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Mass spectrometry data formats

Here the main mass spectrometry data formats are listed.



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. An open source project known as Sashimi[3] offers a collection of converter programs for some common mass spectrometric file formats. Currently there are converters available at Sashimi for ThermoFinnigan (Xcalibur), MassWolf (Micromass MassLynx) and mzStar (SCIEX/ABI Analyst). Bruker's free CompassXport tool will nicely generate mzXML (and now mzData) files for many of their native file formats.


The Human Proteome Organization (HUPO) has developed a common file format called mzData which offers similar functionality to mzXML.[4]


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.[4][5]


Known viewers for mzXML and mzData:

Complex Tracker (CovalX website)
Insilicos (Insilicos website)
MS-Spectre (MS-Spectre website)
TOPPView (OpenMS and TOPP website)

See also


  1. ^ 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.
  2. ^ Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA (2005). "What is mzXML good for?". Expert review of proteomics 2 (6): 839–45. PMID 17342793.
  3. ^ Sashimi. Retrieved on 2007-10-11.
  4. ^ 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.
  5. ^ mzML. Retrieved on 2007-10-11.
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Mass_spectrometry_data_formats". A list of authors is available in Wikipedia.
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