Principles of the System
The 4000 QTRAP® system includes a hybrid triple quadrupole LIT (linear ion trap) mass spectrometer designed specifically for quantitative and qualitative applications.
The Q3 region can be operated as either a standard quadrupole mass spectrometer, or as a linear ion trap mass spectrometer. The unique scan modes of both configurations can be linked to provide more and higher quality data than either technique alone.
Applications for the System
The 4000 QTRAP® system is best suited to three specific applications:
- Quantitative analysis of small molecules
- Qualitative analysis of small molecules
- Qualitative analysis of proteins and peptides
Quantitative Analysis of Small Molecules
This application involves measurement of specific molecular weight compounds (usually a drug or metabolite in urine or other bodily fluid) and their resulting fragment ions for determining the exact quantity of the compound in the sample of interest. Quantitation is performed using a standard curve of mass spectrometer signal intensity for various known concentrations of the compound. The signal in the test sample is compared to the standard curve to determine the concentration.
The typical scan type used for this application in the 4000 QTRAP system (as well as all triple quadrupole instruments) is MRM (Multiple Reaction Monitoring).
Qualitative Analysis of Small Molecules
This application involves MS analysis of low molecular weight (typically less than 1000 amu) compounds such as drugs and their metabolites. This is for the purpose of identification and structural characterization of the chemical compounds in a sample such as urine or other bodily fluid. In addition, this general application is used when the researcher wants to know what molecular weight species are in the sample.
The typical scan type used for this application in the 4000 QTRAP system is an EMS (Enhanced MS) scan for intact molecular weight analysis. For more detailed structural analysis using tandem mass spectrometry, EPI (Enhanced Product Ion) and MS3 (MS/MS/MS) scans are performed.
Qualitative Analysis of Proteins and Peptides
This application involves determination of molecular weights and sequences of protein and peptide samples. This is for the purposes of identification of the compounds and structural characterization. This general application is used when the researcher wants to know what molecular weight species and what sequences of peptides or proteins are in the sample.
The typical scan types used for this application in the 4000 QTRAP system are EMS (Enhanced MS) and EMC (Enhanced Multi-Charge) scans for intact molecular weight analysis. ER (Enhanced Resolution) scans are used to obtain higher resolution molecular weight information such as determining the charge state of a multiply charged peptide ion. This allows for more accurate identification of the sample using protein database searching. For more detailed structural analysis using tandem mass spectrometry (MS/MS), EPI (Enhanced Product Ion) scans are performed.
How the System Works
The 4000 QTRAP® system has a number of enhanced modes of operation. A common feature of the enhanced modes is that ions are trapped in the Q3 quadrupole region and then scanned out to produce full spectrum data. Many spectra are rapidly collected in a short period of time and are significantly more intense than spectra collected in a comparable standard quadrupole mode of operation.
During the collection phase, ions pass through the Q2 collision cell, where CAD gas focuses the ions into the Q3 region. The Q3 quadrupole is operated with only the main RF voltage applied. Ions are prevented from passing through the Q3 quadrupole rod set and are reflected back by an exit lens to which a DC barrier voltage is applied. After the fill time elapses (a time defined by the user, or determined by the Dynamic Fill Time feature), a DC barrier voltage is applied to a Q3 entrance lens (ST3). This confines the collected ions in Q3 and stops further ions from entering. The entrance and exit lens DC voltage barriers and the RF voltage applied to the quadrupole rods confine the ions within Q3.
During the scan out phase, the voltage on the exit lens and the auxiliary RF voltage are ramped simultaneously with the main RF voltage for increased resolution and sensitivity. An auxiliary AC frequency is applied to the Q3 quadrupole. The main RF voltage amplitude is ramped from low to high values, which sequentially brings masses into resonance with the auxiliary AC frequency. When ions are brought into resonance with the AC frequency, they acquire
enough axial velocity to overcome the exit lens barrier and are axially ejected towards the mass spectrometer ion detector. Full spectra data can be acquired from the ions collected in Q3 by rapidly scanning the main RF voltage.
The unique scan modes of both configurations can be linked to provide more and higher quality data than either instrument alone. For example, a precursor ion scan in transmission mode can be used as a survey scan in order to target specific ions to be used in an EPI scan (in LIT mode). Conversion between the two modes of operation is rapid, since it involves only the addition or removal of the resolving DC voltages.
The 4000 QTRAP system offers the following benefits over a standard triple quadrupole and a traditional 3-D ion trap mass spectrometer:
- The proven quadrupole quantitation capabilities of the API 4000™ instrument with additional scan types: Enhanced MS, Enhanced Multiply Charged, Enhanced Product Ion, Enhanced Resolution, MS/MS/MS, and Time Delayed Fragmentation.
- Higher sensitivity in all RF/DC scan modes.
- Scanning to a mass range of m/z 3–2800 quadrupole mode, 50–2800 LIT mode.
- Enhanced resolution at reduced scan speeds.
Guide: https://sciex.com/documents/downloads/literature/4000-qtrap-hardware-guide.pdf