Saturn GC/MS System

Minimizes Spectral
Skew
Varian Application Note
Number 5
John Sullivan and Robert D. Brittain
Varian Chromatography Systems

Key Words: Spectral Skewing, DFTPP

All GC/MS systems exhibit a certain degree of spectral
skew in the full scan mode (see Figure 1) that is
dependent on the time required for data collection.
This skewing is caused by the changing concentration
of the analyte in the MS system as the GC peak
elutes. For instance, if the spectral scan takes 500
msec to complete and the analyte concentration
changes appreciably during this time, then the
resulting spectrum is distorted. When capillary
columns are used, GC peaks are sufficiently narrow
that large concentration changes can occur in the time
required for one spectral scan.
To minimize spectral skewing, the mass range should
be scanned as rapidly as possible. Unfortunately, most
GC/MS systems cannot be operated at scan rates
high enough to eliminate spectral skewing. While most
benchtop GC/MS systems can operate at high scan
rates (1000-3000 mass units per second), in practice
they are normally used at lower scan rates (<1000 per
second) due to various operational limitations (e.g.,
sensitivity, mass intensity, consistency, etc.) This is
illustrated in Figure 2, which shows spectra for the
EPA tuning compound decafluorotriphenyl- phosphine
(DFTPP) on the leading and trailing sides of the GC
peak using a conventional quadrupole GC/MS.

Hypothetical Isointensity
Mass Spectrum without Skew

m/z

SCAN PERIOD

Figure 1. Spectral skewing of a hypothetical compound with an isointensity spectrum. Skewing occurs when scan rate is slow
with respect to concentration change of the analyte. Example assumes scan from low to high mass.
The Saturn GC/MS system is designed to minimize System A, whereas minimal change is observed on
spectral skewing by acquiring data at much higher the Saturn system.
rates than other systems; the resulting Saturn mass
spectra are representative of the analyte eluting from
Minimizing spectral skew has several advantages
the GC and free of distortion by spectral skewing.
when resulting data are interpreted. One of the
Furthermore, data file size is maintained at acceptable
primary advantages of an information-rich detector
levels by advanced data averaging algorithms which
such as the Saturn is the ability to detect co-eluting
condense the data acquired at these high scan rates.
analytes. This is done by looking for spectral changes
Saturn data collection and storage processes are
across the width of a peak. When coeluting peaks are
illustrated in Figure 3. The spectrum is always
present at different concentration levels, these
scanned from low to high mass at 5600 mass
spectral shifts are much more difficult to detect if
units/sec; each resulting spectrum is called a
spectral skewing is also occurring. In addition, since
“microscan”. Several of these microscans are
the intensities of individual mass peaks are important
averaged to create the “analytical scan”. This
to both library search and quantitation routines,
averaging increases the S/N ratio while reducing the
identification and quantitation accuracy may be
data file size. The result is a true “average spectrum”
compromised by spectral skewing. A further
for the analyte that is representative of the spectrum at
consideration is the use of compounds such as
the center of the analytical scan.
DFTPP for mass spectrometer tuning in EPA
environmental analyses. It is more difficult to obtain
For comparison with Figure 2 (acquired with System A accurate and reproducible spectra for these EPA
which is a widely used benchtop quadrupole mass tuning compounds when spectral skewing is present.
spectrometer), Saturn GC/MS spectra of DFTPP are
shown in Figure 4. Mass spectrometer and
The Saturn GC/MS system combines rapid spectral
chromatographic parameters for the Saturn and
scanning with advanced data averaging techniques to
System A were set to obtain 8 spectral scans across
provide the analyst with the highest quality mass
identical peak widths for the DFTPP, typical of GC/MS
spectral data free of significant spectral skewing. This
analyses. The comparative data are summarized in
ensures the highest degree of confidence in mass
Figure 5, which shows the ratio of ion intensities at m/z
spectrometer tuning, compound identification, and
198 and 442 for every scan across the DFTPP peak.
quantitation.
This ratio changes markedly across the GC peak on

Figure 2. Spectra from the leading and trailing sides of a GC peak on System A, a widely used benchtop quadrupole mass
spectrometer that scans from high to low mass. Note the differences in ratio of ion intensities for m/z 198 and 442.
 SIGNAL AVERAGING ANALYTICAL SCAN 2
AFTER SIGNAL AVERAGING

4 5

3 6

2 7

1 8

Figure 3. Data collection process in the Saturn GC/MS system involves averaging several microscans to obtain a single
analytical scan.
 Figure 4. Spectra from the leading and trailing sides of a GC peak on the Saturn GC/MS system.

Figure 5. Ratio of 198 m/z to 442 m/z for each individual scan across a DFTPP peak on Saturn and System A. System A is a
widely used benchtop quadrupole mass spectrometer.

These data represent typical results.

For further information, contact your local Varian Sales Office.
GCMS5:0792