OpenMS protocols

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OpenMS specifications

Information


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
Wikipedia https://en.wikipedia.org/wiki/OpenMS

Subtools


  • ConsensusID
  • ProteinQuantifier
  • TOPP

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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

Publications for OpenMS

OpenMS in pipelines

 (10)
2017
PMCID: 5499783
PMID: 28713550
DOI: 10.5256/f1000research.12693.r23454

[…] 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 , the openms framework , compomics tools, such as peptideshaker , the pride database, as the world-leading proteomics repository (also coordinating the global proteomexchange consortium of proteomics […]

2017
PMCID: 5547443
PMID: 28673088
DOI: 10.1021/acs.jproteome.7b00248

[…] the “de novo” approach to feature detection (illustrated in , top). this classical approach is used by many important software tools for label-free quantification, including superhirn, maxquant, and openms (e.g., featurefindercentroided). however, decoupling feature detection from peptide identification in the “de novo” approach leads to a common problem: some peptides that were identified […]

2016
PMCID: 4795486
PMID: 26997865
DOI: 10.4137/BMI.S26229

[…] approach is based on two types of measurements. in the first case, the intensity of each peptide deriving from fragmentation of proteins is evaluated by dedicated softwares (eg, maxquant, openms, and demix-q). in the second case, the peak area or the spectral counting in the ms/ms analysis relative to a peptide is determined. there are several advantages in the label-free […]

2016
PMCID: 5311252
PMID: 27477696
DOI: 10.1038/onc.2016.242

[…] and n-termini, and carbamidomethylation on cysteine residues, a variable modification was used for oxidation on methionine residues. quantification of tmt-10plex reporter ions was carried out using openms project's isobaricanalyzer (v2.0). peptide spectrum matches found at 1% false discovery rate were used to infer gene identities, which were quantified using the medians of peptide spectrum […]

2015
PMCID: 5217390
PMID: 28248281
DOI: 10.3390/proteomes3040467

[…] database search results by means of gene ontology functional annotation, pathway analysis, and prediction of signal peptides and interaction networks [,,,,]. in addition, perseus/maxquant [], the openms proteomics platform [], and peptideshaker [] are commendable and freely available tools to extract and visualize biologically meaningful information from shotgun proteomics data., […]


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OpenMS in publications

 (83)
PMCID: 5864088
PMID: 29529084
DOI: 10.1371/journal.pntd.0006344

[…] mass)., lc-ms/ms raw data files were lock mass-corrected and converted to mzxml format using compass data analysis software (bruker daltonics). ms1 feature identification was performed using an openms-based [] workflow (optimus version 1.1.0 https://github.com/alexandrovteam/optimus, see for parameters), restricting to features with ms2 data available. feature abundance was normalized […]

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

[…] 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 […]

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 […]

PMCID: 5829137
PMID: 29487294
DOI: 10.1038/s41598-018-21541-4

[…] well in the case of a low number of samples and a high number of dimensions (molecular features and microbial taxa). molecular features are identified by inputting lc-ms/ms spectral data into the openms. molecular features are defined as molecule’s atomic weight through mass to charge ratio (m/z) and retention time (rt). rt reflects the hydrophobicity property of the molecule. by combining […]

PMCID: 5736515
PMID: 29260340
DOI: 10.1186/s13321-017-0252-9

[…] metabolome, with novel molecules generated using promiscuous enzymatic reaction rules. these novel molecules are searched on the ms spectra of an e. coli cell lysate interfacing our workflow with openms through the knime analytics platform., we provide an easy to use and modify, modular, and open-source workflow. we demonstrate its versatility through a variety of use cases including […]


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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

 (2)
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Anonymous user #552

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Desktop
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.