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Mass spectrometry data format

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"SeeMS" redirects here. Not to be confused with seems.

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.[1] These data formats are described here.

Open formats

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JCAMP-DX

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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.[2] Together with the American Society for Mass Spectrometry a JCAMP-DX format for mass spectrometry was developed with aim to preserve legacy data.[3]

ANDI-MS or netCDF

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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.[5]

AnIML

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AnIML is a joined effort of IUPAC and ASTM International to create an XML based standard that covers a wide variety of analytical techniques including mass spectrometry.[6]

mzData

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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.[7] This format is now deprecated, and replaced by mzML.[8]

mzXML

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mzXML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data.[9][10] 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.

YAFMS

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Yet Another Format for Mass Spectrometry (YAFMS) is a suggestion to save data in four table relational server-less database schema with data extraction and appending being exercised using SQL queries.[11]

mzML

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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.[12] The first specification was published in June 2008.[13] 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.

mzAPI

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Instead of defining new file formats and writing converters for proprietary vendor formats a group of scientists proposed to define a common application program interface to shift the burden of standards compliance to the instrument manufacturers' existing data access libraries.[14]

mz5

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The mz5 format addresses the performance problems of the previous XML based formats. It uses the mzML ontology, but saves the data using the HDF5 backend for reduced storage space requirements and improved read/write speed.[15]

imzML

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The imzML standard was proposed to exchange data from mass spectrometry imaging in a standardized XML file based on the mzML ontology. It splits experimental data into XML and spectral data in a binary file. Both files are linked by a universally unique identifier.[16]

mzDB

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mzDB saves data in an SQLite database to save on storage space and improve access times as the data points can be queried from a relational database.[17]

Toffee

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Toffee is an open lossless file format for data-independent acquisition mass spectrometry. It leverages HDF5 and aims to achieve file sizes similar to those from the proprietary and closed vendor formats.[18]

mzMLb

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mzMLb is another take on using a HDF5 backend for performant raw data saving. It, however, preserves the mzML XML data structure and stays compliant to the existing standard.[19]

Proprietary formats

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Below is a table of different file format extensions.

Company Extension File type
ACD/Labs *.spectrus Imports LC/MS and GC/MS data from most major instrument vendors listed here
Agilent
Bruker 		.D (folder) Agilent MassHunter, Agilent ChemStation, or Bruker BAF/YEP/TDF data format
Agilent/Bruker .YEP instrument data format
Agilent .AEV, .ASR ASCII Report format (for Analytical Studio Reviewer)
Bruker .BAF instrument data format
Bruker .FID instrument data format
Bruker .TDF timsTOF instrument data format
ABI/Sciex .WIFF, .WIFF2 instrument data format
ABI/Sciex .t2d 4700 and 4800 file format
ABI/Sciex .dat Voyager-DE series file format
Waters .PKL MassLynx peak list format
Thermo
PerkinElmer 		.RAW* Thermo Xcalibur
PerkinElmer TurboMass
Micromass**/Waters .RAW* (folder) Waters MassLynx
Chromtech
Finnigan***
VG 		.DAT Finnigan ITDS file format; MAT95 instrument data format
MassLab data format
Finnigan*** .MS ITS40 instrument data format
Shimadzu .QGD GCMSSolution format
Shimadzu .qgd instrument data format
Shimadzu .lcd QQQ/QTOF instrument data format
Shimadzu .spc library data format
Bruker/Varian .SMS instrument data format
Bruker/Varian .XMS instrument data format
ION-TOF .itm raw measurement data
ION-TOF .ita analysis data
Physical Electronics/ULVAC-PHI .raw* raw measurement data
Physical Electronics/ULVAC-PHI .tdc spectrum data

(*) 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

Software

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Viewers

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There are several viewers for mzXML, mzML and mzData. These viewers are of two types: Free Open Source Software (FOSS) or Proprietary.

In the FOSS viewer category, one can find MZmine,[20] mineXpert2 (mzXML, mzML, native timsTOF, xy, MGF, BafAscii)[21] MS-Spectre,[22] TOPPView (mzXML, mzML and mzData),[23] Spectra Viewer,[24] SeeMS,[25] msInspect,[26] jmzML.[27]

In the proprietary category, one can find PEAKS,[28] Insilicos,[29] Mascot Distiller,[30] Elsci Peaksel.[31]

There is a viewer for ITA images.[32] ITA and ITM images can be parsed with the pySPM python library.[33]

Converters

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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[34][35]
FileConverter: A command line tool that converts to/from various mass spectrometry formats,[36] part of TOPP[37]

Known converters for mzXML:

The Institute for Systems Biology maintains a list of converters[38]

Known converters for mzML:

msConvert:[39][40] A command line tool converting to/from various mass spectrometry formats. A GUI is also available for Windows users.
ReAdW:[41] The Institute for Systems Biology command line converter for Thermo RAW files, part of the TransProteomicPipeline.[42] 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,[36] part of TOPP[37]

Converters for proprietary formats:

msConvert:[39][40] 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)[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[43] and PerkinElmer.[44] Purchased from Palisade by John Wiley and Sons in 2020 and incorporated into KnowItAll Spectroscopy software.(list of file formats supported).
Aston,[45] native support for several Agilent Chemstation, Agilent Masshunter and Thermo Isodat file formats
unfinnigan,[46] native support for Finnigan (*.RAW) file formats
OpenChrom, an open source software with support to convert various native file formats including its own open .ocb format to store chromatograms, peaks and identification results[47]

Currently available converters are :

MassWolf, for Micromass MassLynx .Raw format
mzStar, for SCIEX/ABI SCIEX/ABI Analyst format
wiff2dta[48] for SCIEX/ABI SCIEX/ABI Analyst format to mzXML, DTA, MGF and PMF

See also

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References

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  1. ^ Deutsch EW (December 2012). "File formats commonly used in mass spectrometry proteomics". Molecular & Cellular Proteomics. 11 (12): 1612–21. doi:10.1074/mcp.R112.019695. PMC 3518119. PMID 22956731.
  2. ^ McDonald, Robert S.; Wilks, Paul A. (1988). "JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form" (PDF). Applied Spectroscopy. 42 (1): 151–162. Bibcode:1988ApSpe..42..151M. doi:10.1366/0003702884428734.
  3. ^ Lampen P, Hillig H, Davies AN, Linscheid M (December 1994). "JCAMP-DX for mass spectrometry". Applied Spectroscopy. 48 (12): 1545–52. Bibcode:1994ApSpe..48.1545L. doi:10.1366/0003702944027840. S2CID 96773027.
  4. ^ ASTM E1947 – 98(2009) Standard Specification for Analytical Data Interchange Protocol for Chromatographic Data
  5. ^ Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, et al. (January 2014). "Controlled vocabularies and ontologies in proteomics: overview, principles and practice". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1844 (1 Pt A): 98–107. doi:10.1016/j.bbapap.2013.02.017. PMC 3898906. PMID 23429179.
  6. ^ Davies, Tony (2007). "Herding AnIMLs (no, it's not a spelling mistake): Update on the IUPAC and ASTM Collaboration on Analytical Data Standards". Chemistry International. 29 (6).
  7. ^ Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, et al. (October 2007). "Five years of progress in the Standardization of Proteomics Data 4th 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. S2CID 22837325.
  8. ^ "mzData". HUPO-PSI. Archived from the original on 7 July 2018. Retrieved 26 April 2021.
  9. ^ Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, et al. (November 2004). "A common open representation of mass spectrometry data and its application to proteomics research". Nature Biotechnology. 22 (11): 1459–66. doi:10.1038/nbt1031. PMID 15529173. S2CID 25734712.
  10. ^ Lin SM, Zhu L, Winter AQ, Sasinowski M, Kibbe WA (December 2005). "What is mzXML good for?". Expert Review of Proteomics. 2 (6): 839–45. doi:10.1586/14789450.2.6.839. PMID 16307524. S2CID 24914725.
  11. ^ Shah AR, Davidson J, Monroe ME, Mayampurath AM, Danielson WF, Shi Y, et al. (October 2010). "An efficient data format for mass spectrometry-based proteomics". Journal of the American Society for Mass Spectrometry. 21 (10): 1784–8. doi:10.1016/j.jasms.2010.06.014. PMID 20674389.
  12. ^ "mzML". HUPO-Proteomics Standards Initiative. Retrieved 19 April 2013.
  13. ^ Deutsch E (July 2008). "mzML: a single, unifying data format for mass spectrometer output". Proteomics. 8 (14): 2776–7. doi:10.1002/pmic.200890049. PMID 18655045. S2CID 28297899.
  14. ^ Askenazi M, Parikh JR, Marto JA (April 2009). "mzAPI: a new strategy for efficiently sharing mass spectrometry data". Nature Methods. 6 (4): 240–1. doi:10.1038/nmeth0409-240. PMC 2691659. PMID 19333238.
  15. ^ Wilhelm M, Kirchner M, Steen JA, Steen H (January 2012). "mz5: space- and time-efficient storage of mass spectrometry data sets". Molecular & Cellular Proteomics. 11 (1): O111.011379. doi:10.1074/mcp.O111.011379. PMC 3270111. PMID 21960719.
  16. ^ Schramm T, Hester Z, Klinkert I, Both JP, Heeren RM, Brunelle A, et al. (August 2012). "imzML--a common data format for the flexible exchange and processing of mass spectrometry imaging data" (PDF). Journal of Proteomics. 75 (16): 5106–5110. doi:10.1016/j.jprot.2012.07.026. PMID 22842151. S2CID 25970597.
  17. ^ Bouyssié D, Dubois M, Nasso S, Gonzalez de Peredo A, Burlet-Schiltz O, Aebersold R, Monsarrat B (March 2015). "mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets". Molecular & Cellular Proteomics. 14 (3): 771–81. doi:10.1074/mcp.O114.039115. PMC 4349994. PMID 25505153.
  18. ^ Tully B (June 2020). "Toffee – a highly efficient, lossless file format for DIA-MS". Scientific Reports. 10 (1): 8939. Bibcode:2020NatSR..10.8939T. doi:10.1038/s41598-020-65015-y. PMC 7265431. PMID 32488104.
  19. ^ Bhamber RS, Jankevics A, Deutsch EW, Jones AR, Dowsey AW (January 2021). "mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements". Journal of Proteome Research. 20 (1): 172–183. doi:10.1021/acs.jproteome.0c00192. PMC 7871438. PMID 32864978.
  20. ^ "MZmine website".
  21. ^ "mineXpert2 website".
  22. ^ "MS-Spectre website". Ms-spectre.sourceforge.net. Retrieved 29 November 2011.
  23. ^ "OpenMS and TOPP website". Open-ms.sourceforge.net. Retrieved 29 November 2011.
  24. ^ "An open source viewer developed under academic projects". Staff.icar.cnr.it. Retrieved 29 November 2011.
  25. ^ "An open source viewer developed by Matt Chambers at Vanderbilt". Proteowizard.sourceforge.net. Retrieved 29 November 2011.
  26. ^ "An open source viewer developed by at the Fred Hutchinson Cancer Center". Proteomics.fhcrc.org. Retrieved 29 November 2011.
  27. ^ "jmzML". Retrieved 29 November 2011.
  28. ^ "BSI: PEAKS website". Bioinfor.com. Retrieved 29 November 2011.
  29. ^ "Insilicos website". Archived from the original on 20 December 2014. Retrieved 28 March 2020.
  30. ^ Matrix Science Limited. "Commercial software with free viewer mode for mzXML and many proprietary formats". Matrixscience.com. Retrieved 29 November 2011.
  31. ^ "Peaksel - software to read and process proprietary and open HPLC formats".
  32. ^ "ITAviewer online".
    "ITAviewer source". GitHub. 9 November 2017.
  33. ^ "pySPM website". GitHub. 17 June 2022.
  34. ^ Hermes Archived 3 March 2016 at the Wayback Machine
  35. ^ "Hermes website". Icecoffee.ch. Retrieved 29 November 2011.
  36. ^ a b "FileConverter". Open-ms.sourceforge.net. Retrieved 29 November 2011.
  37. ^ a b TOPP Archived 15 April 2008 at the Wayback Machine
  38. ^ "mzXML". Retrieved 30 June 2008.
  39. ^ a b "msconvert". ProteoWizard. Retrieved 20 April 2013.
  40. ^ a b "ProteoWizard". Retrieved 20 April 2013.
  41. ^ "ReAdW". Tools.proteomecenter.org. Retrieved 29 November 2011.
  42. ^ "TransProteomicPipeline". Tools.proteomecenter.org. 25 May 2011. Retrieved 29 November 2011.
  43. ^ MASSTransit by Palisade Archived 9 May 2008 at the Wayback Machine
  44. ^ "Gas Chromatography (GC)". PerkinElmer. Retrieved 29 November 2011.
  45. ^ aston – Open source chromatography and mass spectrometry software – Google Project Hosting
  46. ^ unfinnigan – Painless extraction of mass spectra from Thermo "raw" files – Google Project Hosting
  47. ^ Dąbrowski Ł (7 August 2015). "Review of free data processing software for chromatography". Mediterranean Journal of Chemistry. 4 (4): 193–200. doi:10.13171/mjc.4.4.2015.15.09.16.35/dabrowski.
  48. ^ wiff2dta at sourceforge
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