Introduction
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_______________________________________________________________ Experiment Types
_______________________ Finnigan LTQ Hardware Manual _____________________
1-23
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In an Ion Tree experiment, you can specify either of two options that prioritize
how the LTQ gathers information: Depth Focus and Breadth Focus.
• Depth Focus characterizes an ion by performing a series of MS
n
-level
fragmentations (for example, MS/MS, MS
3
, MS
4
, etc.) before
characterizing the next most intense ion in the MS
n
series.
• Breadth Focus characterizes all ions to the same MS
n
level before
advancing to the next MS
n
level.
For example, if you specify a Maximum Depth of 3 and a Maximum Breadth
of 2 in an Ion Tree experiment, the following occurs:
• First, with either Depth or Breadth Focus, the LTQ scans for parent ions
(MS) over the specified mass range. The most intense ion of the MS
spectrum is selected for fragmentation (MS/MS).
• Second, if you chose the Depth Focus, after the most intense ion of the
MS spectrum is fragmented — producing an MS/MS spectrum — the
LTQ selects and fragments the most intense ion of the MS/MS spectrum.
This results in an MS
3
spectrum, the level specified as the maximum
depth for this example. The LTQ then backs up one level and fragments
the second most intense ion of the MS/MS spectrum, creating more
product ions on the level of MS
3
from this parent ion. This process is then
repeated for the second most intense ion in the MS spectrum.
• If you chose the Breadth Focus, after the most intense ion of the MS
spectrum is fragmented — producing an MS/MS spectrum — the LTQ
selects and fragments the second-most intense ion of the same MS
spectrum. The fragmentation of parent ions continues to the Max Breadth
level that you specified (2, for this example). After the two most intense
peaks on the MS level are fragmented, the LTQ scans the first MS/MS
spectrum to select and fragment the two most intense ions. This results in
product ions on the level of MS
3
, the level specified as the maximum
depth for this example. This process is then repeated for the second most
intense ion in the MS spectrum.
The results of a Data-Dependent Ion Tree experiment can be viewed in the
Xcalibur Qual Browser window. The results are displayed as a structure tree
that originates from a particular parent ion.
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