MassBank and RMassBank

Published on October 31, 2017   31 min

Other Talks in the Series: Bioinformatics for Metabolomics

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Hello and welcome to my talk on MassBank and RMassBank. My name is Emma Schymanski, I'm a research scientist at Eawag, the Swiss Federal Institute of Aquatic Science and Technology in Dubendorf, Switzerland.
Just to set the scene to this presentation, this presentation is actually part of a series on Bioinformatics for Metabolomics and forms Part D, for Metabolomics Resources and Computational Tools. And this talk being about MassBank and RMassBank actually covers both. So, MassBank itself is an open access library of mass spectra, and in this respect is a resource for identification of metabolites and small molecules. RMassBank is actually an open source R package enabling data upload into MassBank and computational tool to form part of this talk, and this is aimed really at increasing the number of publicly available mass spectra in MassBank and thus, also in the open space.
MassBank actually started in 2006, as one of the first public repositories of mass spectra. And you can see the website at the bottom of the slide, and this screenshot here, shows an overview of the database service from the MassBank website itself. One of the strengths but also in some people's minds, also one of the weaknesses of MassBank is that it had no standard analytical method. This meant that MassBank was actually suitable for all types of data, which in my opinion is actually a strength. You can basically include many different types of mass spectrum data so you can have gas chromatography, liquid chromatography, mass spectra, single scan mass spectra, or tandem mass spectra, high resolution, low resolution, and accurate mass data. So, that's just going through, in order of the acronyms on the slide, and the contributor is responsible for data quality, which is in some cases a good thing and in some cases not such a good thing and I will go through this in a few later slides. If you want to read up more about MassBank itself, then I'd recommend you look at the publication that I've also got referenced on this slide.