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OpenMS specifications


Unique identifier OMICS_02387
Name OpenMS
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


  • ConsensusID
  • ProteinQuantifier
  • TOPP




No version available



  • person_outline Oliver Kohlbacher
  • person_outline jpfeuffer

Additional information ConsensusID: ProteinQuantifier:

Publications for OpenMS

OpenMS citations


KniMet: a pipeline for the processing of chromatography–mass spectrometry metabolomics data

PMCID: 5856871
PMID: 29576760
DOI: 10.1007/s11306-018-1349-5

[…] XML or CDF format (previously converted with, for instance, Proteowizard [14]) can be deconvoluted internally with the R (R Core Team ) library XCMS (Smith et al. ), or by integrating into KniMet the OpenMS nodes (Pfeuffer et al. ). Alternatively, this step can be performed externally with either the locally installed R instance, XCMS online [17] or a vendor software. In this case, the obtained da […]


Proteomic analysis of corneal endothelial cell descemet membrane tissues reveals influence of insulin dependence and disease severity in type 2 diabetes mellitus

PLoS One
PMCID: 5846724
PMID: 29529022
DOI: 10.1371/journal.pone.0192287

[…] .1%.In order to identify peptides, mass spectrometer RAW data files were converted to mzML format using msconvert [], then MGF files were generated from mzML using the Peak Picker HiRes tool from the OpenMS framework []. All searches required 10 parts per million precursor mass tolerance, 0.02 Dalton fragment mass tolerance, strict tryptic cleavage, up to 2 missed cleavages, fixed modification of […]


Elongator and codon bias regulate protein levels in mammalian peripheral neurons

Nat Commun
PMCID: 5832791
PMID: 29497044
DOI: 10.1038/s41467-018-03221-z

[…] . XML output files were parsed and non-redundant protein sets determined using Proteome Cluster (10.1002/pmic.200900370). MS1-based features were detected and peptide peak areas were calculated using OpenMS (10.1186/1471-2105-9-163). Proteins were required to have one or more unique peptides across the analyzed samples with E-value scores of 0.01 or less. Proteome data are available at ProteomeXch […]


Creating a 3D microbial and chemical snapshot of a human habitat

Sci Rep
PMCID: 5829137
PMID: 29487294
DOI: 10.1038/s41598-018-21541-4
call_split See protocol

[…] Feature finding is used to identify and distinguish detectible ions (molecules) from the complex sample mixture. Open-source OpenMS/TOPP software was used to identify molecular features from processed featureXML format. Unique features, represented by MS1 molecular mass, were identified based on detected precursor mass and […]


QCloud: A cloud based quality control system for mass spectrometry based proteomics laboratories

PLoS One
PMCID: 5764250
PMID: 29324744
DOI: 10.1371/journal.pone.0189209

[…] etriculator [], and others [], introduced web-based interfaces, interactive plots and comparison capabilities to assist instrument operators in monitoring quality control metric. Other tools, such as OpenMS [], iMonDB [] and AutoQC [], have also contributed to automate the extraction of quality metrics from raw files and, thus, to generate automatic pipelines for quality control. In parallel, meth […]


Expression Atlas: gene and protein expression across multiple studies and organisms

Nucleic Acids Res
PMCID: 5753389
PMID: 29165655
DOI: 10.1093/nar/gkx1158

[…] ine for microarray data has not changed since the last release. Proteomics data are currently processed in custom-designed way for each data set, using open source and/or free to use software such as OpenMS () and MaxQuant (). […]

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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

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Anonymous user #552's avatar image No country

Anonymous user #552

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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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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.