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Running on a Real Instrument

Although ViMMS is primarily a simulator, controllers can also drive a Thermo Orbitrap Fusion Tribrid mass spectrometer via Thermo Fisher's IAPI. The vimms_fusion extension mirrors the in silico classes with instrument aware counterparts.

Requirements

  • A valid installation of the IAPI libraries from Thermo Fisher Scientific.
  • The optional vimms-fusion package available in the ViMMS repository.

Basic Usage

from vimms_fusion.MassSpec import IAPIMassSpectrometer
from vimms_fusion.Environment import IAPIEnvironment
from vimms.Controller import TopNController

mass_spec = IAPIMassSpectrometer(polarity="positive")
controller = TopNController("positive", N=5, isolation_width=1)

with IAPIEnvironment(mass_spec, controller, min_time=0, max_time=900) as env:
    env.run()

The same controller implementations used for simulation can therefore be deployed directly on the instrument. Refer to the examples in examples/04. DDAvsDIA (Wandy et al 2023) for notebook demonstrations.