Blog
New computer tool helps advance chemical analysis to protect the marine ecosystem
MassQL software was developed by an international research group in collaboration with a Brazilian scientist
Open source software to be used in Brazilian research on coral bleaching – Photo: Freepik
Modern natural product chemistry relies on analytical methods that produce vast amounts of data, mass spectrometry, for instance, detects molecules of interest and measures their mass, helping to determine their chemical structure. Typically, scientists focus on a specific research question and end up using only a small portion of the data generated. Meanwhile, the rest, which could support numerous other analyses and studies, often remains unexplored.
An international research group has produced software that promises to make research more efficient, using mass spectrometry and metabolomics – the study of the products of metabolism in living beings – as its main analysis tools. Called Mass Spectrometry Query Language (MassQL), the open-source tool allows an expressive set of molecule mass patterns to be analyzed from raw data.
The tool was designed in collaboration with Anelize Bauermeister, a professor at the Laboratory of Chemical Ecology of Microorganisms and Innovation (Lequim) at USP’s Institute of Chemistry (IQ). Anelize studies coral bleaching, a phenomenon that happens when coral reefs suffer some kind of stress, such as rising ocean temperatures, and expel the zooxanthellae—microalgae that live on their surface and provide much of the nutrients necessary for their survival.
In this context, her research group intends to apply the Mass Spectrometry Query Language to analyze the metabolome of corals and their associated microorganisms, deepen our understanding of the interactions between these individuals, and help formulate strategies to prevent or remediate damage. The goal is to protect the marine ecosystem from growing environmental threats.
According to Anelize, MassQL provides the means for researchers from different laboratories, with various equipment, to compare their data in search of relevant information about the chemical profiles of the samples analyzed.
Anelize Bauermeister - Photo: Lattes
“I can access the database and analyze samples from other people and from different places in the world, which I wouldn’t have access to here in my lab. I can compare a coral from the coast of São Paulo with a coral from Australia,” she explains.
Collaboration
While studying the metabolomics of marine organisms through mass spectrometry, the researcher identified the need to detect structural patterns representing specific classes of compounds. Her goal was to compare the chemical profiles of bacteria collected from beach sand and the seabed, in order to understand how environmental conditions influence their similarities and differences. However, amid the vast amount of data generated, she encountered a major limitation: “There was no software that allowed me to specifically search for chemical functions, I could only access this information through complex programming code.”
The scientist then shared her concerns with colleagues in the field of bioinformatics, which combines biology, computing, mathematics, and statistics. Led by researcher Mingxun Wang from the Department of Computer Science at UCSD, the team began developing a new computational tool to assist with data mining: MassQL. The platform offers access to spectral databases, information obtained through mass spectrometry and publicly shared by researchers, and to computer codes that allow users to search for specific mass patterns. These functionalities were designed and refined based on the prior experiences, needs, and challenges reported by Anelize and other researchers working with metabolomics.
Good for the environment
Another advantage of the software is that it allows for reanalyzing previously acquired but underutilized data. The method protects the environment by avoiding the collection of more coral samples from their natural habitat, as well as the time of researchers, who can focus on extracting relevant information from publicly available databases. “I can revisit this data using MassQL. It’s much more sustainable for the environment and for people too,” the researcher says.
An article detailing the tool’s design has been published in Nature Methods.
More information: e-mail anelize@iq.usp.br, with Anelize Bauermeister
*Science Media Fellow – Scientific Journalism/Fapesp at LarFarMar
**Intern under the supervision of Moisés Dorado
English version: Nexus Traduções, edited by Denis Pacheco
Política de uso
A reprodução de matérias e fotografias é livre mediante a citação do Jornal da USP e do autor. No caso dos arquivos de áudio, deverão constar dos créditos a Rádio USP e, em sendo explicitados, os autores. Para uso de arquivos de vídeo, esses créditos deverão mencionar a TV USP e, caso estejam explicitados, os autores. Fotos devem ser creditadas como USP Imagens e o nome do fotógrafo.
A reprodução de matérias e fotografias é livre mediante a citação do Jornal da USP e do autor. No caso dos arquivos de áudio, deverão constar dos créditos a Rádio USP e, em sendo explicitados, os autores. Para uso de arquivos de vídeo, esses créditos deverão mencionar a TV USP e, caso estejam explicitados, os autores. Fotos devem ser creditadas como USP Imagens e o nome do fotógrafo.