OpenMS specifications

Information


Unique identifier OMICS_02387
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
License BSD 3-clause “New” or “Revised” License, GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.2.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/OpenMS

Subtools


  • ConsensusID
  • ProteinQuantifier
  • TOPP

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Versioning


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Documentation


Maintainers


  • person_outline Oliver Kohlbacher <>
  • person_outline jpfeuffer <>

Additional information


https://github.com/OpenMS/OpenMS/wiki ConsensusID: http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/TOPP_ConsensusID.html ProteinQuantifier: http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html

OpenMS articles

OpenMS citations

 (5)
2017
PMCID: 5499783

[…] sweden). in addition, europe also hosts worldwide renowned groups that are focused on the development and application of widely-used bioinformatics tools and resources, including maxquant 4, the openms framework 5, compomics 6 tools, such as peptideshaker 7, the pride database, as the world-leading proteomics repository 8 (also coordinating the global proteomexchange consortium of proteomics […]

2016
PMCID: 5703597

[…] we present an automated pipeline for proteogenomic data analysis that is implemented within the openms framework for computational mass spectrometry. this pipeline is largely based on existing software (openms, mascot, ms-gf+, and percolator) but also benefits from custom extensions and new […]

2016
PMCID: 4895710

[…] human tissues., each raw file was converted to the standard mzml format using the proteowizard (v3.0.6485) msconvert tool35. following conversion, the data was processed with topp tools from openms (pre-v2.0 development build) (fig. 1)36. all spectra were centroided using the peakpickerhires tool, and files from fractionated experiments were merged using the filemerger tool (up […]

2014
PMCID: 4212285

[…] and 3) identification of differentially expressed proteins., several software packages support these tasks including the freely available trans-proteomic pipeline [33], the cpas system [34], the openms framework [35], and maxquant [36] (table 1). each of these packages has their advantages and shortcomings, and a detailed discussion goes beyond the scope of this review. for example, maxquant […]

2012
PMCID: 3477001

[…] method for identification assessment, the out files (containing assignments produced by sequest) of each set was converted to a unique idxml (v1.1) file. this is the format used by the algorithm (openms v1.4) for retention time prediction described by pfeifer et al. [18]., following elias et al. [19] recommendation, all searches used a database constructed as a composition of target protein […]

OpenMS institution(s)
Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Tuebingen, Germany; Center for Bioinformatics, University of Tuebingen, Tuebingen, Germany; Center for Quantitative Biology, University of Tuebingen, Tuebingen, Germany; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tuebingen, Germany; Chair for Bioinformatics and Information Mining, Department of Computer and Information Science, University of Konstanz, Konstanz, Germany; Institute of Molecular Medicine and Cell Research, Freiburg University, Freiburg, Germany; Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Berlin, Germany; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
OpenMS funding source(s)
Supported by BMBF (grant numbers 031A535A, 031A430C, and 01ZX1301F) and Deutsche Forschungsgemeinschaft (SFB685/B1, Core Facilities Initiative QBiC2).

OpenMS reviews

 (2)
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achimt

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great set of tools with a steep learning curve
Marc Dubois's avatar image No country

Marc Dubois

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Desktop
OpenMS is a C++ library for developers. Their programming interface is well done and very clear. A Python binding exposing most classes C ++ was created, an initiative that should be welcomed. It includes many algorithms for metabolomics and proteomics, all of which can be finely set. It brings new concepts of data reduction rather interesting (concept RawMap, PeakMap, FeatureMap) to theoretically manage large amounts of data. In theory only, since the development team announced reviewing the kernel openMS to greatly improve performance.

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