AB Sciex QTRAP 4500 LC/MS/MS system, System User'S Manual, Page: 56 / 138

Operating Instructions — Acquisition Methods
4500 Series of Instruments System User Guide
56 of 138 RUO-IDV-05-0264-A
MS/MS/MS (MS3) : In this scan mode, a precursor ion is selected by the Q1 quadrupole and
fragmented with collisionally activated dissociation in the Q2 collision cell. The resulting product
ions are all transmitted to the linear ion trap, where a single product ion is then isolated. The
isolated ion is further fragmented in the linear ion trap, and the resulting product ions are
scanned out of the ion trap at one of three scan speeds. As with any in-trap Collision Induced
Disassociation (CID) technique, there is a low mass cut-off for the second MS/MS step due to the
condition that the lowest mass fragment and precursor must be simultaneously stable in the trap.
For QTRAP
®
systems, this results in the loss of ions lower than 28 percent of the mass of the
precursor ion during MS3 experiments. This phenomenon is often referred to as the one-third
cut-off rule.
About Spectral Data Acquisition
Spectral data can be acquired in one of three modes, as shown in the following table.
Parameters
The working parameters are the set of instrument parameters currently being used.
• Source and gas parameters (these parameters can change depending on the ion
source used)
• Compound parameters
• Resolution parameters
• Detector parameters
For more information about instrument parameter values and ranges, refer to Appendix A:
Parameters for 4500 Series Instruments .
Table 8-1 Spectral Data Acquisition
Mode Description
Profile The preset value is 0.1 Da. Profile data is the data generated by the
mass spectrometer and corresponds to the intensity recorded at a
series of evenly spaced discrete mass values. For example, for a
mass range 100 Da to 200 Da and step size 0.1, the mass
spectrometer scans 99.95 to 100.05 (records as value 100), 100.05 to
101.15 (records as value 101)…199.95 to 200.05 (records as value
200).
Peak Hopping The preset value is 1.0 Da. Peak Hopping is a mode of operating a
mass spectrometer in which large steps (approximately 1 Da) are
made. It has the advantage of speed (fewer data steps are made) but
with the loss of peak shape information.
Centroid The mass spectrometer scans as in profile mode, but creates a
centroid of the data, replacing found peaks with the intensity-weighted
center of gravity for each peak. Centroid data has the advantage of
significantly reducing file size. The disadvantage is that peak shape
information is lost, and if data has been collected as a centroid it
cannot be altered. We recommend the use of profile mode and
centroiding of the data post-acquisition.