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==
 | 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: 4.0.2, July 2008; see [[Software:ReAdW|ReAdW]] 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: 4.0.2, July 2008; see [[Software:massWolf|wolf]] 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: 4.0.2, July 2008: see [[Software:mzWiff|mzWiff]] 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: 4.1.0-pr, July 2008: see [[Software:trapper|trapper]] 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 || ? || ? || ? || ?
+|-
 |}
 ==Converting mzXML '''to''' other formats==
 ===MzXML2Search===
-This program can convert to dta, mgf, and pkl formats.
+This program can convert to dta, mgf, pkl, and ms2 formats.
 ===msconvert===
-This program can convert to many output formats, including mzML.
+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.
 ==Viewing mzXML files==
 ==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

Current revision

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

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Reference

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