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RMassBank specifications


Unique identifier OMICS_02657
Name RMassBank
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.8.0
Stability Stable
methods, gplots, Biobase, S4Vectors, Rcpp, RUnit, RCurl, digest, rjson, XML, MSnbase, mzR, rcdk, yaml, RMassBankData, xcms(>=1.37.1), CAMERA, ontoCAT, enviPat
Maintained Yes


No version available


RMassBank citations


Navigating freely available software tools for metabolomics analysis

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

[…] atabases all contain authenticated MS/MS spectra. Unlike the other spectral databases MassBank allows for the automatic upload of user-generated data to the database, using either the Mass++ (C++) or RMassBank (Stravs et al. ) (R) software.Both ESI-MS/MS and GC–MS spectra acquired using authenticated chemical standards are present in the HMDB (Wishart et al. ). Whilst the commercially available NI […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] ed spectra or simply by typing in spectral features, mass, or targeted compound name. It furthermore allows users to directly extract spectra during data processing through many tools like RAMClustR, RMassBank, and Mass++. Metabolite Link (METLIN) [] currently contains 961 829 molecules, from which 200 000 have in silico MS/MS data. Additionally, over 14 000 metabolites were analyzed, and mass spe […]


Critical Assessment of Small Molecule Identification 2016: automated methods

J Cheminform
PMCID: 5368104
DOI: 10.1186/s13321-017-0207-1

[…] t was (A/B): 95/5 at 0 min, 95/5 at 1 min, 0/100 at 13 min, 0/100 at 24 min (A = water, B = methanol, both with 0.1% formic acid) at a flow rate of 300 μL/min.The MS/MS peak lists were extracted with RMassBank [] using the ion mass and a retention time window of 0.4 min around the expected retention time and reported as absolute ion intensities. To obtain high-quality spectra, the data was cleaned […]


MetFrag relaunched: incorporating strategies beyond in silico fragmentation

J Cheminform
PMCID: 4732001
PMID: 26834843
DOI: 10.1186/s13321-016-0115-9

[…] ID (HCD) 15, 30, 45, 60, 75 and 90 normalized units (see [] for more details) coupled with liquid chromatography (LC) with a 25 min program on an Xbridge C18 column. The raw files were processed with RMassBank [, ], yielding the “EA” records in MassBank. These spectra were merged using the mzClust_hclust function in xcms [] (parameters eppm = 5×10-6 and eabs = 0.001 Da) to create peaks with the me […]


Data standards can boost metabolomics research, and if there is a will, there is a way

PMCID: 4648992
PMID: 26612985
DOI: 10.1007/s11306-015-0879-3

[…] e standards which were measured for the development and validation of MassCascade (Beisken et al. ). This data was used by M. Stravs (Eawag, CH), during a training workshop, to demonstrate the use of RMassBank (Stravs et al. ) to extract, annotate and recalibrate MS/MS data, and finally create 58 new reference spectra from MetaboLights (Haug et al. ) in MassBank (Horai et al. ).The deposited data […]


The Critical Assessment of Small Molecule Identification (CASMI): Challenges Solutions

PMCID: 3901296
PMID: 24958137
DOI: 10.3390/metabo3030517

[…] formed during MS/MS measurements, a phenomenon observed with several aromatic compounds (e.g., [,]). One result of the adduct detection was the expansion of the fragment formula annotation option in RMassBank to include adducts by adding N2 and O to the allowed elements of the subformulas []. The spectrum of Challenge 17 is shown in . The fragment at m/z 105.044 corresponding to a C6H5(N ≡ N)+ fr […]


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