Formats:mzXML

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Revision as of 18:16, 13 November 2008 Ntasman (Talk | contribs) (→Converters: status and summary table) ← Previous diff		Current revision Jeng (Talk | contribs) (→MzXML2Search)
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-	'''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.		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==		==Converters: status and summary table==
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	| Bruker || (?) || .baf || [[Software:CompassXport|CompassXport]] page || no (Bruker supported) || || refer to vendor; see [[Software:CompassXport|CompassXport]] page		| 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 || (?) || (?) || 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]
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	==Converting mzXML '''to''' other formats==		==Converting mzXML '''to''' other formats==
	===MzXML2Search===		===MzXML2Search===
-	This program can convert to dta, mgf, and pkl formats.	+	This program can convert to dta, mgf, pkl, and ms2 formats.
	===msconvert===		===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==		==Viewing mzXML files==
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	==Reference==		==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.		*Learn more at the [http://sashimi.sourceforge.net/ Sashimi project website], the original website for the mzXML format.

---

Current revision

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.

Contents 1 Converters: status and summary table 2 Converter Overview 2.1 direct vendor support 2.1.1 Bruker 2.2 SPC/TPP supported proprietary formats 2.2.1 Thermo/XCalibur 2.2.2 Analyst (ABI/MDS Sciex) 2.2.3 Waters Masslynx 2.2.4 Agilent MassHunter 2.3 Other SPC/TPP supported MS file formats 2.3.1 dta 2.3.2 pkl 2.3.3 mgf 2.4 Other external converter projects 2.4.1 SCIEX/ABI 4700/4800 MALDI TOFTOF 2.4.2 ABI Mariner, Voyager 3 Converting mzXML to other formats 3.1 MzXML2Search 3.2 msconvert 4 Viewing mzXML files 4.1 Pep3D 4.2 Insilicos viewer 5 Additional Resources 6 Parsing mzXML data 6.1 RAMP 7 Related Formats 8 Reference

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:

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	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

Other Compatible MS File Formats:

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	pkl2mzXML
.mgf	mascot	?	?	?	?

Converter Overview

The first step in processing ms or ms/ms data with SPC proteomics software is conversion of raw data to our open mzXML format.

direct vendor support

Bruker

Bruker directly supports the mzXML format, using their CompassXport program:

• CompassXport is the recommended converter for Bruker (.baf) files. (And for historical reasons only, we provide a page on our own (SPC-created) retired open-source Bruker converter, mzBruker.) Also, see Additional Resources, below.

SPC/TPP supported proprietary formats

The TPP project supports a wide variety of mass-spec instrument formats. Currently, we provide software tools (converters) for the following vendor formats. Follow the links for more specific information for each converter:

Thermo/XCalibur

• ReAdW: Thermo/XCalibur raw data (.RAW files) to mzXML converter

Analyst (ABI/MDS Sciex)

• mzWiff: Analyst (ABI/MDS Sciex) software's raw data (.wiff files) to mzXML converter.

Waters Masslynx

• massWolf: MassLynx (Waters) raw data (.raw directories) to mzXML converter

Agilent MassHunter

• trapper: MassHunter (Agilent) raw data (.d directories) to mzXML converter

Other SPC/TPP supported MS file formats

dta

• 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

• 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. Supports RAW, mzML and mzXML as of 6/08.

SCIEX/ABI 4700/4800 MALDI TOFTOF

• T2Extractor - SCIEX/ABI 4700/4800 MALDI TOFTOF Data to mzXML: Java application to convert data from a SCIEX/ABI 4000 series MALDI TOFTOF instruments into mzXML format. This application is provided courtesy of Phil Andrews lab at the University of Michigan. Please see this link: [1]

ABI Mariner, Voyager

• PyMsXML - ABI Mariner, Voyager raw data to mzXML: python-based converter. (Also supports Analyst .wiff files, but we recommend our own mzWiff program for that purpose.) Please see this link: 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

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 summary of what it can do and can't do in its installation at the Institute for Systems Biology.

Viewing mzXML files

Pep3D

The Pep3D program, included with the TPP, produces a gel-like image, which is very useful for getting an overview of an entire run. It can also link to CID and peptide probability information.

Insilicos viewer

We also recommend the free InSilicos Viewer, which can display mzXML, mzData, and other formats.

Additional Resources

• out2linux.pl: working with Bioworks Sequest output. See Software:Out2XML page.
• working with Bruker ion trap and DataAnalysis software. See Software:da2tpp page.

Parsing mzXML data

RAMP

RAMP: C/C++ API, contained in TPP and basis for TPP tools. Also parses mzData.

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 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 mzML development page. As of version 4.0, the TPP supports mzML through an interface between RAMP and Proteowizard.

Reference

• 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. Download PDF
• Learn more at the Sashimi project website, the original website for the mzXML format.