AB Sciex 4000 QTRAP Installation instructions

Hardware Guide
4000 QTRAP®System
D1000092200 B
May 2010

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Document Number: D1000092200 B 3
Contents
Chapter 1 System Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Principles of the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Applications for the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Quantitative Analysis of Small Molecules . . . . . . . . . . . . . . . . . . . . 5
Qualitative Analysis of Small Molecules. . . . . . . . . . . . . . . . . . . . . . 6
Qualitative Analysis of Proteins and Peptides . . . . . . . . . . . . . . . . . 6
How the System Works. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Features of the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Parts of the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Component Descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Shutting Down and Turning on the System . . . . . . . . . . . . . . . . . . . . 9
Instrument Safe Fluids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Source/Gas Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Turbo V™ Ion Source Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Compound Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Technical Support. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Chapter 2 4000 Series Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 15

Contents
4 Document Number: D1000092200 B

Document Number: D1000092200 B 5
1
System Overview
The 4000 QTRAP®system includes a hybrid triple quadrupole/LIT (linear ion trap)
mass spectrometer, a Turbo V™ ion source, a computer, and the Analyst®
software.
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).
WARNING! If you need to move the system, contact an FSE to assist you. Risk of
personal injury or instrument damage
Note: Before you operate the instrument, make sure you have read the Safety Practices
guide.

System Overview
6 Document Number: D1000092200 B
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

Hardware Guide
Document Number: D1000092200 B 7
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.
Features of the System
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.
Parts of the Instrument
This section contains diagrams of the instrument and general descriptions of its
components.
Figure 1-1 Front view of the instrument
Source Exhaust
Vacuum Chamber Detector

System Overview
8 Document Number: D1000092200 B
Figure 1-2 Back view of the instrument
Component Descriptions
This section contains general descriptions of the components of the instrument.
B BA A
RF FEEDBACK RF FEEDBACK
Gas and Vacuum Panel
Turbo Pump
Turbo Pump
I/O Panel
Table 1-1 Component Descriptions
Component Description
I/O Panel The external power supply, the IEEE-488 (GPIB) connections
to the computer, the AUX I/O to your peripherals and the
Sources connection are made through the I/O panel on the
right side of the chassis.
Gas and Vacuum Panel The vacuum lines to the external roughing pump are
connected through the gas and vacuum panel. The panel also
houses the gas supply connections and the external
connection for the source exhaust pump.
Control Panel The control panel contains the main power switch, four fuses,
and two Indicator/Reset buttons.
Source Exhaust System Most ion sources produce both sample and solvent vapors.
These vapors are a potential hazard to the laboratory
environment. The source exhaust system is designed to safely
remove and allow for the appropriate handling of the ion
source exhaust products.
Vacuum Chamber The vacuum chamber houses the quadrupole rod sets, most
of the ion optics, the collision cell, and the ion detector.

Hardware Guide
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Figure 1-3 Ion Optics
Shutting Down and Turning on the System
Use the following procedures if you need to shut down or turn on the system.
To shut down the system
1. In the Analyst®software, complete or stop any ongoing scans.
2. Turn off the sample flow to the instrument.
CAUTION! Potential Instrument Damage: Shut off the sample flow before you
shut down the instrument.
3. In the Analyst software, deactivate the hardware profile and then close the
application software.
4. Stop the Analyst®Service. (See the Software Reference Guide for the
Analyst software.)
CAUTION! Leave the roughing pump running for a minimum of 15 minutes
after turning off the instrument’s main power switch. When the main power
switch is turned off, the turbo pumps continue to rotate without power for a
few minutes and continue to provide vacuum to the vacuum chamber. If, during
this time, the roughing pump is turned off, the pressure in the vacuum line
between the roughing pump and the turbo pumps increases. The increase in
back pressure can create an incorrect load on the turbo pumps’ bearings and
can cause a catastrophic failure of the turbo pumps.
CAUTION! If the instrument is to be shut down for any length of time, we
recommend that the vacuum chamber be vented to prevent exhaust from the
roughing pump being sucked back into the vacuum chamber. To vent the
vacuum chamber, follow steps 5 to 7.
CEM
Q3
LINAC®
Collision
Cell
Q1
IQ2
Curtain Gas™ flow
Q0 ST
IQ1
Skimmer
Orifice
Curtain Plate
IQ3
ST3
Q2
Aux RF
Exit
Lens
ST2
Deflector

System Overview
10 Document Number: D1000092200 B
CAUTION! If the vacuum chamber is not going to be vented while the
instrument is shut down, we recommend the roughing pump remain turned on
to prevent the pump exhaust from being sucked back into the vacuum chamber.
If you do not want to vent the vacuum chamber, skip steps 6 and 7.
5. Turn off the main power to the instrument. As you face the instrument
where the instrument name is visible and with the source to your left, the
switch is located on the bulkhead at the back right corner of the chassis.
6. After fifteen minutes, turn off the roughing pump. The power switch is
located beside the power supply input attachment on the roughing
pump.
7. Let the vacuum chamber vent naturally through the orifice for ten minutes
to allow the instrument to reach atmospheric pressure.
8. Unplug the mains power cord to the instrument from the rear bulkhead
near the main power switch for the instrument.
To turn on the system
Certain conditions outside the direct control of the instrument firmware must be
satisfied before the turbo pumps will be initiated. The Curtain Gas™ supply must
be turned on at the source, and the roughing pump must be turned on manually.
Interlocks (pressure switches) monitored by the firmware detect if the Curtain Gas
supply and the roughing pump are switched on. If the interlocks are not satisfied,
the turbo pumps are not initiated.
CAUTION! If the ion source is removed, the system electronics will be disabled,
interrupting any data acquisition tasks. The turbo pump and the vacuum system will not
be affected.
1. Turn on the roughing pump, if it was turned off. The power switch is
located beside the power supply input attachment on the roughing
pump.
2. Make sure that all gas supplies are flowing correctly to the instrument.
3. Plug the mains power cord into the bulkhead.
4. Turn on the main power switch.
5. Make sure that the GPIB (general purpose interface bus) cable is
connected to both the instrument and the computer.
Note: The roughing pump has its own power toggle switch and must be turned
off manually. The roughing pump is not controlled remotely by the system
controller.
Note: The roughing pump has its own power toggle switch and must be turned
on manually. The roughing pump is not controlled remotely by the system
controller.

Hardware Guide
Document Number: D1000092200 B 11
6. Turn on the computer, if it was turned off, and then start the Analyst®
software.
Instrument Safe Fluids
The following fluids can safely be used with the instrument:
•Methanol (0 to 100%)
•Acetonitrile (0 to 100%)
•Water
•Formic acid (0 to 1%)
•Ammonium acetate (0 to 1%)
Source/Gas Parameters
The parameters in Table 1-2 are optimized for different LC conditions involving
flow rate. For more information about the parameters, see the Analyst®software
Help system.
Turbo V™ Ion Source Settings
Table 1-3 shows the recommended starting values for the X- and Y-axis
parameters. For more information, see the Turbo V™ Ion Source Operator’s
Guide.
Note: This list is not complete. If you are uncertain about a specific fluid, do not use the
fluid until confirmation is received from AB SCIEX that it will not present a hazard.
Note: We recommend that you run the instrument with the Curtain Gas™flow set to at
least 20 to maintain good instrument performance.
Table 1-2 Source/Gas Parameters
Parameter Value
Curtain Gas (CUR) 20
IonSpray Voltage (IS) 5000
Temperature (TEM) 700
Ion Source Gas (GS1) 60
Ion Source Gas 2 (GS2) 60
Table 1-3 Vertical and Horizontal Parameters
Parameter Value
X-axis 5
Y-a xis 5

System Overview
12 Document Number: D1000092200 B
Compound Parameters
In general, you can use the preset values for most of the parameters in Table 1-4.
For more information about the parameters, see the Analyst®software Help
system.
Table 1-4 Compound Parameters
Parameter Value
CAD Gas Use the preset value and optimize for your
compound.
DP (Declustering Potential) Use the preset value and optimize for your
compound.
EP (Entrance Potential) Use the preset value.
CXP (Collision Cell Exit
Potential)
Use the preset value and optimize for your
compound.
CE (Collision Energy) Use the preset value and optimize for your
compound.
CES (Collision Energy Spread) Use the preset value and optimize for your
compound.
Fixed LIT Fill Time Use the preset value.
DFT (Dynamic Fill Time) Either select or deselect the feature based on your
experiment.
In the Tool s > Settings > Method Options dialog
box, the Dynamic Fill Time settings are optimized for
the 10000 Da/s scan speed. These settings are also
suitable for other LIT scan speeds.
Q0 Trapping Either select or deselect the feature based on your
experiment.
The recommended fixed fill time to use with Q0
trapping is 20 ms or greater.
MCS (Multi-Charge Separation)
Barrier
Use the preset value.
Q3 Entry Barrier Use the preset value.
Q3 Empty Time Use the preset value.
MS/MS/MS Fragmentation Time Use the preset value.
Q3 Cool Time Use the preset value.
TDF CE (Time Delayed
Fragmentation Collision Energy)
Use the preset value.
IE1 (Ion Energy 1) — For
experienced instrument
operators only
Do not adjust.
IE3 (Ion Energy 3) — For
experienced instrument
operators only
Do not adjust.

Hardware Guide
Document Number: D1000092200 B 13
Related Documentation
The guides and tutorials for the instrument and the Analyst®software are
installed automatically with the software and are available from the Start menu:
All Programs > AB SCIEX. A complete list of the available documentation can be
found in the online Help. To view the Analyst software Help, press F1.
Technical Support
AB SCIEX and its representatives maintain a staff of fully-trained service and
technical specialists located throughout the world. They can answer questions
about the instrument or any technical issues that may arise. For more information,
visit the web site at http://www.absciex.com.

System Overview
14 Document Number: D1000092200 B

Document Number: D1000092200 B 15
2
4000 Series Parameters
The following tables contains generic parameters for the 4000 series of
instruments. The first number under each scan type is the preset value; the range
of numbers is the accessible range for each parameter.
Table 2-1 4000 Series Instrument Parameters
Parameter
ID Access ID
Positive Ion Mode Negative Ion Mode
Q1 Q3 MS/MS Q1 Q3 MS/MS
CUR CUR 10 10 10 10 10 10
10 to 50 10 to 50 10 to 50 10 to 50 10 to 50 10 to 50
CAD CAD016 0 1 6
0 to 12 0 to 12 0 to 12 0 to 12 0 to 12
IS(1)(2) IS(1)(2) 5000 5000 5000 –4200 –4200 –4200
0 to
5500
0 to
5500
0 to 5500 –4500 to
0
–4500 to
0
–4500 to
0
NC(3) NC(3) 3 3 3 –3 –3 –3
0 to 5 0 to 5 0 to 5 –5 to 0 –5 to 0 –5 to 0
TEM(2)(3) TEM(2)(3) 000 0 0 0
0 to 750 0 to 750 0 to 750 0 to 750 0 to 750 0 to 750
OR DP 20 20 20 –20 –20 –20
(DP = OR) 0 to 400 0 to 400 0 to 400 –400 to 0 –400 to 0 –400 to 0
Q0 EP 10 10 10 –10 –10 –10
(EP = –Q0) 15 to 2 15 to 2 15 to 2 –2 to –15 –2 to –15 –2 to –15
IQ1 IQ1 Q0 +
(–1)
Q0 +
(–1)
Q0 + (–1) Q0 + 1 Q0 + 1 Q0 + 1
(IQ1 = Q0 + offset) –0.5 to
–2
–0.5 to
–2
–0.5 to
–2
0.5 to 2 0.5 to 2 0.5 to 2
ST ST Q0 +
(–5)
Q0 +
(–5)
Q0 + (–5) Q0 + 5 Q0 + 5 Q0 + 5
(ST = Q0 + offset) –7 to –4 –7 to –4 –7 to –4 4 to 7 4 to 7 4 to 7
RO1 IE1 1 n/a 1 –1 n/a –1
(IE1 = Q0 – RO1) 0.5 to 2 0.5 to 2 –2 to
–0.5
–2 to
–0.5
RO1 RO1 n/a Q0 +
(–1)
n/a n/a Q0 + 1 n/a
(IE1 = Q0 + offset) –0.5 to
–2
0.5 to 2
(1)IonSpray™ ion source (2)TurboIonSpray®ion source (3)Heated Nebulizer (4) 1 =ON and 0
= OFF (5)DuoSpray™ ion source, 1 = TIS and 2= HN

4000 Series Parameters
16 Document Number: D1000092200 B
IQ2 IQ2 Q0+ (–8) Q0+ (–8) Q0+ (–8) Q0 + 8 Q0 + 8 Q0 + 8
(IQ2 = Q0 + offset) n/a n/a n/a n/a n/a n/a
RO2 RO2 –60 –20 n/a 60 20 n/a
–145 to
–20
–145 to
–20
60 to 100 20 to 145
RO2 CE n/a n/a 30 n/a n/a –30
(CE = Q0 – RO2) 5 to 130 –130 to
–5
ST3 ST3 –80 n/a n/a 80 n/a n/a
–80 to
–200
80 to 200
ST3 CXP n/a 15 15 n/a –15 –15
(CXP = RO2 – ST3) 0 to 55 0 to 55 –55 to 0 –55 to 0
RO3 RO3 –62 n/a n/a 62 n/a n/a
–60 to
–200
60 to 200
RO3 IE3 n/a 2 2 n/a –2 –2
(IE3 = RO2 – RO3) –0.5 to 5 –0.5 to 5 –5 to 0 –5 to 0
C2 C2 RO3 + 0 RO3 + 0 RO3 + 0 RO3 + 0 RO3 + 0 RO3 + 0
n/a n/a n/a n/a n/a n/a
DF DF 0 0 0 0 0 0
–400 to
0
–400 to
0
–400 to 0 0 to 400 0 to 400 0 to 400
CEM CEM 1800 1800 1800 1800 1800 1800
500 to
3297
500 to
3297
500 to
3297
500 to
3297
500 to
3297
500 to
3297
GS1 GS1 20 20 20 20 20 20
0 to 90 0 to 90 0 to 90 0 to 90 0 to 90 0 to 90
GS2 GS2000 0 0 0
0 to 90 0 to 90 0 to 90 0 to 90 0 to 90 0 to 90
ihe(4) ihe111 1 1 1
0 or 1 0 or 1 0 or 1 0 or 1 0 or 1 0 or 1
IHT IHT 40 40 40 40 40 40
10 to
250
10 to
250
10 to 250 10 to 250 10 to 250 10 to 250
svp(5) svp111 1 1 1
1 or 2 1 or 2 1 or 2 1 or 2 1 or 2 1 or 2
Table 2-1 4000 Series Instrument Parameters (cont’d)
Parameter
ID Access ID
Positive Ion Mode Negative Ion Mode
Q1 Q3 MS/MS Q1 Q3 MS/MS
(1)IonSpray™ ion source (2)TurboIonSpray®ion source (3)Heated Nebulizer (4) 1 =ON and 0
= OFF (5)DuoSpray™ ion source, 1 = TIS and 2= HN

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Table 2-2 4000 QTRAP®System Parameters for LIT Scan Types Only
Parameter ID Access ID Positive Ion Mode Negative Ion Mode
CAD CAD High High
Low–High Low–High
AF2** AF2 100 100
0 to 200 0 to 200
AF3 AF3 Mass-Speed
Dependent
Mass-Speed Dependent
0 to 5 0 to 5
EXB EXB Mass-Speed
Dependent
Mass-Speed Dependent
–200 to 0 0 to 200
CES CES 0 0
–50 to 50 –50 to 50
ROS CE 30 –30
(Q0 – ROS) 5 to 130 –5 to –130
** MS/MS/MS only

4000 Series Parameters
18 Document Number: D1000092200 B