Department Environmental Chemistry

RMassBank:
Workflow to process tandem MS files and build MassBank records

RMassBank is a workflow to enable the creation of high quality accurate mass MS/MS spectral records for the MassBank database. The workflow includes automatic recalibration and processing of mass spectra within R from mzML files and the retrieval of compound information via web services to minimise the user efforts in record generation. At this stage RMassBank is designed and tested on Orbitrap XL and Q-Exactive (Thermo) data. Extensions to other instrument and acquisition types is in progress, through collaboration with the IPB, UFZ and the NORMAN Network. As RMassBank involves automated interpretation of the raw MS and MS/MS data, extensions to alternative formats relies on both the contributions of data and expertise from external parties.

Those directly involved in RMassBank development/maintenance include Michael Stravs & Emma Schymanski (Eawag), Steffen Neumann (IPB), Erik Müller (IPB/UFZ) and Tobias Schulze (UFZ). We also gratefully acknowledge the support of Prof. Nishioka (NAIST, Japan).

Further details are available in the Vignette included in the R package "RMassBank" available from Bioconductor and in the publication (citation below).

  • RMassBank (R package)
  • RMassBankData (raw test data: ~50 MB)
    Example spectra processed with RMassBank can be found on massbank.jp and massbank.eu, including

All MassBank records marked with a "CC" license can also be downloaded.

Feedback and contributions to RMassBank and MassBank are welcomed. Contact us (Michael Stravs, Emma Schymanski) via:

Citation

M. A. Stravs, E. L. Schymanski, H. P. Singer and J. Hollender, 2013: Automatic Recalibration and Processing of Tandem Mass Spectra Using Formula Annotation, Journal of Mass Spectrometry, 48 (1), 89-99. DOI: 10.1002/jms.3131