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ProteoWizard v.1.0
The ProteoWizard Library is a set of software libraries and tools for rapid development of proteomics data analysis software. The libraries are cross-platform and built from the ground up using modern C++ techniques.
The ProteoWizard Library is a set of software ...
The ProteoWizard Library is a set of software libraries and tools for rapid development of proteomics data analysis software.
The libraries are cross-platform and built from the ground up using modern C++ ...
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+ 136.64Stanford UniversityShow more authorsAbstractThe ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform prot the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library.
Availability: Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for pr consequently, code use, contribution and further development are strongly encouraged.
Contact: darren@proteowizard. parag@ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.Discover the world's research14+ million members100+ million publications700k+ research projectsFigures
BIOINFORMATICS APPLICATIONS NOTEVol. 24 no. 21 2008, pages doi:10.1093/bioinformatics/btn323Genome analysisProteoWizard: open source software for rapid proteomics toolsdevelopmentDarren Kessner1,*, Matt Chambers2, Robert Burke1, David Agus1and Parag Mallick1,3,*1Spielberg Family Center for Applied Proteomics, Cedars-Sinai Medical Center,2Department of Biochemistry,Vanderbilt University, Nashville, TN and3Department of Chemistry & Biochemistry, University of California,Los Angeles, CA, USAReceived on April 18, 2008; revised on May 21, 2008; accepted on June 18, 2008Advance Access publication July 7, 2008Associate Editor: John QuackenbushABSTRACTSummary: The ProteoWizard software project provides a modularand extensible set of open-source, cross-platform tools and libraries.The tools perform proteomics data
the libraries enablerapid tool creation by providing a robust, pluggable developmentframework that simplifies and unifies data file access, and performsstandard proteomics and LCMS dataset computations. The librarycontains readers and writers of the mzML data format, which hasbeen written using modern C++ techniques and design principlesand supports a variety of platforms with native compilers. Thesoftware has been specifically released under the Apache v2 licenseto ensure it can be used in both academic and commercial projects.In addition to the library, we also introduce a rapidly growing setof companion tools whose implementation helps to illustrate thesimplicity of developing applications on top of the ProteoWizardlibrary.Availability: Cross-platform software that compiles usingnative compilers (i.e. GCC on Linux, MSVC on Windows andXCode on OSX) is available for download free of charge, athttp://proteowizard.sourceforge.net. This website also providescode examples, and documentation. It is our hope the ProteoWizardproject will become a standard platform for proteomics consequently, code use, contribution and further development arestrongly encouraged.Contact: darren@proteowizard.org; parag@ucla.eduSupplementary information: Supplementary data are available atBioinformatics online.1 INTRODUCTIONHistorically, three factors have led to a significant overhead indeveloping proteomics software. The first challenge of writinganalysis tools is supporting data generated by different
eachvendor typically encodes their data in a vendor-specific, proprietary,closed format, with access restricted to a particular operating system.To simplify cross-vendor software development two open formatswere created (Pedrioli et al., 2004), which led to the secondchallenge: reading and writing of these open formats. No single,natively-compiling cross-platform, open-source software library,has emerged to allow academic and commercial groups to encode or*To whom correspondence should be addressed.access encoded data. Despite this, the existence of open standardsgreatly simplified development, and numerous open source softwareprojects, such as the Trans-Proteomic Pipeline (TPP) (Keller et al.,2005), the OpenMS Proteomic Pipeline (TOPP) (Kohlbacher et al.,2007) and the Computational Proteomics Analysis System (CPAS)(Rauch et al., 2006) were built upon the open formats. More recently,the HUPO-PSI and Institute for Systems Biology have taken animportant step in simplifying proteomics software development bycreating the mzML data format standard to be released in June 2008(Orchard et al., 2007). The third challenge is the lack of a single,standard cross-platform library that performs common calculations,such as protein digestion, mass computation, peak integration,charge state detection and isotope deconvolution. Consequently,these calculations have been repeatedly implemented in the courseof developing more sophisticated tools.2 DESIGN AND IMPLEMENTATIONProteoWizard has been designed from the ground-up with testabilityin mind. Each code module has a unit test that runs automaticallyduring the build process. In addition, the data model has ‘diff’calculations built in, for validating data after format conversion orpreprocessing.As illustrated in Figure 1, ProteoWizard is built from manyindependent libraries, grouped together in dependency levels. Eachlibrary depends only on libraries in lower levels of the hierarchy.The lowest layer, the utility layer, contains independent classes thatperform computations applicable in a wide variety of situationssuch as binary to text encoding, XML parsing and mathematicalcalculations that are common in data analysis. Abstract interfaces areused in analysis modules to facilitate comparison between differentalgorithms. Below we describe the data and analysis layers in greaterdetail.2.1 The data layerThe ProteoWizard data layer abstracts the source data file, hidingany format-specific details. The underlying data model of the datalayer is a one-to-one translation from mzML data elements to C++data structures. This mapping is shown in the data model detailsin the Supplementary Material. Metadata fields are encoded in&cvParam& elements, which refer to terms (by their accessionnumber) in a controlled vocabulary (CV) maintained in a central(C) 2008 The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
ProteoWizardFig. 1. ProteoWizard architecture.repository by the HUPO-PSI. ProteoWizard parses the CV file atcompile time and generates C++ code, which allows convenient,typesafe handling of the CV terms.The data model uses a virtual interface for accessing spectrumlists, to allow lazy evaluation when accessing the spectra containedin a data file, improving data access time, as files can be readincrementally as needed.Vendor proprietary formats are handled with a plug-in readerinterface. ProteoWizard currently supports reading of mzML,mzXML and Thermo RAW files. As vendor libraries are subjectto platform restrictions some features of ProteoWizard may onlybe available if a vendor library is found at runtime. Collaborationwith other labs (Vanderbilt, Nashville, TN, ISB, Seattle, WA) areunderway to implement readers for all vendor formats.Data writing is also handled in a modular, extensible manner,with C++ iostream serialization currently supported for mzML andmzXML. Because ProteoWizard has been released with a permissivelicense, it can be incorporated in commercial software projects.2.2 The analysis layerThe analysis layer contains all scientific computation, in reusablemodules that are independent of platform and data format. Currentlyavailable are modules for convenient access to the underlying datamodel, spectrum data caching, data and metadata extraction, selectedion chromatogram calculation and pseudo-2D-gel image creation.There are also independent modules for handling chemical formulas,peptide calculations and isotope envelopes. More analysis modulesare currently in development, with an emphasis on establishingstandard interfaces for common proteomics computations, such aspeak picking, isotope de-convolution and precursor estimation. Ourgoal is to work collaboratively to create an analysis infrastructure inwhich experts in a particular area will be able to contribute a modulethat can then be plugged into various software tools. This will allow,for example, an expert in signal processing to create and contributea peak picker, without having to handle details about file formats,operating system or command line configuration.2.3 The tools layerThe tools layer code is responsible only for regulating interactionbetween the user and the analysis modules. Several tools have beenimplemented using the ProteoWizard Library including:o msConvert: data format conversion from vendor proprietaryformats to mzML and mzXML.o msDiff : comparison of two data files, for validation ofconversion and preprocessing.Fig. 2. Architecture of msAccess tool (utility and data layers).Fig. 3. msPicture output.o msAccess : command line access to mass spec data files,including spectrum binary data and metadata, selected ionchromatograms. The modular layout of msAccess is shown inFigure 2.o msPicture: pseudo-2D gel image creation tool. msPicture canread from a variety of formats to generate dataset images.In addition, if given a pepXML file, msPicture can denotetriggered MS/MS, colored by peptideProphet score. We showan example output in Figure 3.The hello_analyzer program has been provided in the codeexample supplement as a demonstration of how easily one can useProteowizard for creating analysis tools.3 SUMMARY AND FUTURE DIRECTIONSAs the proteomics field continues to grow, an increasing number ofresearch groups are writing custom software for data analysis. Ourgoal is for ProteoWizard to become a repository where proteomicssoftware developers can share their work, and benefit from thework of others. We welcome contributions of existing code, or newprojects that will benefit the proteomics community. Already, theTPP tools will be using ProteoWizard to support mzML in the nextmajor release, in advance of the formal release of mzML at ASMS2008. SWIG bindings are currently being developed to allow accessto the ProteoWizard Library from JAVA, Python, PERL and R.2535
D.Kessner et al.ACKNOWLEDGEMENTSThe authors would like to thank Roland Luethy and JonathanKatz for contributing towards the development and application ofProteoWizard, Natalie Tasman for code contributions, Brian Pratt forRAMP implementation and Eric Deutsch, the ISB NHLBI ProteomeCenter and the HUPO-PSI for help with ProteoWizard’s mzMLinterfaces.Funding: This work has been supported by the NCI CCNE-TR, theWunderkinder Foundation and by the Bennioff Foundation. M.C. issupported by NIH Grants: R01 CA126218 and U24 CA126479.Conflict of Interest: none declared.REFERENCESKeller,A. et al. (2005) A uniform proteomics MS/MS analysis platform utilizing openXML file formats. Mol. Syst. Biol., 1, 1–8.Kohlbacher,O. et al. (2007) TOPP–the OpenMS proteomics pipeline. Bioinformatics,23, e191–e197.Orchard,S. et al. (2007) Five years of progress in the standardization of proteomicsdata 4th annual spring workshop of the HUPO-proteomics standards initiativeApril 23–25, 2007 Ecole Nationale Superieure (ENS), Lyon, France. Proteomics,7, .Pedrioli,P.G. et al. (2004) A common open representation of mass spectrometry dataand its application to proteomics research. Nat. Biotechnol., 22, .Rauch,A. et al. (2006) Computational Proteomics Analysis System (CPAS): anextensible, open-source analytic system for evaluating and publishing proteomicdata and high throughput biological experiments. J. Proteome Res., 5, 112–121.2536
· ArticleFull-text availableFeb 2018ArticleFeb 2018ArticleFull-text availableJan 2018Show moreFederal University of Rio de JaneiroI'm trying to convert subsets of a single .Raw data into .mzML with 2
minutes sequential sections using command line. For that I'm usinge.g.:
--filter &scanTime [1,300]&--filter &scanTime [301,600]&such as:&& msconvert #2MEOH.RAW --mzML -z --mz32 --filter &peakPicking true 1-2& --filter &scanNumber [1,100]& --outfile #2MEOH_1.mzML -o mzML_section&& msconvert #2MEOH.RAW --mzML -z --mz32 --filter &peakPicking true 1-2& --filter &scanNumber [101,200]& --outfile #2MEOH_2.mzML -o…ProjectPrivate Profile[...]ArticleOctober 2007 · Metabolomic studies generate large quantities of data. Metabolomics data sets have complex structure and will typically be subjected to a variety of processing and analysis techniques. The data sets are expensive to collect and can be expected to hold more useful information than is extracted and used by the studies, which collected them. These aspects of metabolomics have caused workers to... [Show full abstract]ArticleJanuary 2006ArticleApril 2006 ·
· Impact Factor: 4.25Conference PaperJanuary 2009ArticleData provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.This publication is from a journal that may support self archiving.Last Updated: 04 Jan 18Project web is currently offline pending the final migration of its data to our new datacenter.}