setting: Class Representing the Setting of a Mass Spectrometer

In zeehio/msProcess: Protein Mass Spectra Processing

Description

Class slots:

dist.drift

a numeric scalar denoting the length of drift tube in meters.

dist.focus

a numeric scalar denoting the distance between charged grids in millimeters.

dist.accel

a numeric scalar denoting the distance from sample plate to first grid in millimeters.

volt.accel

a numeric scalar denoting the voltage between charged grids in volts.

volt.focus

a numeric scalar denoting the voltage used in ion focusing phase in volts.

time.delay

a numeric scalar denoting the delay time before focus voltage is applied in nanoseconds.

time.resol

a numeric scalar denoting the time between detector records in seconds.

vel0.mean

a numeric scalar denoting the mean initial velocity in meters/second.

vel0.std

a numeric scalar denoting the standard deviation of initial velocity.

The model of a linear MALDI-TOF instrument with time-lag focusing depends on the nine parameters. In a real instrument, the three distance parameters (dist.drift, dist.focus, and dist.accel) are unchanging characteristics of the design. The user has direct control over volt.accel, volt.focus, time.delay, and time.resol. The parameters that determine the normal distribution of initial velocities, i.e., vel0.mean and vel0.std, are controlled indirectly by the choice of EAM and by the laser intensity.

S3 METHODS

show

Display a setting object.

Usage: show(object) or object

object

a setting object.

References

Coombes, K.R., Koomen, J.M., Baggerly, K.A., Morris, J.S., Kobayashi, R., “Understanding the characteristics of mass spectrometry data through the use of simulation," Cancer Informatics, 2005(1):41–52, 2005.

See Also

spectrometer.

zeehio/msProcess documentation built on May 4, 2019, 10:15 p.m.