Formats:mzXML

From SPCTools

(Difference between revisions)

Revision as of 20:04, 23 January 2008

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.

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.

1 Converter Overview
2 Converters: status and summary table
3 Viewing mzXML files
- 3.1 Pep3D
- 3.2 Insilicos viewer
4 Additional Resources
5 Parsing mzXML data
- 5.1 RAMP
6 Related Formats
7 Reference

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)

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 mzWiff converter.

Waters Masslynx

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

Other external converter projects

These projects are not supported by the SPC, but may be of use.

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

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 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	known issues: does not centroid orbi/ft data correctly	official release: Nov 2006; see ReAdW page; contact spctools-discuss newsgroup if interested in beta ReAdW version
Waters	MassLynx	.RAW directory	wolf	yes, SPC	no centroiding	offical release: 2007 Jul 18; see wolf page; contact spctools-discuss newsgroup if interested in beta wolf version
MDS/Sciex for ABI and Agilent	Analyst, AnalystQS	.wiff file	mzStar (official release); mzWiff (beta, not yet released)	yes, SPC	mzStar is known to have many bugs which are fixed in mzWiff	mzStar page; contact spctools-discuss newsgroup if interested in beta mzWiff
Agilent	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	link
ABI	(?)	(?)	PyMsXML	no	ABI Mariner, Voyager converter	external link

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 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.

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

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML"

 | [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.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: 2007 Jul 18; 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]]