Mass spectrometry
(MS) is uniquely powerful for measuring
the mass
of intact proteins and other biomolecules. New applications have expanded
intact protein analysis into biopharmaceuticals, native MS, and top-down
proteomics, all of which have driven the need for more automated data-processing
pipelines. However, key metrics in the field are often not precisely
defined. For example, there are different views on how to calculate
uncertainty from spectra. This Critical Insight will explore the different
definitions of mass, error, and uncertainty. It will discuss situations
where different definitions may be more suitable and provide recommendations
for best practices. Targeting both beginners and experts, the goal
of the discussion is to provide a common foundation of terminology,
enhance statistical rigor, and improve automation of data analysis.