Introduction
Experiment Types
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1-22 ______________________ Finnigan LTQ Hardware Manual _______________________
The LTQ includes the following Ion Mapping templates in Instrument Setup
so you can get started with an Ion Mapping experiment:
• Total (or full scan) Ion Map
• Neutral Loss Ion Map
• Parent Ion Map
These Ion Mapping experiments, in general, require that sample solution enter
the MS Detector at a composition that is constant throughout. Therefore, you
use infusion to introduce your sample for these Ion Mapping experiments.
In a Total (or full scan) Ion Mapping experiment, you get product ion scans
for each parent ion, so you can determine which parent ions lost a particular
fragment to yield a particular product ion. Furthermore, you can determine
which parent ions are related to specific product ions. For example, you can
map the spectral peaks in a mass range from m/z 400 to m/z 2000 and specify
to scan for MS/MS product ions in incremental steps of every mass-to-charge
ratio, every fifth mass-to-charge ratio, or every tenth mass-to-charge ratio.
A Neutral Loss Ion Mapping experiment collects scans for masses that have
lost neutral fragments. As with full scan Ion Mapping, you can get product ion
scans on every parent ion. However, a Neutral Loss Ion Map identifies which
parent ions lost a neutral fragment of a particular mass. For example, you can
specify a neutral loss of 80 u (as in the case of a phosphorylated peptide in a
tryptic digest). A Neutral Loss Ion Mapping experiment can step through each
product mass in the mixture. The experiment searches for evidence of the loss
of a neutral moiety of mass 80 u.
A Parent Ion Mapping experiment identifies all the ions that produce a
particular molecular ion that you specify. For example, if you specify a
product ion mass of m/z 50, a Parent Ion Map includes all the parent ions that
yielded the specified product ion, m/z 50.
A Data-Dependent Zoom Map is an Ion Mapping experiment that collects
ZoomScan data on every scan interval in a mass range that you specify, as
well as Data-Dependent MS/MS product spectra on every mass above an
intensity threshold.
The results of any of the Ion Mapping experiments can be viewed in the
Xcalibur Qual Browser window.
Ion Tree Experiments
In an Ion Tree experiment, the LTQ can collect MS
n
data automatically. You
can specify a particular parent ion for fragmentation, or you can let the LTQ
find the parent ions automatically and fragment them to any level between
MS
2
and MS
10
. The LTQ automates the collection of data by deciding what
actions need to occur next for the experiment to progress.
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