Mass spectrometry data format

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.{{cite journal |doi=10.1366/0003702884428734 |url=http://old.iupac.org/jcamp/protocols/dxir01.pdf |title=JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form |date=1988 |last1=McDonald |first1=Robert S. |last2=Wilks |first2=Paul A. |journal=Applied Spectroscopy |volume=42 |issue=1 |pages=151–162 |bibcode=1988ApSpe..42..151M }} Together with the American Society for Mass Spectrometry a JCAMP-DX format for mass spectrometry was developed with aim to preserve legacy data.{{cite journal | vauthors = Lampen P, Hillig H, Davies AN, Linscheid M | title = JCAMP-DX for mass spectrometry. | journal = Applied Spectroscopy | date = December 1994 | volume = 48 | issue = 12 | pages = 1545–52 | doi = 10.1366/0003702944027840 | bibcode = 1994ApSpe..48.1545L | s2cid = 96773027 | url = https://www.osapublishing.org/as/abstract.cfm?uri=as-48-12-1545 }}

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.[http://www.astm.org/Standards/E1947.htm ASTM E1947 – 98(2009) Standard Specification for Analytical Data Interchange Protocol for Chromatographic Data] 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.{{cite journal | vauthors = Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M | display-authors = 6 | title = Controlled vocabularies and ontologies in proteomics: overview, principles and practice | journal = Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics | volume = 1844 | issue = 1 Pt A | pages = 98–107 | date = January 2014 | pmid = 23429179 | doi = 10.1016/j.bbapap.2013.02.017 |pmc=3898906 | doi-access = free }}

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.{{cite journal |last1=Davies |first1=Tony |title=Herding AnIMLs (no, it's not a spelling mistake): Update on the IUPAC and ASTM Collaboration on Analytical Data Standards |journal=Chemistry International |volume=29 |issue=6 |year=2007 |url=https://old.iupac.org/publications/ci/2007/2906/pp1_animls.html}}

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.{{cite journal | vauthors = Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H | display-authors = 6 | title = 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 | journal = Proteomics | volume = 7 | issue = 19 | pages = 3436–40 | date = October 2007 | pmid = 17907277 | doi = 10.1002/pmic.200700658 | s2cid = 22837325 }} This format is now deprecated, and replaced by mzML.{{cite web|title=mzData|url=https://www.psidev.info/mzdata|publisher=HUPO-PSI|access-date=26 April 2021|archive-url=https://web.archive.org/web/20180707193136/https://www.psidev.info/mzdata |archive-date=2018-07-07}}

mzXML is a XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data.{{cite journal | vauthors = 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 | display-authors = 6 | title = A common open representation of mass spectrometry data and its application to proteomics research | journal = Nature Biotechnology | volume = 22 | issue = 11 | pages = 1459–66 | date = November 2004 | pmid = 15529173 | doi = 10.1038/nbt1031 | s2cid = 25734712 }}{{cite journal | vauthors = 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 | date = December 2005 | pmid = 16307524 | doi = 10.1586/14789450.2.6.839 | s2cid = 24914725 }} 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.

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.{{cite journal | vauthors = Shah AR, Davidson J, Monroe ME, Mayampurath AM, Danielson WF, Shi Y, Robinson AC, Clowers BH, Belov ME, Anderson GA, Smith RD | display-authors = 6 | title = An efficient data format for mass spectrometry-based proteomics | journal = Journal of the American Society for Mass Spectrometry | volume = 21 | issue = 10 | pages = 1784–8 | date = October 2010 | pmid = 20674389 | doi = 10.1016/j.jasms.2010.06.014 | doi-access = free | bibcode = 2010JASMS..21.1784S }}

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.{{cite web|title=mzML|url=http://www.psidev.info/mzml|publisher=HUPO-Proteomics Standards Initiative|access-date=19 April 2013}} The first specification was published in June 2008.{{cite journal | vauthors = Deutsch E | title = mzML: a single, unifying data format for mass spectrometer output | journal = Proteomics | volume = 8 | issue = 14 | pages = 2776–7 | date = July 2008 | pmid = 18655045 | doi = 10.1002/pmic.200890049 | s2cid = 28297899 | doi-access = free }} 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.

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.{{cite journal | vauthors = Askenazi M, Parikh JR, Marto JA | title = mzAPI: a new strategy for efficiently sharing mass spectrometry data | journal = Nature Methods | volume = 6 | issue = 4 | pages = 240–1 | date = April 2009 | pmid = 19333238 | pmc = 2691659 | doi = 10.1038/nmeth0409-240 }}

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.{{cite journal | vauthors = Wilhelm M, Kirchner M, Steen JA, Steen H | title = mz5: space- and time-efficient storage of mass spectrometry data sets | journal = Molecular & Cellular Proteomics | volume = 11 | issue = 1 | pages = O111.011379 | date = January 2012 | pmid = 21960719 | pmc = 3270111 | doi = 10.1074/mcp.O111.011379 | doi-access = free }}

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.{{cite journal | vauthors = Schramm T, Hester Z, Klinkert I, Both JP, Heeren RM, Brunelle A, Laprévote O, Desbenoit N, Robbe MF, Stoeckli M, Spengler B, Römpp A | display-authors = 6 | title = imzML--a common data format for the flexible exchange and processing of mass spectrometry imaging data | journal = Journal of Proteomics | volume = 75 | issue = 16 | pages = 5106–5110 | date = August 2012 | pmid = 22842151 | doi = 10.1016/j.jprot.2012.07.026 | s2cid = 25970597 | url = https://hal.archives-ouvertes.fr/hal-00741330/file/imzML%20-%20JoP-%20submitted%20revision%20JPROT-D-12-00290R11%20%282%29.pdf }}

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.{{cite journal | vauthors = Bouyssié D, Dubois M, Nasso S, Gonzalez de Peredo A, Burlet-Schiltz O, Aebersold R, Monsarrat B | title = mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets | journal = Molecular & Cellular Proteomics | volume = 14 | issue = 3 | pages = 771–81 | date = March 2015 | pmid = 25505153 | doi = 10.1074/mcp.O114.039115 | doi-access = free | pmc = 4349994 }}

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.{{cite journal | vauthors = Tully B | title = Toffee – a highly efficient, lossless file format for DIA-MS | journal = Scientific Reports | volume = 10 | issue = 1 | pages = 8939 | date = June 2020 | pmid = 32488104 | doi = 10.1038/s41598-020-65015-y|pmc=7265431 | doi-access = free | bibcode = 2020NatSR..10.8939T }}

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.{{cite journal | vauthors = Bhamber RS, Jankevics A, Deutsch EW, Jones AR, Dowsey AW | title = mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements | journal = Journal of Proteome Research | volume = 20 | issue = 1 | pages = 172–183 | date = January 2021 | pmid = 32864978 | pmc = 7871438 | doi = 10.1021/acs.jproteome.0c00192 }}

The Allotrope Foundation curates a HDF5 and Triplestore based file format named Allotrope Data Format (ADF) and a flat JSON representation ASM short for Allotrope Simple Model. Both are based on the Allotrope Foundation Ontologies (AFO) and contain schemas for mass spectrometry and chromatography coupled with MS detectors.{{cite journal |last1=Rauh |first1=David |last2=Blankenburg |first2=Claudia |last3=Fischer |first3=Tillmann G. |last4=Jung |first4=Nicole |last5=Kuhn |first5=Stefan |last6=Schatzschneider |first6=Ulrich |last7=Schulze |first7=Tobias |last8=Neumann |first8=Steffen |title=Data format standards in analytical chemistry |journal=Pure and Applied Chemistry |date=27 June 2022 |volume=94 |issue=6 |pages=725–736 |doi=10.1515/pac-2021-3101|hdl=2086/22122 |hdl-access=free }}

Below is a table of different file format extensions.

:

(*) 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

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,{{Cite journal |last1=Katajamaa |first1=Mikko |last2=Miettinen |first2=Jarkko |last3=Oresic |first3=Matej |date=2006-03-01 |title=MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data |url=https://pubmed.ncbi.nlm.nih.gov/16403790 |journal=Bioinformatics |volume=22 |issue=5 |pages=634–636 |doi=10.1093/bioinformatics/btk039 |issn=1367-4803 |pmid=16403790}} mineXpert2 (mzXML, mzML, native timsTOF, xy, MGF, BafAscii){{Cite journal |last1=Langella |first1=Olivier |last2=Rusconi |first2=Filippo |date=2021-04-07 |title=mineXpert2: Full-Depth Visualization and Exploration of MSn Mass Spectrometry Data |url=https://pubmed.ncbi.nlm.nih.gov/33683899 |journal=Journal of the American Society for Mass Spectrometry |volume=32 |issue=4 |pages=1138–1141 |doi=10.1021/jasms.0c00402 |issn=1879-1123 |pmid=33683899}} MS-Spectre,{{cite web|url=http://ms-spectre.sourceforge.net |title=MS-Spectre website |publisher=Ms-spectre.sourceforge.net |access-date=29 November 2011}} TOPPView (mzXML, mzML and mzData),{{Cite journal |last1=Sturm |first1=Marc |last2=Kohlbacher |first2=Oliver |date=2009-07-06 |title=TOPPView: An Open-Source Viewer for Mass Spectrometry Data |journal=Journal of Proteome Research |volume=8 |issue=7 |pages=3760–3763 |doi=10.1021/pr900171m |pmid=19425593 |issn=1535-3893}} Spectra Viewer,{{cite web|url=http://staff.icar.cnr.it/cannataro/projects/SpectraViewer/ |title=An open source viewer developed under academic projects |publisher=Staff.icar.cnr.it |access-date=29 November 2011}} SeeMS,{{cite web|url=http://proteowizard.sourceforge.net |title=An open source viewer developed by Matt Chambers at Vanderbilt |publisher=Proteowizard.sourceforge.net |access-date=29 November 2011}} msInspect,{{cite web|url=http://proteomics.fhcrc.org/CPL/msinspect.html |title=An open source viewer developed by at the Fred Hutchinson Cancer Center |publisher=Proteomics.fhcrc.org |access-date=29 November 2011}} jmzML.{{Cite journal |last1=Côté |first1=Richard G. |last2=Reisinger |first2=Florian |last3=Martens |first3=Lennart |date=2010 |title=jmzML, an open-source Java API for mzML, the PSI standard for MS data |journal=Proteomics |language=en |volume=10 |issue=7 |pages=1332–1335 |doi=10.1002/pmic.200900719 |pmid=20127693 |issn=1615-9861}}

In the proprietary category, one can find PEAKS,{{cite web|url=http://www.bioinfor.com/peaks |title=BSI: PEAKS website |publisher=Bioinfor.com |access-date=29 November 2011}} Insilicos,{{Cite web |url=http://www.insilicos.com/ |title=Insilicos website |access-date=28 March 2020 |archive-url=https://web.archive.org/web/20141220185618/http://insilicos.com/ |archive-date=20 December 2014 |url-status=dead }} Mascot Distiller,{{cite web|author=Matrix Science Limited |url=http://www.matrixscience.com/distiller.html |title=Commercial software with free viewer mode for mzXML and many proprietary formats |publisher=Matrixscience.com |access-date=29 November 2011}} Elsci Peaksel.{{cite web|url=https://elsci.io/peaksel/ |title=Peaksel - software to read and process proprietary and open HPLC formats}}

There is a viewer for ITA images.{{cite web|url=https://scholi.github.io/ITAviewer|title=ITAviewer online}}
{{cite web|url=https://github.com/scholi/ITAviewer|title=ITAviewer source|website=GitHub |date=9 November 2017 }} ITA and ITM images can be parsed with the pySPM python library.{{cite web|url=https://github.com/scholi/pySPM|title=pySPM website|website=GitHub |date=17 June 2022 }}

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[http://blogs.ethz.ch/andreas/2008/05/09/mzdata-to-mzxml-converter/ Hermes] {{webarchive |url=https://web.archive.org/web/20160303202924/http://blogs.ethz.ch/andreas/2008/05/09/mzdata-to-mzxml-converter/ |date=3 March 2016 }}{{cite web|url=http://www.icecoffee.ch/hermes/converter.html |title=Hermes website |publisher=Icecoffee.ch |access-date=29 November 2011}}

:FileConverter: A command line tool that converts to/from various mass spectrometry formats, part of TOPP{{Cite journal |last1=Kohlbacher |first1=Oliver |last2=Reinert |first2=Knut |last3=Gröpl |first3=Clemens |last4=Lange |first4=Eva |last5=Pfeifer |first5=Nico |last6=Schulz-Trieglaff |first6=Ole |last7=Sturm |first7=Marc |date=2007-01-15 |title=TOPP—the OpenMS proteomics pipeline |journal=Bioinformatics |volume=23 |issue=2 |pages=e191–e197 |doi=10.1093/bioinformatics/btl299 |pmid=17237091 |issn=1367-4803}}

Known converters for mzXML:

: The Institute for Systems Biology maintains a list of converters{{cite web|url=http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML |title=mzXML |access-date=30 June 2008}}

Known converters for mzML:

:msConvert: A command line tool converting to/from various mass spectrometry formats. A GUI is also available for Windows users.{{Cite journal |last1=Kessner |first1=Darren |last2=Chambers |first2=Matt |last3=Burke |first3=Robert |last4=Agus |first4=David |last5=Mallick |first5=Parag |date=2008-11-01 |title=ProteoWizard: open source software for rapid proteomics tools development |journal=Bioinformatics |volume=24 |issue=21 |pages=2534–2536 |doi=10.1093/bioinformatics/btn323 |pmid=18606607 |pmc=2732273 |issn=1367-4803}}

: ReAdW:{{cite web|url=http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW |title=ReAdW |publisher=Tools.proteomecenter.org |access-date=29 November 2011}} The Institute for Systems Biology command line converter for Thermo RAW files, part of the TransProteomicPipeline.{{cite web|url=http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP |title=TransProteomicPipeline |publisher=Tools.proteomecenter.org |date=25 May 2011 |access-date=29 November 2011}} 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, part of TOPP

Converters for proprietary formats:

:msConvert: 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) files for many of their native file formats (.baf).{{Cite web |last=Guillaume |first=Erny |date=2016-02-29 |title=Converting Bruker files to the mzML format using CompassXport. |url=https://finneeblog.wordpress.com/2016/02/29/converting-bruker-files-to-the-mzml-format-using-compassxport/ |access-date=2025-04-11 |website=finnee blog |language=en}}

: MASSTransit, a software to change data between proprietary formats, by Palisade Corporation and distributed by Scientific Instrument Services, Inc[http://www.sisweb.com/software/masstransit.htm MASSTransit by Palisade] {{webarchive |url=https://web.archive.org/web/20080509121844/http://www.sisweb.com/software/masstransit.htm |date=9 May 2008 }} and PerkinElmer.{{cite web|url=http://www.perkinelmer.com/gc |title=Gas Chromatography (GC) |publisher=PerkinElmer |access-date=29 November 2011}} Purchased from Palisade by John Wiley and Sons in 2020 and incorporated into KnowItAll Spectroscopy software.[https://sciencesolutions.wiley.com/wp-content/uploads/2021/08/210421-Wiley_KnowItAll_Software_File_Format_Datasheet.pdf (list of file formats supported).]

: Aston,[http://code.google.com/p/aston aston – Open source chromatography and mass spectrometry software – Google Project Hosting] native support for several Agilent Chemstation, Agilent Masshunter and Thermo Isodat file formats

: unfinnigan,[http://code.google.com/p/unfinnigan unfinnigan – Painless extraction of mass spectra from Thermo "raw" files – Google Project Hosting] 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{{Cite journal| vauthors = Dąbrowski Ł |date=2015-08-07 |title=Review of free data processing software for chromatography |journal=Mediterranean Journal of Chemistry |volume=4 |issue=4 |pages=193–200 |doi=10.13171/mjc.4.4.2015.15.09.16.35/dabrowski |doi-access=free}}

Currently available converters are :

:: MassWolf, for Micromass MassLynx .Raw format

:: mzStar, for SCIEX/ABI SCIEX/ABI Analyst format

:: wiff2dta[https://sourceforge.net/projects/protms/files/wiff2dta/ wiff2dta at sourceforge] for SCIEX/ABI SCIEX/ABI Analyst format to mzXML, DTA, MGF and PMF

• Mass spectrometry software

{{reflist}}

Category:Bioinformatics software

Category:Mass spectrometry software

Category:Proteomics