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Introduction
Scan Modes
Thermo Scientific TSQ Series Hardware Manual 9
Figure 4. Examples of compounds with a common neutral-loss fragment
Data Dependent Scan Mode
The TSQ mass spectrometer uses the information in a data-dependent scan mode experiment
to make automatic decisions about the next step of the experiment without input from a user.
In data-dependent scan mode you specify criteria to select one or more ions of interest on
which to perform subsequent scans, such as MS/MS. You can approach the setup of
data-dependent experiments in either of two ways:
• If you have some idea of what the parent ion is, or if you expect a certain kind of parent,
you can set up a list of possible parent ions. Then, when one of the parent ions you
specified is detected, you can acquire product spectra and analyze the information.
Conversely, you can also set up a list of ions that you do not want selected for
fragmentation.
• If you have little information about your compound, you can set up the parameters of a
data-dependent experiment so that if the intensity of the ion signal is above a specified
threshold, the TSQ system generates product spectra. Later, you can decide if the
information is useful.
Because a data-dependent scan needs to use a target ion from a previous scan, the first scan
event cannot be a data-dependent scan.
N
N
N
N
N
OH
N
N
N
N
N
2
H
N
2
H
N
N
N
2
H
N
2
H
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