ProteoWizard specifications


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


  • msConvert
  • SeeMS
  • idConvert
  • msPicture



Add your version


  • person_outline Samuel H. Payne <>

ProteoWizard articles

ProteoWizard citations

PMCID: 5916935

[…] 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 software33. the resulting mzxml files were used to identify proteins by searching against human uniprotkb database on the labkey server using x!tandem algorithm34–36. […]

PMCID: 5397609

[…] 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 […]

PMCID: 5516859

[…] dissociation ms2 event for each selected precursor ion. the analysis of the normal proteome was performed with a top 10 higher-energy dissociation method., peak list data were extracted using the proteowizard software ( 3.0.3201) and searched against the swissprot mouse database (release 2012.05) appended with common contaminants, using mascot […]

PMCID: 5311252

[…] 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 target/decoy analysis. […]

PMCID: 4279952

[…] collision energies (ces) were calculated according to the formulas: ce = 0.044 x m z−1 precursor + 5.5 for doubly charged precursor ions. raw data files (wiff) were converted into mzxml format using msconvert from proteowizard (version 1.6.1455). qtrap ms2 spectra were assigned to peptide sequences using the sequest algorithm and peptideprophet. the software skyline43 was used to generate […]

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's avatar image No country

Marc Dubois

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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.