Technical data

Methods with Acquisition Parameters 3
Setup of TOF and Q-TOF reference mass correction (recalibration)
Agilent 6200 Series TOF and 6500 Series Q-TOF LC/MS System Concepts Guide 89
For example, if a Time Segment contains one Experiment with
Fragmentor voltage at 225 V and another Experiment with
Fragmentor voltage at 200 V, then a spectral cycle contains two
successive spectra, one at 225 V and another at 200 V.
Spectra from scans of different fragmentor voltage (or other
scan specific parameters) should not be summed and averaged
because they yield different masses.
Example The “Scans To Average” is 5. If the spectrum of interest is in the
nth cycle, then spectral data of the same Fragmentor voltage
from cycles n-2, n-1, n, n+1, n+2 are used in the average with
equal weights. If this Time Segment has defined one Fragmentor
voltage of 225 Experiment #1, and one Fragmentor voltage of
220 Experiment #2, and the current spectrum is the
Fragmentor voltage of 225 Experiment #1 of the nth cycle, the
spectra n-4, n-2, n, n+2, n+4 will be used for the average.
Reference Mass Window When the software attempts to find
the reference mass, it searches for the highest spectral peak in
the defined reference mass window, which is the window width
in parts per million (ppm). Recalibration using reference
masses of the internal reference standard does not replace
normal or external mass calibration. You must set the window
for recalibration small enough so the software does not pick
a spectral peak from the sample as the reference mass peak. 100
ppm is the recommended default value.
Reference Mass Minimum Height The “Reference Mass
Minimum Height” is the abundance in counts. The software uses
this height to exclude noise peaks and peaks of reference
masses that may fall within the detection window but that are
too small to be used for calibration. This is especially important
if you use reference masses that may be present in the tryptic
digest, such as the y1 ion (147 m/z for N-terminal Lys or 175 m/z
for N-terminal Arg), but may not be present in all spectra in the
run. Signals below 1,000 counts are generally too low to be used.
Signals above 75,000 counts for the reference mass ion can
negatively affect the reference mass correction.