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

Samuel H. Payne <>

Publications for ProteoWizard

Correcting systematic bias and instrument measurement drift with mzRefinery.

2015 Bioinformatics

PMCID: 4653383

PMID: 26243018

DOI: 10.1093/bioinformatics/btv437

A cross-platform toolkit for mass spectrometry and proteomics.

2012 Nat Biotechnol

PMCID: 3471674

PMID: 23051804

DOI: 10.1038/nbt.2377

ProteoWizard: open source software for rapid proteomics tools development.

2008 Bioinformatics

PMCID: 2732273

PMID: 18606607

DOI: 10.1093/bioinformatics/btn323

ProteoWizard IN pipelines

(12)

An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation

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 […]

An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation

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 […]

Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing

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) […]

Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing

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. […]

microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network

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

Marc Dubois

2015-12-24, 12:39

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.