ProteoWizard protocols

ProteoWizard specifications

Information


Unique identifier OMICS_03354
Name ProteoWizard
Software type Toolkit/Suite
Interface Command line interface, Web user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ProteoWizard

Subtools


  • idConvert
  • msConvert
  • msPicture
  • SeeMS

Download


Versioning


Add your version

Maintainer


  • person_outline Samuel H. Payne <>

Publications for ProteoWizard

ProteoWizard IN pipelines

 (12)
2017
PMCID: 5397609
PMID: 28065881
DOI: 10.1093/dnares/dsw057

[…] to extract fragment ions with 10–50 ppm accuracy., the trans-proteomic pipeline was used for data analysis.13,14 all the .wiff files obtained in ida experiments were converted to .mzml format using msconvert from proteowizard version 3.0.4624 selecting vendor-specific peak picking algorithm.15 all the .mzml files were then independently searched against rat protein sequence file using […]

2017
PMCID: 5397609
PMID: 28065881
DOI: 10.1093/dnares/dsw057

[…] ions with 10–50 ppm accuracy., the trans-proteomic pipeline was used for data analysis.13,14 all the .wiff files obtained in ida experiments were converted to .mzml format using msconvert from proteowizard version 3.0.4624 selecting vendor-specific peak picking algorithm.15 all the .mzml files were then independently searched against rat protein sequence file using x!tandem16 and comet17 […]

2016
PMCID: 5270547
PMID: 27791479
DOI: 10.1080/15476286.2016.1249092

[…] energy of 35%., we performed peptide identification using x! tandem incorporated in a trans-proteomic pipeline (version 4.6 occupy rev 2).56 each raw data file was first converted to mzxml using the msconvert tool incorporated in proteowizard (version 3.0.4205).57 ms/ms scans in the converted mzxmls were then searched in x!! tandem against the homo sapiens swiss-prot database (release 2013 08) […]

2016
PMCID: 5270547
PMID: 27791479
DOI: 10.1080/15476286.2016.1249092

[…] identification using x! tandem incorporated in a trans-proteomic pipeline (version 4.6 occupy rev 2).56 each raw data file was first converted to mzxml using the msconvert tool incorporated in proteowizard (version 3.0.4205).57 ms/ms scans in the converted mzxmls were then searched in x!! tandem against the homo sapiens swiss-prot database (release 2013 08) containing 20,272 proteins. […]

2016
PMCID: 5311252
PMID: 27477696
DOI: 10.1038/onc.2016.242

[…] was used with 60 s duration. precursors with unassigned charge state or charge state 1 were excluded. an underfill ratio of 1% was used., raw ms/ms files were converted to mzml format using msconvert from the proteowizard tool suite.54 spectra were then searched using msgf+55 (v10072) and percolator56 (v2.08), where eight subsequent search results were grouped for percolator […]

ProteoWizard institution(s)
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA, USA; USC Stevens Institute for Innovation, University of Southern California, Los Angeles, CA, USA; Insilicos, Seattle, WA, USA; Matrix Science, Boston, MA, USA; Department of Stress & Developmental Biology, Leibniz Institute for Plant Biochemistry, Halle (Saale), Germany; Proteomics Services, Cambridge Centre for Proteomics, Cambridge,UK; AB SCIEX, Foster City, CA, USA; AB SCIEX, Concord, ON, Canada; Agilent Technologies, Santa Clara, CA, USA; Bruker Daltonik GmbH, Bremen, Germany; Thermo Fisher Scientific, San Jose, CA, USA; Waters Corporation, Manchester, UK; LabKey Software, Seattle, WA, USA; Institute for Systems Biology, Seattle, WA, USA; Genome Biology, EMBL Heidelberg, Heidelberg, Germany; Canary Center for Cancer Early Detection, Stanford University, Stanford, CA, USA
ProteoWizard funding source(s)
This work is supported by the Wunderkinder Foundation, Redstone Family Foundation, and National Cancer Institute and National Institutes of Health grants and contracts P41 RR011823, CCNE-TR 5U54CA119367, CCNE-T 1U54CA151459, PSOC-MCSTART 5U54CA143907, R01CA126218 and U24CA126479, by National Science Foundation MRI grant No. 0923536, and by the European Union 7th Framework Program PRIME-XS project, grant agreement number 262067.

ProteoWizard review

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Marc Dubois

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Desktop
Proteowizard written in C ++, provides a clear and readable interface programming. It is based on modern design and application of new standards c ++ 11 (including smart pointers). It also provides many algorithms for processing data spectrometry (peak picking ...) and allows the reading of many raw files owners. This is an indispensable tool for application developers proteomics / metabolomics. The only downside is that it still uses a build system based on bjam that requires a long learning curve.