 29 November 2011. 
  31. ^ "Sashimi". http://sashimi.sourceforge.net. Retrieved 2007-10-11. 
  32. ^ "mzSquash". Sourceforge.net. https://sourceforge.net/projects/mzsquash/. Retrieved 29 November 2011. 
  33. ^ pymzml.github.com
  34. ^ The cElementTree Module
  35. ^ Bald, Till; Barth, Johannes; Niehues, Anna; Specht, Michael; Hippler, Michael; Fufezan, Christian (2012). "pymzML - Python module for high throughput bioinformatics on mass spectrometry data". Bioinformatics. doi:10.1093/bioinformatics/bts066. 
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