Maximizing information usage

For genome analysis it is commonly accepted that one can hypothesize the function of genes based on sequence similarity, using annotated reference sequences. Once a homology hypothesis has been made based on reference annotations, it allows one to build hypothesis in terms of function and ultimately understand the underlying biology. In contrast, mass spectrometry (MS) can detect many molecules, as ions, yet we often cannot link a MS signal to a molecule. The reference libraries to annotate fragmented molecular data only cover a small portion of the known molecular space. The use of computational (in silico) fragmentation predictions from structural libraries offers a promising alternative. One of the weaknesses of the molecular annotation using such in silico approaches is that they currently annotate the molecules individually. However, molecular relationships, based on spectral similarity, can be used to enhance the structural hypothesis inferred from the annotation of molecules detected by mass spectrometry. We introduce an online tool called “Network Annotation Propagation” that uses a combination of molecular networks, based on spectral similarity, from which we infer molecular similarity, together with in silico fragmentation, to enable the scientific community to strengthen their MS annotations.

Propagating annotations of molecular networks using in silico fragmentation
Ricardo R. da Silva, et al.
PLoS Comput Biol April 18, 2018

Data integration

Metabolomic profiles were explored to understand environmental and taxonomic influences on the metabolism of two congeneric zoanthids, Palythoa caribaeorum and P. variabilis, collected across distinct geographical ranges. Integrated mass spectrometry data suggested the major influence of geographical location on chemical divergence when compared to species differentiation.

Chemical profiling of two congeneric sea mat corals along the Brazilian coast: adaptive and functional patterns.
L. V. Costa-Lotufo, F. Carnevale-Neto, A. E. Trindade-Silva, R. R. Silva, et al.
Chemical Communications Dec 2017



Data analysis workflow

Mass spectrometry instruments measure the mass to charge ratio of ions, from which we infer the molecular structures. They are key tools for investigating the incredibly diverse chemistry that is associated with biological systems. Typically, when one thinks about the chemistry of biology, one thinks of biochemical pathways, structural lipids or carbohydrates. However, numerous additional chemistries are part of various biological systems. These include molecules that originate from diet, water treatment, personal care, medications, pollutants and environmental exposures including plastics, clothes and furniture. These principles apply not only to people but to all of biology, from the worms at the bottom of the ocean, to the bacteria in our belly buttons and to the birds that fly over Mount Everest. In the past decade, our capacity to inventory the chemistry of biological systems using mass spectrometry at a global level has been revolutionized. In this Review, we discuss the informatics and hardware tools that are available for small-molecule analysis and provide an overview of the tools that could transform how we study the chemistry of biological systems; perhaps in the future this will be as easy as taking a photograph with a smartphone.

Global chemical analysis of biology by mass spectrometry
Alexander A. Aksenov, Ricardo da Silva, et al
Nature Reviews Chemistry July 2017