I am on the cheminformatics side and have done a lot of querying of data from mass spec files and having this as a DSL is highly convenient.
Typically we would use R/Python and the wetlab focused chemists would use GUI tools to inspect and compare spectra. I have also experimented with loading data into an SQL database for the obvious reasons and because the amount of data collected in the lab was such that indexing could be highly useful.
The major convenience in MassQL is the ppm thresholding that is build into every query, it makes any SQL you might write super long and ugly. Both the built-in support for isotope ratios and to be able to query both the full scan and the individual MS2 simultaneously is super useful. The wetlab people also found it much more intuitive than building a script in python or making convoluted SQL queries that could do the same.
Found this[1] page which includes an explanation of how it works, and also shows some analysis using the Spectra R package.
The SpectraQL[2] package adds MassQL support to Spectra, so one can compare a bit.
General-purpose data analysis tools tend not to be well suited to most types of scientific data. And it’s not only mass spectrometry, but also microscopy, diffraction, etc. There are huge improvements to be made in these areas.
