Abstract: The disclosure features systems and methods that include: exposing a biological sample to an ion beam that is incident on the sample at a first angle to a plane of the sample by translating a position of the ion beam on the sample in a first direction relative to a projection of a direction of incidence of the ion beam on the sample; after each translation of the ion beam in the first direction, adjusting a focal length of an ion source that generates the ion beam; and measuring and analyzing secondary ions generated from the sample by the ion beam after adjustment of the focal length to determine mass spectral information for the sample, where the sample is labeled with one or more mass tags and the mass spectral information includes populations of the mass tags at locations of the sample.

Abstract: The disclosure features methods and systems that include directing an ion beam to a region of a sample to liberate charged particles from the region of the sample, where the directed ion beam is pulsed at a first repetition rate, deflecting a first subset of the liberated charged particles from a first path to a second path different from the first path in response to a gate signal synchronized with the repetition rate of the pulsed ion beam, and detecting the first subset of the liberated charged particles in a time-of-flight (TOF) mass spectrometer to determine information about the sample, where the gate signal sets a common reference time for the TOF mass spectrometer for the first subset of charged particles liberated by each pulse of the ion beam.

Abstract: The disclosure features systems and methods that include: exposing a biological sample to an ion beam that is incident on the sample at a first angle to a plane of the sample by translating a position of the ion beam on the sample in a first direction relative to a projection of a direction of incidence of the ion beam on the sample; after each translation of the ion beam in the first direction, adjusting a focal length of an ion source that generates the ion beam; and measuring and analyzing secondary ions generated from the sample by the ion beam after adjustment of the focal length to determine mass spectral information for the sample, where the sample is labeled with one or more mass tags and the mass spectral information includes populations of the mass tags at locations of the sample.