ProteoWizard protocols

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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

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Versioning


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Maintainer


  • person_outline Samuel H. Payne <>

Publications for ProteoWizard

ProteoWizard in pipelines

 (16)
2018
PMCID: 5768655
PMID: 29375523
DOI: 10.3389/fmicb.2017.02658

[…] data file was first analyzed using the mascot distiller software (version 2.4.3.2, matrix science, london, united kingdom) and the resulting mgf files were converted into the mzml file format using msconvert (). the saprolegnia protein database (20,088 entries) was then searched using several search engines in parallel, i.e., ms-gf+ () v1.0 (v8299), myrimatch () (version 2.1.120), comet () […]

2018
PMCID: 5916935
PMID: 29695737
DOI: 10.1038/s41598-018-24270-w

[…] events of the top 10 most intense +2 or +3 ions from the ms1 spectrum over an acquisition time of 140 minutes., the raw files obtained from lc-ms/ms were converted to mzxml format using msconvert from the proteowizard software. the resulting mzxml files were used to identify proteins by searching against human uniprotkb database on the labkey server using x!tandem algorithm–. search […]

2017
PMCID: 5354518
PMID: 28191870
DOI: 10.7554/eLife.21069.038

[…] waltham, ma) as previously described (). each cross-linked sample was run four times and the data were combined before analysis (technical replicate). mass spectra were converted into mzml using msconvert from proteowizard (). standard linear peptide searches were performed using comet to identify all proteins in the sample (). cross-linked peptides were identified using the kojak version […]

2016
PMCID: 5025507
PMID: 27729833
DOI: 10.1007/s11306-016-1109-3

[…] raw-files) were directly imported into progenesis qi (nonlinear dynamics, newcastle upon tyne, uk) for peak picking and run alignment. in addition, raw data was converted into mzxml-format using proteowizard (chambers et al. ) for processing with the ‚xcms’-package for r (https://masspec.scripps.edu/xcms/download.php) according to previously published protocols (patti et al. ; tautenhahn et […]

2016
PMCID: 5059416
PMID: 27572102
DOI: 10.1007/s13361-016-1460-7

[…] as described in moruz et al. []. we will refer to this set as the “hm_yeast” set., converting the raw files to two separate files in the ms1 and ms2 formats [], respectively, was done with proteowizard [] with vendor peak picking for the ms2 spectra and all other options left at their default values. next, we assigned high-resolution precursor masses and charges using information […]


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ProteoWizard in publications

 (269)
PMCID: 5940703
PMID: 29740076
DOI: 10.1038/s41598-018-25552-z

[…] with mass hunter (version b.05.01, agilent technologies, usa) and analyst tf (version 1.7.1, ab sciex, usa) qualitative analysis software. ms raw data files were converted to the mzxml format using proteowizard and processed by the r package xcms (version 1.41.0), which can perform peak finding, filtering, alignment, and scaling. the r package camera was used for peak annotation after xcms data […]

PMCID: 5916935
PMID: 29695737
DOI: 10.1038/s41598-018-24270-w

[…] events of the top 10 most intense +2 or +3 ions from the ms1 spectrum over an acquisition time of 140 minutes., the raw files obtained from lc-ms/ms were converted to mzxml format using msconvert from the proteowizard software. the resulting mzxml files were used to identify proteins by searching against human uniprotkb database on the labkey server using x!tandem algorithm–. search […]

PMCID: 5949002
PMID: 29686101
DOI: 10.1073/pnas.1801247115

[…] with a smartbeam-ii laser (355 nm). detailed instrument settings are available in si appendix., in brief, maldi-tof ms raw data were first converted to the open-source mzml format () by using proteowizard’s command-line msconvert (). the mzml files were read into r through mzr () and custom code and processed into peak lists by using maldiquant (). lastly, the peak lists informed […]

PMCID: 5912195
PMID: 29696081
DOI: 10.1080/20013078.2018.1463779

[…] repeated fragmentation. ions clustering for more than once within 25 s were excluded from the selection. mass spectrum raw files were converted to a peak list format (mgf) by ms convert software (proteowizard), and data processing was performed using mascot version 2.2 (matrix science) against the t. cruzi database downloaded from uniprot, with the following parameters: ms1 mass tolerance […]

PMCID: 5915062
PMID: 29719595
DOI: 10.18632/oncotarget.24773

[…] ms/ms were excluded from further fragmentation for the next 60 seconds., proteins from the lcm-derived samples were assigned by exporting features, for which ms/ms spectra were recorded, using the proteowizard software (version 3.0.9248; http://proteowizard.sourceforge.net). resulting .mgf files were submitted to mascot (version 2.3.01, matrix science, london, uk) and applied to the human […]


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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.