Lit-Mode Scan Types - AB Sciex QTRAP 4500 LC/MS/MS system System User's Manual

Operating Instructions — Acquisition Methods
Q1 Multiple Ions (Q1 MI): A zero width scan type using the Q1 quadrupole. The ion intensity is
returned for the specified masses only.
Q3 MS (Q3): A full scan using the third quadrupole (Q3). The ion intensity is returned for every
mass in the scan range.
Q3 Multiple Ions (Q3 MI): A zero width scan type using the Q3 quadrupole. The ion intensity is
returned for the specified masses only.
MRM (MRM): An MS/MS scan in which a user-selected ion is passed through the Q1 quadrupole
and fragmented in the Q2 collision cell. The Q3 quadrupole is then used to specify which
fragment ion enters the detector. This scan mode is used primarily for quantitation.
Product Ion (MS2): An MS/MS full scan where the Q1 quadrupole is fixed to transmit a specific
precursor ion and the Q3 quadrupole scans a defined mass range. Used to identify all of the
products of a particular precursor ion.
Precursor Ion (Prec): An MS/MS scan where the Q3 quadrupole is fixed at a specified mass-to-
charge ratio to transmit a specific product ion and the Q1 quadrupole scans a mass range. Used
to confirm the presence of a precursor ion or more commonly used to identify compounds
sharing a common product ion.
Neutral Loss (NL): An MS/MS scan where both the Q1 quadrupole and the Q3 quadrupole scan
a mass range, a fixed mass apart. A response is observed if the ion chosen by the first analyzer
fragments by losing the neutral loss (the fixed mass) specified. Used to confirm the presence of a
precursor ion or more commonly used to identify compounds sharing a common neutral loss.

LIT-Mode Scan Types

The LIT-mode scans use the Q3 quadrupole as a linear ion trap. Ions are trapped and stored in
the trap before being scanned out, giving increased sensitivity. In addition, MS/MS/MS analysis
can be performed in the linear ion trap, providing more information about the sample.
Enhanced MS (EMS): Ions are scanned in the Q1 quadrupole to the linear ion trap where they
are collected. These ions are scanned out of the Q3 quadrupole to produce single MS type
spectra.
Enhanced Multi-Charge (EMC): This scan is similar to the EMS scan except that before
scanning the ions out of the linear ion trap, there is a delay period during which low-charge state
ions (primarily singly-charged ions) are allowed to preferentially escape from the linear ion trap.
When the retained ions are scanned out, the multiply-charged ion population dominates the
resulting spectrum.
Enhanced Product Ion (EPI): This scan type is used to obtain a high quality MS/MS spectrum
on a specific ion. The fragmentation is done in the Q2 collision cell and thus provides the
information-rich MS/MS spectrum typical of collisionally activated dissociation fragmentation. In
this scan mode, the precursor ion to be fragmented is first selected in the Q1 quadrupole with a
mass window that is 1 to 4 Da wide, filtering out all other ions. The precursor ion is fragmented by
collisionally activated dissociation (CAD) gas in the Q2 collision cell. The fragment ions
generated are captured in the linear ion trap and then scanned out at one of three scan speeds,
depending on the required fragment ion resolution.
For IDA experiments, the Product Of field is set to 30 Da by default, and this value should not be
changed.
Enhanced Resolution (ER): This scan is similar to the EMS scan except that a small 30 Da
mass around the precursor mass is scanned out of the linear ion trap at the slowest scan rate to
produce a narrow window of the best-resolved spectra.
System User Guide 4500 Series of Instruments
RUO-IDV-05-0264-A 55 of 138