Formats:mzXML

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mzXML is an open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for Systems Biology. mzXML provides a standard container for ms and ms/ms proteomics data and is the foundation of our proteomic pipelines. Raw, proprietary file formats from most vendors can be converted to the open mzXML format.

Patrick Pedrioli was the primary original author; please see the references below for the often-cited Nature Biotech publication.

Several versions of this format exist. Currently these are 1.0 (also called "msXML"), 2.0, 2.1, 3.0, and 3.1. 3.1 is the current version. The offical XML Schema components for the format are available at mzXML schema.

-'''mzXML''' is a open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for Systems Biology.  mzXML provides a standard container for ms and ms/ms proteomics data and is the foundation of our proteomic pipelines.  Raw, proprietary file formats from most vendors can be converted to the open mzXML format.
+'''mzXML''' is an open data format for storage and exchange of mass spectroscopy data, developed at the SPC/Institute for Systems Biology.  mzXML provides a standard container for ms and ms/ms proteomics data and is the foundation of our proteomic pipelines.  Raw, proprietary file formats from most vendors can be converted to the open mzXML format.
 Patrick Pedrioli was the primary original author; please see the references below for the often-cited Nature Biotech publication.
-Several versions of this format exist. Currently these are 1.0 (also called "msXML"), 2.0, 2.1 and 3.0. '''2.1''' is the most common version currently in use.
+Several versions of this format exist. Currently these are 1.0 (also called "msXML"), 2.0, 2.1, 3.0, and 3.1. '''3.1''' is the current version.  The offical XML Schema components for the format are available at [http://sashimi.sourceforge.net/schema_revision/ mzXML schema].
+==Converters: status and summary table==
+All known formats and their converters are summarized in the table below:
+'''Compatible Mass-Spectrometer Instrument-Specific Software and File Formats:'''
+{| class="wikitable" style="text-align:center;" border="2" cellpadding="2"
+|+ Compatible Mass-Spec instrument-specific file formats
+|-
+! raw file vendor !! instrument acquisition software !! raw file type !! raw-to-mzXML converter !! SPC maintained? !! converter status/notes !! download
+|-
+| Bruker || (?) || .baf || [[Software:CompassXport|CompassXport]] page || no (Bruker supported) || || refer to vendor; see [[Software:CompassXport|CompassXport]] page
+|-
+| [http://www.thermo.com/ Thermo] || [http://www.thermo.com/com/cda/product/detail/1,,1000001009250,00.html XCalibur ]|| .RAW file || [[Software:ReAdW|ReAdW]] || yes, SPC ||  || official release: 4.3.0, August 2009; see [[Software:ReAdW|ReAdW]] page
+|-
+| [http://www.waters.com/watersdivision/ContentD.asp?watersit=JDRS-5KEKAJ  Waters] || [http://www.waters.com/watersdivision/ContentD.asp?watersit=JDRS-5WQP7W MassLynx] || .RAW directory || [[Software:massWolf|wolf]] || yes, SPC || no centroiding || offical release: 4.3.0, August 2009; see [[Software:massWolf|wolf]] page
+|-
+| [http://www.mdssciex.com/ MDS/Sciex] for [https://products.appliedbiosystems.com/ab/en/US/adirect/ab;jsessionid=Gn0ZFF66S2ZTv1cfLTLn2nGxCH5L1gYVGv39d92hdr4PqSBglGVG!1672817600?cmd=catNavigate2&catID=600832 ABI] and [http://www.chem.agilent.com/Scripts/PCol.asp?lPage=38192 Agilent] || [https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600927 Analyst], [https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600910 AnalystQS] || .wiff file|| [[Software:mzWiff|mzWiff]]|| yes, SPC ||  || official release: 4.3.0, August 2009: see [[Software:mzWiff|mzWiff]] page
+|-
+| [http://www.chem.agilent.com/Scripts/PCol.asp?lPage=38192 Agilent] || [http://www.chem.agilent.com/scripts/pds.asp?lpage=40460 MassHunter] || .d directory || trapper || yes, SPC || || official release: 4.3.0, August 2009: see [[Software:trapper|trapper]] page
+|-
+| ABI || (?) || (?) || T2DExtractor || no (Andrews Lab)|| 4700/4800 MALDI TOFTOF converter; known issue: correct instrument name is not recorded in mzXML; charge state info is not recorded in mzXML || [http://tools.proteomecenter.org/T2DE.php link]
+|-
+| ABI || (?) || (?) || PyMsXML || no || ABI Mariner, Voyager converter || [http://www.umiacs.umd.edu/~nedwards/research/PyMsXML.html external link]
+|}
+'''Other Compatible MS File Formats:'''
+{| class="wikitable" style="text-align:center;" border="2" cellpadding="2"
+|+ Other compatible MS file formats
+|-
+! format !! original use !! text-to-mzXML converter !! SPC maintained? !! converter status/notes !! download
+|-
+| .dta || sequest || dta2mzXML || yes || in TPP release || refer to TPP page
+|-
+| .pkl || ? || pkl2mzXML || yes || in TPP release || [[Software:pkl2mzXML|pkl2mzXML]]
+|-
+| .mgf|| mascot || ? || ? || ? || ?
+|-
+|}
 ==Converter Overview==
 ====Analyst (ABI/MDS Sciex)====
-*[[Software:mzStar|mzStar]]: Analyst (ABI/MDS Sciex) software's raw data (.wiff files) to mzXML converter; please note, mzStar is about to be retired in favor of the much-improved [[Software:mzWiff|mzWiff]] converter.
+*[[Software:mzWiff|mzWiff]]: Analyst (ABI/MDS Sciex) software's raw data (.wiff files) to mzXML converter.
 ====Waters Masslynx====
 *[[Software:massWolf|massWolf]]: MassLynx (Waters) raw data (.raw directories) to mzXML converter
+====Agilent MassHunter====
+*[[Software:trapper|trapper]]: MassHunter (Agilent) raw data (.d directories) to mzXML converter
+===Other SPC/TPP supported MS file formats===
+====dta====
+*[[Software:dta2mzXML|dta2mzXML]]
+The dta format is a simple text file describing precursor m/z and a peaklist table.  This format was originally developed for Sequest.  No annotation metadata is stored in this format, so you will loose information going from raw to dta then back to mzXML.
+====pkl====
+*[[Software:pkl2mzXML|pkl2mzXML]]
+Command-line program to convert pkl files to mzXML files.
+====mgf====
+The mgf format is another simple text format developed for the Mascot search engine.
 ===Other external converter projects===
 These projects are not supported by the SPC, but may be of use.
+*'''msConvert'''.  Part of the ProteoWizard Library.  Available from [http://proteowizard.sourceforge.net http://proteowizard.sourceforge.net].  Supports RAW, mzML and mzXML as of 6/08.
 ====SCIEX/ABI 4700/4800 MALDI TOFTOF====
 *'''PyMsXML''' - ABI Mariner, Voyager raw data to mzXML: python-based converter.  (Also supports Analyst .wiff files, but we recommend our own [[Software:mzWiff|mzWiff]] program for that purpose.)  Please see this link: [http://www.umiacs.umd.edu/~nedwards/research/PyMsXML.html http://www.umiacs.umd.edu/~nedwards/research/PyMsXML.html]
+==Converting mzXML '''to''' other formats==
+===MzXML2Search===
+This program can convert to dta, mgf, pkl, and ms2 formats.
+===msconvert===
-==Converters: status and summary table==
+This program can convert to many output formats, including mzML. Eventually, this program will be a general purpose converter, converting from all common raw formats into both mzML and mzXML. Here is a [[Msconvert Capabilities | summary]] of what it can do and can't do in its installation at the Institute for Systems Biology.
-All known formats and their converters are summarized in the table below:
-'''Compatible Mass-Spectrometer Instrument-Specific Software and File Formats:'''
-{| class="wikitable" style="text-align:center;" border="2" cellpadding="2"
-|+ Compatible Mass-Spec file formats
-|-
-! raw file vendor !! instrument acquisition software !! raw file type !! raw-to-mzXML converter !! SPC maintained? !! converter status/notes !! download
-|-
-| Bruker || (?) || .baf || [[Software:CompassXport|CompassXport]] page || no (Bruker supported) || || refer to vendor; see [[Software:CompassXport|CompassXport]] page
-|-
-| [http://www.thermo.com/ Thermo] || [http://www.thermo.com/com/cda/product/detail/1,,1000001009250,00.html XCalibur ]|| .RAW file || [[Software:ReAdW|ReAdW]] || yes, SPC || known issues: does not centroid orbi/ft data correctly || official release: Nov 2006; see [[Software:ReAdW|ReAdW]] page; contact spctools-discuss newsgroup if interested in beta ReAdW version
-|-
-| [http://www.waters.com/watersdivision/ContentD.asp?watersit=JDRS-5KEKAJ  Waters] || [http://www.waters.com/watersdivision/ContentD.asp?watersit=JDRS-5WQP7W MassLynx] || .RAW directory || [[Software:massWolf|wolf]] || yes, SPC || no centroiding || offical release: ???; see [[Software:massWolf|wolf]] page; contact spctools-discuss newsgroup if interested in beta wolf version
-|-
-| [http://www.mdssciex.com/ MDS/Sciex] for [https://products.appliedbiosystems.com/ab/en/US/adirect/ab;jsessionid=Gn0ZFF66S2ZTv1cfLTLn2nGxCH5L1gYVGv39d92hdr4PqSBglGVG!1672817600?cmd=catNavigate2&catID=600832 ABI] and [http://www.chem.agilent.com/Scripts/PCol.asp?lPage=38192 Agilent] || [https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600927 Analyst], [https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600910 AnalystQS] || .wiff file|| [[Software:mzStar|mzStar]] (official release); [[Software:mzWiff|mzWiff]] (beta, not yet released) || yes, SPC || mzStar is known to have many bugs which are fixed in mzWiff || [[Software:mzStar|mzStar]] page; contact spctools-discuss newsgroup if interested in beta [[Software:mzWiff|mzWiff]]
-|-
-| [http://www.chem.agilent.com/Scripts/PCol.asp?lPage=38192 Agilent] || [http://www.chem.agilent.com/scripts/pds.asp?lpage=40460 MassHunter] || .d directory || trapper (beta, not yet released) || yes, SPC || || currently internal only for development purposes
-|-
-| ABI || (?) || (?) || T2DExtractor || no (Andrews Lab)|| 4700/4800 MALDI TOFTOF converter; known issue: correct instrument name is not recorded in mzXML; charge state info is not recorded in mzXML || [http://tools.proteomecenter.org/T2DE.php link]
-|-
-| ABI || (?) || (?) || PyMsXML || no || ABI Mariner, Voyager converter || [http://www.umiacs.umd.edu/~nedwards/research/PyMsXML.html external link]
-|}
 ==Viewing mzXML files==
 ==Parsing mzXML data==
-RAMP: C/C++ API, contained in TPP and basis for TPP tools.  Also parses mzData: link
+===RAMP===
+[[Software:RAMP|RAMP]]: C/C++ API, contained in TPP and basis for TPP tools.  Also parses mzData.
-JRAP: java
+[[Software:JRAP|JRAP]]: java API
 ==Related Formats==
-Please note that while widely accepted in the proteomics community mzXML is format, not a standard.  There are two other open ms/ms proteomic formats: mzData and mzML.  mzData was the first attempt, created by the HUPO/PSI committee process.  Many vendors wanted to wait until the format was finalized (a process which took two years); in the meanwhile, mzXML was developed to fill the need.  mzML is an upcoming format which aims to marry the best elements of mzXML and mzData, and represents a joint effort of the HUPO/PSI committee, SPC/ISB, instrument vendors, and other proteomics software groups.
+Please note that while widely accepted in the proteomics community mzXML is format, not a standard.  There are two other open ms/ms proteomic formats: mzData and mzML.  mzData was the first attempt, created by the HUPO/PSI committee process.  Many vendors wanted to wait until the format was finalized (a process which took two years); in the meantime, mzXML was developed to fill the need.
+mzML is a new format released 6/2008 which aims to marry the best elements of mzXML and mzData, and represents a joint effort of the HUPO/PSI committee, SPC/ISB, instrument vendors, and other proteomics software groups. It is intended and expected that mzML will replace the use of mzXML and mzData. For more information, visit the [http://psidev.info/index.php?q=node/257 mzML development page].  As of version 4.0, the TPP supports mzML through an interface between RAMP and [http://proteowizard.sourceforge.net Proteowizard].
 ==Reference==
-*Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti R, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK Jr, 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 in a Proteomics Research Environment." Nature Biotechnology 22(11):1459-1466.  [http://www.proteomecenter.org/PDFs/Desiere.GenomeBiology.04.pdf Download PDF]
+* mzXML 2.0 format guide by Patrick Pedrioli: outdated but a very useful reference document.  http://sashimi.sourceforge.net/schema_revision/mzXML_2.0/Doc/
+*Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti R, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK Jr, 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 in a Proteomics Research Environment." Nature Biotechnology 22(11):1459-1466.  [http://www.proteomecenter.org/PDFs/Pedrioli.NatureBiotech.04.pdf Download PDF]
 *Learn more at the [http://sashimi.sourceforge.net/  Sashimi project website], the original website for the mzXML format.

raw file vendor	instrument acquisition software	raw file type	raw-to-mzXML converter	SPC maintained?	converter status/notes	download
Bruker	(?)	.baf	CompassXport page	no (Bruker supported)		refer to vendor; see CompassXport page
Thermo	XCalibur	.RAW file	ReAdW	yes, SPC		official release: 4.3.0, August 2009; see ReAdW page
Waters	MassLynx	.RAW directory	wolf	yes, SPC	no centroiding	offical release: 4.3.0, August 2009; see wolf page
MDS/Sciex for ABI and Agilent	Analyst, AnalystQS	.wiff file	mzWiff	yes, SPC		official release: 4.3.0, August 2009: see mzWiff page
Agilent	MassHunter	.d directory	trapper	yes, SPC		official release: 4.3.0, August 2009: see trapper page
ABI	(?)	(?)	T2DExtractor	no (Andrews Lab)	4700/4800 MALDI TOFTOF converter; known issue: correct instrument name is not recorded in mzXML; charge state info is not recorded in mzXML	link
ABI	(?)	(?)	PyMsXML	no	ABI Mariner, Voyager converter	external link

format	original use	text-to-mzXML converter	SPC maintained?	converter status/notes	download
.dta	sequest	dta2mzXML	yes	in TPP release	refer to TPP page
.pkl	?	pkl2mzXML	yes	in TPP release	pkl2mzXML
.mgf	mascot	?	?	?	?

Formats:mzXML

From SPCTools

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Contents

Converters: status and summary table

Converter Overview

direct vendor support

Bruker

SPC/TPP supported proprietary formats

Thermo/XCalibur

Analyst (ABI/MDS Sciex)

Waters Masslynx

Agilent MassHunter

Other SPC/TPP supported MS file formats

dta

pkl

mgf

Other external converter projects

SCIEX/ABI 4700/4800 MALDI TOFTOF

ABI Mariner, Voyager

Converting mzXML to other formats

MzXML2Search

msconvert

Viewing mzXML files

Pep3D

Insilicos viewer

Additional Resources

Parsing mzXML data

RAMP

Related Formats

Reference

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