User`s guide

Chapter 6 Acquiring Mass Spectra
6-26 PerSeptive Biosystems
6
• Signal intensity of reference and analyte peaks is in
the same range—Signal intensity of reference and
analyte peaks should be of similar magnitude. If they
are not in the same range, you may see weak analyte
peaks with poor signal-to-noise ratio while the internal
standard is adequate, or saturated internal standard
peaks with adequate analyte peaks.
• No contaminants present—Unresolved contaminants
can affect peak shape.
• Two internal reference masses that bracket the
mass range of interest—Best results are obtained
when masses above and below the mass of interest are
correctly identified.
NOTE: Although not required, using more than two
reference masses can help to minimize the effects of
an asymmetrical reference peak.
• Internal reference masses are within the same
range as analyte masses—Best results are obtained
when masses are in the same range. For example,
reference masses of 904 and 1,570 are adequate when
evaluating an analyte mass of 1,296 Da.
During mass
calibration and
peak detection
When calibrating mass (described in the Data Explorer
Software User’s Guide,
Section 5.3, Manual Calibration) and
detecting peaks (described in the
Data Explorer Software
User’s Guide,
Section 3.2, Peak Detection), the following
factors contribute to the accuracy of mass measurements:
• Use Centroid mass instead of Apex mass—Before
calibrating, set peak labels to Centroid. Centroid mass
is the best representation of peak position. Apex mass
represents the highest data point.
• Set Centroid Percent to 50%—Lower settings can
include noise or contaminant peaks. Higher settings
may not include adequate data to ensure accurate
mass assignment.