ISQ User Guide - Write Frame of Mind

4 Creating a Method
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 1100 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 created. You can also use a specific
tune file for each of the scans.
• The Mass List or Range column is used to indicate to the ISQ the 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.
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.
• In SIM mode, the Dwell or Scan Times column is used to define 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 between scans. 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 signal becomes less precise. This column must be set to
a value between .0005 and 10 s. The default is .1 s.
• The Tune File Name is used to select a tune file to be used for this scan. It should
be the automatic tune file you created in Tuning the ISQ.
• The Scan Name column is used to enter a description of the scan. The name
may be used as a label to indicate the compound used with the scan.
• The SIM Widths column is used to set 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, but lower intensity.
• 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.
• The Data Type column is used to select 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.
Thermo Scientific ISQ User Guide 37