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MassSpecWavelet specifications


Unique identifier OMICS_10872
Name MassSpecWavelet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.46.0
Stability Stable
caTools, waveslim, xcms
Maintained Yes


No version available



  • person_outline Pan Du

Publication for MassSpecWavelet

MassSpecWavelet citations


Navigating freely available software tools for metabolomics analysis

PMCID: 5550549
PMID: 28890673
DOI: 10.1007/s11306-017-1242-7

[…] ted ion list. A suite of modular tools is provided by MeltDB. It includes a number of algorithms for peak picking including matchFilter (Smith et al. ) and centWave (Tautenhahn et al. ) from XCMS and MassSpecWavelet (Du et al. ), as well as retention indices calculation and sum formula annotation.metaMS(Wehrens et al. ) is based on XCMS (Smith et al. ) and CAMERA (Kuhl et al. ) but is adapted for […]


MetMatch: A Semi Automated Software Tool for the Comparison and Alignment of LC HRMS Data from Different Metabolomics Experiments

PMCID: 5192445
PMID: 27827849
DOI: 10.3390/metabo6040039

[…] g is performed on the remaining signals inside each narrowed search frame. Currently three different chromatographic peak picking algorithms have been implemented and can be selected in MetMatch. The MassSpecWavelet algorithm, while being very reliable, has significantly longer runtimes than the other two peak picking algorithms. These are based on Gaussian peak correlation and the Savitzky-Golay […]


A conserved role of the RSC chromatin remodeler in the establishment of nucleosome depleted regions

Curr Genet
PMCID: 5383693
PMID: 27558480
DOI: 10.1007/s00294-016-0642-y

[…] .2() function from the “gplots” package.Nucleosome positions were computed for each dataset as the local maximum of nucleosome occupancy in a 100 bp window using the localMaximum() function from the “MassSpecWavelet” package. Promoter NDR length is computed as the distance in bases between the position of the first nucleosome before the TSS and the first nucleosome after the TSS. This metric was c […]


Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry

PLoS One
PMCID: 4521892
PMID: 26230717
DOI: 10.1371/journal.pone.0134256

[…] for improving peak detection in simulated mass spectra. We present comparisons of our algorithm of peak detection to the two peak detection algorithms of high efficiency published in the literature, MassSpecWavelet (based on continuous wavelet transform, CWT, approach) [] and Cromwell (based on spectra differentiation) []. Comparisons are based on a large number of artificially generated datasets […]


Visualization of proteomics data using R and Bioconductor

PMCID: 4510819
PMID: 25690415
DOI: 10.1002/pmic.201400392

[…] preprocessing for relative quantitation and statistical analysis and enables visualization throughout the pipeline. Other packages provide functionality to process raw MS data, such as, among others MassSpecWavelet [] continuous wavelet transform for peak detection (used internally by xcms), BRAIN [] to to calculate the aggregated isotopic distribution, PROcess [] for SELDI-TOF data processing. T […]


Identifying and quantifying metabolites by scoring peaks of GC MS data

BMC Bioinformatics
PMCID: 4307155
PMID: 25492550
DOI: 10.1186/s12859-014-0374-2

[…] ject home page: system: Platform independentPrograming language: R [] version 3.0.0 or higherOther requirements: R packages xcms [], svDialogs [], pander [] and MassSpecWavelet []License: General Public License version 3 […]


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MassSpecWavelet institution(s)
Robert H Lurie Comprehensive Cancer Center, Northwestern UniversityChicago, IL, USA

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