Peer Reviewed Journal via three different mandatory reviewing processes, since 2006, and, from September 2020, a fourth mandatory peer-editing has been added.
Tandem mass spectrometry (MS/MS) is a popular technology for identifying small molecules
involved in metabolism, better known as metabolites. Coupled with liquid chromatography
(LC), LC-MS/MS instruments first separate, ionize, and fragment metabolites, then measure
mass-to-charge ratios (m/z) and intensities of metabolite fragments. Understanding
metabolite fragmentation is crucial to develop computational tools for identifying
metabolites based on this spectroscopic data. Metabolite fragmentation patterns have large
variations making it especially difficult for computer scientists to design and implement
metabolite identification approaches. To address this interdisciplinary challenge, this
article presents FragView, a web-based application providing the web service for
visualizing metabolite fragmentation. Users can break chemical bonds to produce
metabolite fragments and export 3D fragment structures for 3D printing. Developing
FragView is an opportunity for exposing student participants to this interdisciplinary
bioinformatics project. This paper summarizes the experience of training student
participants in bootcamps and designing the implementation plan based on student
backgrounds. Students were exposed to project meeting discussions on coding and raw data
visualization and visited a lab with an LC-MS/MS instrument. FragView is an open source,
freely accessible tool, released under the GPLv3 license. We will continue to improve and
update FragView in the future based on feedback.
