Thermo Scientific ISQ, User Manual

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4
Creating a Method
Creating a Method for the ISQ Mass Spectrometer
40 ISQ User Guide Thermo Scientific
As an example, in this method, the mass range of 50-550 amu will be scanned in
0.2 seconds. Beginning from the same start time, three different SIM masses at
100, 150, and 200 will be looked at for 0.2 seconds each. These simultaneous
full scan and SIM scans will begin 2.5 minutes into the GC run. You will get a
complete set of scans every 0.816 seconds.
At 4 minutes into the GC run, the scanning is completely changed. Now the full
scan range is 35-150 amu, which is scanned every 0.1 seconds, and the two SIM
masses are 450 and 614 amu, which are scanned for 0.1 and 0.2 seconds
respectively. All these scans will repeat every 0.412 seconds until the GC run is
complete.
All of these scans use the last tune file that was saved to the instrument.
b. The Mass List or Range column tells the ISQ system what masses it needs to scan.
In full-scan mode, enter the start and end mass separated by a dash. In SIM mode,
enter individual masses or multiple values in this field (as long as they are separated
by a comma). You must put each full-scan range on a separate line.
c. In SIM mode, the Dwell or Scan Times column defines the amount of time (in
seconds) that the ISQ will look at your SIM ion mass. If you are in Full-Scan mode,
the
Dwell or Scan Times column determines the amount of time for each individual
scan. You should set this value to have 5-20 scans across your GC peak. If you have
too few scans, the GC peak area is too imprecise. If you have too many scans, the ISQ
instrument’s signal becomes less precise. The default is 0.2 s.
d. The Tune File Name column selects a tune file to be used for this scan. It should be
the automatic tune file you created in Tuning the ISQ . You can also use a specific
tune file for each of the scans.
e. The Scan Name column contains a description of the scan. The name may be used as
a label to indicate the compound used with the scan.
f. The SIM Widths column sets the width range of the SIM window. The range of
values can be between 0.01 and 10. The default is 1 amu, which means the ISQ will
collect all the ions from your SIM mass +/- 0.5 amu. Narrower SIM widths lead to
greater specificity.
g. The Ion Polarity column is only used in CI mode, which is the only mode for
generating positive and negative ions. In EI mode, this column should be always be
set to
Positive .
h. The Data Type column determines whether you want to collect Profile or
Centroided Mass Spectra . Centroided mass spectra is most common because it is
used by most of the libraries and provides the smallest data files. Profiled mass spectra
provides detailed mass spectral peaks, which results in a large data file that contains
details a centroided spectra does not contain.
Note Each line in a scan must only contain a Full-Scan range or individual SIM masses.
They cannot be mixed in a single line.