New DSL "MassQL" lets scientists query mass spectrometry data

Summary

Biologists and chemists have a new programming language to uncover previously unknown environmental pollutants at breakneck speed – without requiring them to code. By making it easier to search massive chemical datasets, the tool has already identified toxic compounds hidden in plain sight. UCR computer scientist Mingxun Wang in his laboratory. Wang created the new programming language for scientists. (Stan Lim/UCR) Mass spectrometry data is like a chemical fingerprint, showing scientists what molecules are in a sample such as air, water, or blood, and in what amounts. It helps identify everything from pollutants in water to chemicals in new medicines. Developed at UC Riverside, Mass Query Language, or MassQL, functions like a search engine for mass spectrometry data, enabling researchers to find patterns that would otherwise require advanced programming skills. Technical details about the language, and an example of how it helped identify flame retardant chemicals in public waterways, are described in a new Nature Methods journal article. “We wanted to give chemists and biologists, who are generally not also computer scientists, the ability to mine their data exactly how they want to, without having to spend months or years learning to code,” said Mingxun Wang, UCR assistant professor of computer science, who created the language. Demonstrating the effectiveness of the language, Nina Zhao, a postdoctoral student at UC San Diego, used MassQL to sift through the entire world’s mass spectrometry data on water samples that has been made available to the public. She was looking for organophosphate esters, which are generally found in flame retardants. “There are quite literally a billion measurements of molecules in this data. You cannot go through it manually,” said Wang. “However, the language acts like a filter, in a sense, for these chemicals, and it pulled out thousands of them.” In addition to finding known chemicals in the water samples, they also found organopho...