Proteowizard msconvert

Version: 3.0.18205

This container is unmaintained

Please head over to https://github.com/ProteoWizard/container for the new upstream home.

Short Description

Conversion of mass spectrometry vendor formats to mzML.

Description

Please note that there is now a container by the Proteowizard team as part of their continuous integration pipeline which should be used instead of this phnmnl/container-pwiz: https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses

The first step in a metabolomics data processing workflow with Open Source tools is the conversion to an open raw data format like mzML. One of the main routes to mzML-formatted data is using Open Source converter msconvert developed by the Proteowizard team (Chambers et al. 2012), which is one of the reference implementations for mzML. It can convert to mzML from Sciex, Bruker, Thermo, Agilent, Shimadzu, Waters and also the earlier file formats like mzData or mzXML. Although Proteowizard was initially targeting LC/MS data, it can also readily convert GC/MS data for example from the Waters GCT Premier or Agilent instruments.

Key features

• MS raw data conversion

Functionality

• Preprocessing

Approaches

• Metabolomics
• Lipidomics
• Glycomics
• Proteomics

Instrument Data Types

• MS

Screenshots

Tool Authors

• Several hundred labs around the world are using ProteoWizard within their development processes and computational workflows. We'd like to thank the many users who have contributed feedback to the project. We also thank the TPP team for their ongoing support.
• See http://proteowizard.sourceforge.net/team.html for the full list of contributors.

Container Contributors

• Steffen Neumann (IPB Halle)
• Rene Meier (IPB Halle)
• Pablo Moreno (EMBL-EBI)
• Pierrick Roger (CAE)

Website

• http://proteowizard.sourceforge.net/

Git Repository

• https://github.com/phnmnl/container-pwiz.git

Installation

The conversion can be started with e.g.

docker run -v $PWD:/data:rw phnmnl/phnmnl/pwiz-i-agree-to-the-vendor-licenses:latest /data/neg-MM8_1-A,1_01_376.d -o /data/ --mzML

The currently tested vendor formats are:

• mzXML: docker run -it -v $PWD:/data phnmnl/pwiz-i-agree-to-the-vendor-licenses:latest threonine_i2_e35_pH_tree.mzXML
• Bruker .d: docker run -it -v $PWD:/data phnmnl/phnmnl/pwiz-i-agree-to-the-vendor-licenses:latest neg-MM8_1-A,1_01_376.d

To run the MSconvertGUI as shown in the above screenshot, you have to enable X11 access on the client machine, and pass the X11 information to the container:

docker run --rm -v $HOME/.Xauthority:/root/.Xauthority:r -v /tmp/.X11-unix:/tmp/.X11-unix:rw -v $HOME:/data:rw phnmnl/pwiz-i-agree-to-the-vendor-licenses wine MSconvertGUI

Galaxy usage

A rudimentary Galaxy node description is included as msconvert.xml, it was obtained from the msconvert.ctd using python CTD2Galaxy/generator.py -i /vol/phenomenal/vmis/docker-pwiz/msconvert.ctd -m sample_files/macros.xml -o /vol/phenomenal/vmis/docker-pwiz/msconvert.xml

Build instructions

Please note that for licensing reasons we can not include all required files in this repository. Upon container building, the Proteowizard files will be downloaded from http://proteowizard.sourceforge.net/downloads.shtml and included in the created container. By building this container, you agree to all the vendor licenses that are shown at the above download links, and also included in the container and Dockerfile repository. To build, please use

docker build --tag="phnmnl/pwiz-i-agree-to-the-vendor-licenses:latest" .

Also note that the build is known to fail with Docker-1.9, make sure to use Docker-1.10 or above.

Publications

Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, Baker TA, Brusniak MY, Paulse C, Creasy D, Flashner L, Kani K, Moulding C, Seymour SL, Nuwaysir LM, Lefebvre B, Kuhlmann F, Roark J, Rainer P, Detlev S, Hemenway T, Huhmer A, Langridge J, Connolly B, Chadick T, Holly K, Eckels J, Deutsch EW, Moritz RL, Katz JE, Agus DB, MacCoss M, Tabb DL, Mallick P. A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol. 2012 Oct;30(10):918-20. doi: 10.1038/nbt.2377. PubMed PMID: 23051804; PubMed Central PMCID: PMC3471674.

Licensing: APACHE LICENSE

Please see LICENSES/LICENSE, this Apache License Covers Core ProteoWizard Tools and Library. This software does, however, depend on other software libraries which place further restrictions on its use and redistribution, see below.

ADDENDUM TO APACHE LICENSE

To the best of our ability we deliver this software to you under the Apache 2.0 License listed below (the source code is available in the ProteoWizard project). This software does, however, depend on other software libraries which place further restrictions on its use and redistribution. By accepting the license terms for this software, you agree to comply with the restrictions imposed on you by the license agreements of the software libraries on which it depends:

• AB Sciex WIFF Reader Library
• Agilent Mass Hunter Data Access Component Library
• Bruker CompassXtract
• Shimadzu SFCS
• Thermo-Scientific MSFileReader Library
• Waters Raw Data Access Component Library

NOTE: If you do not plan to redistribute this software yourself, then you are the "end-user" in the above agreements.