Extended Data Fig. 1: Resolution-based isotopic envelope calculation.

a) The MS resolution is inversely proportional to the peak width of the acquired signals. When preprocessing raw MS1 data, a centroidization algorithm performs a peak- picking on a continuous profile signal (blue), yielding discrete, centroided signals (red). As resolution increases, the minimal distance to distinguish two adjacent peaks decreases (d2 < d1). b) In practice, this implies that, when acquiring data at lower resolutions, certain isotope signals are masked by close, more intense signals c) By calculating a resolution-based parameter d, HERMES can estimate which close isotopologues can be distinguished in the acquired profile MS1 data and therefore present in the centroided data (See Algorithm 1).