Agilent Technologies 6500 Series Operating manual

Agilent Technologies
Agilent 6500 Series
Q-TOF LC/MS system
Maintenance Guide
Research Use Only. Not for use in Diagnostic
Procedures.

Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Notices
© Agilent Technologies, Inc. 2011
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Manual Part Number
G2581-90065
Edition
Revision B, December 2011
Printed in USA
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Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 3
Content
1 Basic Operation 7
Starting and Shutting Down 13
To start the system in Standby mode 15
To change from Standby to On 18
To change from On to Standby 18
To shut down the instrument 19
Changing Ion Sources 21
To remove an electrospray source 21
To remove the ESI with Agilent Jet Stream Technology 22
To remove a multimode source 22
To remove an APCI or APPI source 23
To remove a nano ESI source 24
To remove a dual nano ESI source 25
To install an electrospray source 26
To install an APCI source 27
To install an APPI source 28
To install a nano ESI, dual nano ESI or multimode source or HPLC-Chip/MS
interface 28
To install the Agilent Jet Stream inlet assembly 29
2 Maintenance 31
Calibrant Delivery System and Divert Valve 32
To prepare tuning mix 35
To prepare the reference mass solution 40
To check calibrant levels 43
To fill a tuning mix or reference mix bottle 44
To check for leaks 45
To replace the LC filter elements 46
To replace the MS selection valve rotor seal 47

4 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Contents
Electrospray Ion Source 49
To flush the nebulizer 49
To clean the electrospray spray chamber daily 50
To clean the electrospray spray chamber weekly 53
To remove the electrospray nebulizer 57
To replace the electrospray nebulizer needle in the analytical or the reference
nebulizer sprayer 58
To adjust the electrospray nebulizer needle 61
To reinstall the electrospray nebulizer 63
To remove the desolvation assembly 64
To clean skimmer 1 (for 6520/6530/6538/6540) 66
To reinstall the desolvation assembly 68
ESI with Agilent Jet Stream Technology 69
To flush the nebulizer daily 69
To flush the nebulizer monthly 70
To clean the spray chamber daily for the ESI with Agilent Jet Stream 71
To clean the spray chamber weekly for the ESI with Agilent Jet Stream 74
To remove the nebulizer for the ESI with Agilent Jet Stream 78
To replace the nebulizer needle for the ESI with Agilent Jet Stream 79
To adjust the nebulizer needle for the ESI with Agilent Jet Stream 83
To reinstall the nebulizer for the ESI with Agilent Jet Stream 85
APCI Source 86
To clean the APCI spray chamber daily 86
To clean the APCI spray chamber weekly 89
To remove the APCI nebulizer 91
To replace the APCI nebulizer needle 92
To adjust the APCI nebulizer needle 95
To reinstall the APCI nebulizer 97
To clean the corona needle 98
To replace the corona needle 100
Multimode Source and HPLC-Chip/MS Interface 102
To clean the multimode source daily 102

Contents
Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 5
To clean the multimode source weekly 104
To adjust the multimode nebulizer 106
To change HPLC-Chip capillaries 109
Ion Transfer Capillary 113
To remove the capillary 113
To clean the capillary 115
To reinstall the capillary 118
To clean skimmer 1 (for 6520/6530/6538/6540) 119
Manifold 121
To open the manifold 121
To close the manifold 122
To clean the ion optics assembly 123
High Pressure Ion Funnel (6550 only) 132
To remove the high pressure ion funnel 132
To clean the high pressure ion funnel 135
To reinstall the high pressure ion funnel process 138
Vacuum System 139
To check the rough pump fluid level 139
To check the oil mist filter 141
To add rough pump fluid 142
To replace the rough pump fluid 144
To replace the fuses 146
3 Reference 149
Safety 150
Environmental Conditions 151
Replaceable Fuses 151

6 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
Contents

7
Agilent 6500 Series Q-TOF LC/MS
Maintenance Guide
Agilent Technologies
1
Basic Operation
Starting and Shutting Down 13
Changing Ion Sources 21
This chapter describes procedures for the basic operation of your Q-TOF
LC/MS instrument.
Figure 1 6520 Q-TOF LC/MS covers. The main power switch is behind the service panel.
Source
CDS cover
Service panel
Power switch
Flight tube
Front cover

8 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
1 Basic Operation
Figure 2 6530 with Agilent Jet Stream Technology
For more details, see the site preparation guide that is sent to customers
before installation. If you move the instrument, you must follow and repeat the
steps detailed in the site preparation guide.
CDS cover
Service panel
Power switch
Flight tube
Front cover

Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 9
Basic Operation 1
Figure 3 6538/6540 Q-TOF LC/MS
CDS cover
Service panel
Power switch
Flight tube
Front cover

10 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
1 Basic Operation
Figure 4 6550 Q-TOF LC/MS
Service panel
Power switch
Flight tube
Front cover
CDS bottles for tuning
and reference mixes

Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 11
Basic Operation 1
Figure 5 6520/6530/6538/6540 gas, LAN, and power connections behind service
panel
LAN connection

12 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
1 Basic Operation
Figure 6 6550 power connections and pump expander box behind service panel
Pump expander box power
switch

Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 13
Basic Operation 1
Starting and Shutting Down
Starting and Shutting Down
This section describes how to start up your Q-TOF LC/MS and how to shut it
down.
The Q-TOF LC/MS instruments have three standard modes of operation that
you can select from the software.
On Mode On is the fully operational status of the system. The instrument and the source
are on. The Q-TOF icon indicates the state of the instrument:
To put an individual device in the On mode, right click the image of the device
in the Instrument Status window and click On. To put all devices in the On
mode, click the On button in the Instrument Status window.
Standby Mode In Standby, the source interface is on, the drying gas remains heated, and
nebulizer flows are maintained. The source and ion optics voltages are turned
off, and the mass spectrometer is not sending spectra to the computer.
However, the Q-TOF high voltage electronics are on.
For APCI and MMI sources, the vaporizer gas heaters are turned down.
For an instrument with Agilent Jet Stream inlet assembly, the sheath gas
temperature, drying gas flow, and drying gas temperatures are reduced.
Table 1 Q-TOF icon color indication
Color State
green idle
blue running, injecting
red error
yellow not ready
purple pre-run, post-run
dark gray offline
light gray standby

14 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
1 Basic Operation
Starting and Shutting Down
This mode lets the instrument remain idle for periods lasting from minutes to
days. You should place the instrument in Standby mode when it is not in use
or when you want to change the ion source.
To put an individual device in the Standby mode, right click the image of the
device in the Instrument Status window and click Standby.
Powered Off
State
When the system is in the powered off state, the system is vented and the
instrument is turned off to allow maintenance or to prepare for long periods
when the instrument is not used.
NOTE
Before you move the instrument to another location, maintain it, or expect it
to be idle for long periods of time, turn off both the front switch and the main
power breaker switch behind the service panel.
CAUTION
If the Q-TOF LC/MS is planned to be shut down for longer than one day, unplug the
instrument from the wall outlet to prevent overheating of the turbo pump power
supplies.

Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 15
Basic Operation 1
To start the system in Standby mode
To start the system in Standby mode
This procedure brings the system from the powered off state to Standby mode.
1Check that nitrogen gas for the drying gas and for the collision cell are
turned on.
When you use an instrument with Agilent Dual Jet Stream Technology or
Agilent Jet Stream Technology, the drying gas requirements are greater
than when operating with ESI, APCI, APPI, or multimode sources. The
supply line must have two hydrocarbon traps (part number BHT-4 or
RMSN-4) plumbed in parallel to achieve these flows without triggering
errors at the instrument. Refer to the Installation Guide for more details.
2Check that the rough pump is connected to the Q-TOF LC/MS.
•Check that the rough pump power cable is connected to the Foreline
Pump power receptacle behind the service panel of the Q-TOF LC/MS.
•For 6550: Check that the rough pump power cable is connected to the
Foreline Pump power receptacle and that the Ion Funnel pump is
connected to the Auxiliary Pump power receptacle in the pump
expander box of the Q-TOF LC/MS.
•Check that the rough pump has the correct voltage rating for your AC
power (230 V or 208 V).
•For 6520/6530/6538/6540: Check that the rough vacuum tubing is
connected to the inlet part of the rough pump.
•For 6550: Check that the rough vacuum hose for the foreline pump is
connected to the foreline vacuum port and that the ion funnel rough
vacuum hose is connected to the ion funnel rough pump inlet.
•Check that the switch on the rough pump is in the On position.

16 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
1 Basic Operation
To start the system in Standby mode
3Check that all pump and spray chamber exhausts are vented outside the
laboratory.
For oil-based rough pumps only: The oil mist filter must be installed on the
rough pump, and the ballast valve must be closed. Open the ballast valve
periodically (must be done on a weekly basis) to return any oil that has
condensed in the oil mist filter to the pump as needed.
For dry pumps (Agilent TS800 or Edwards XDS351i), the ballast does not
need to be emptied regularly.
4Turn on the power for the computer and monitor.
5Check that the instrument is plugged into a power outlet.
6For 6550 only: Check that the power switch on the pump expander box is
connected to the wall outlet and is turned on. The switch is illuminated
green when the power is on.
7Turn on the front switch of the Q-TOF LC/MS.
This starts the pumping system and the electronics.
8After Windows starts, click Start > Programs > Agilent > MassHunter
Workstation > Acq Tools > Q-TOF Diagnostics to start the Q-TOF
diagnostics program.
9From the Connection menu, select Connect and click OK.
NOTE
A silicone rubber septum is placed between the spray shield and the capillary for shipment.
Make sure that this rubber septum is removed if you are starting the system for the first
time.
CAUTION
Do not connect the spray chamber exhaust bottle to the rough pump exhaust tubing or
the rough pump exhaust tubing to the spray chamber exhaust tubing. Doing so can
contaminate the instrument with rough pump fluid.
CAUTION
Vent all exhausts external to the building where they cannot be recirculated by
environmental control systems. Do not vent exhaust into your laboratory. The exhaust
fumes from the vacuum pumps and spray chamber contains trace amounts of the
chemicals you analyze. Health hazards include chemical toxicity from solvents, buffers,
samples and pump fluid vapor, as well as potentially biohazardous aerosols of
biological samples.

Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 17
Basic Operation 1
To start the system in Standby mode
10 Under System Turn-On, mark the check boxes for Pump Down and HV
Condition.
11 Click the Start button under System Turn-On.
The system monitors the vacuum pressure. Once the vacuum pressure
reaches 3 x 10-6 torr, the system will begin conditioning the high voltage
electronics.
12 Once high voltage conditioning has completed, go to Start > Programs >
Agilent > MassHunter Workstation> Data Acquisition to start the Data
Acquisition program.
The system will come up in Standby mode.
By default, the source values are set to:
•Drying gas flow (non iFunnel systems): 3.5 L/minute
•Drying gas flow (6550): 12 L/minute
•Drying gas temperature: 300 °C
•Nebulizing gas pressure: 20 psi
•Sheath gas flow: 3 L/minute
•Sheath gas temperature: 125 °C
13 Allow the instrument to continue pumping down.
The Rough Vac (rough pump) pressure should be about 1.75 to 2.5 torr. The
TOF Vac (flight tube region) pressure should be approximately 3x10-6 torr
within two to three hours. The TOF Vac reading should be in the 10-7 torr
range after pumping overnight to several days.
Leave the instrument in Standby.
NOTE
You will not be able to set the flows while the Q-TOF system is in a “Not Ready” state. The
system will remain in the Not Ready state while the high vacuum pressure is above 3.5 X
10-6 torr.

18 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
1 Basic Operation
To change from Standby to On
To change from Standby to On
Use this procedure when the Q-TOF LC/MS is in Standby mode and you need
to bring it into the On mode.
Before you begin, check that:
•The Q-TOF LC/MS is in Standby mode
•In the Data Acquisition program, click On.
You can only activate the Standby mode or On mode if the ion source is
mounted and closed. You can now select parameters for your measurement.
The instrument is now in the On mode.
To change from On to Standby
Put the Q-TOF LC/MS in Standby mode when you have completed your
analysis of samples.
Before you begin, check that:
•You have completed tuning and data acquisition and you have saved all
data as needed (described in later chapters).
•In the Data Acquisition program, click Standby.
The drying gas flow, drying gas temperature, nebulizer pressure, vaporizer
temperature, and sheath gas temperature are reduced when the instrument
is in Standby mode. The spray chamber high voltages are turned off in
Standby mode. Voltages in the flight tube remain On in Standby mode to
maintain stable operating voltages. The mass spectrometer stops generating
spectra.
The system is now in Standby mode.

Agilent 6500 Series Q-TOF LC/MS Maintenance Guide 19
Basic Operation 1
To shut down the instrument
To shut down the instrument
You can turn off the Q-TOF LC/MS when the instrument will be idle for an
extended time or when you must do maintenance.
Before you begin, check that you have completed tuning and acquiring data,
and that you have saved all data as needed.
1Turn off the solvent flow.
If you have analyte in any of the components in the sample delivery system,
flush the delivery system with pure solvent before you continue.
2Check that the ballast valve on the rough pump is closed.
3In the Data Acquisition program, right-click the Q-TOF device pane and
click Vent.
When you vent the system, these parts are turned off: spray chamber high
voltages, the drying gas heater, the nebulization flow, the detector, and
other lens voltages. The drying gas flow is set to 3.5 L/minute. If the APCI
source is installed, the vaporizer heater is also turned off. If you have an
instrument with Agilent Jet Stream Technology, the sheath gas heater is
also turned off. The Rough Pump turns off when the turbo speed is below 20
percent.
4Wait until the instrument completely vents (reaching 760 torr) to ensure
that the flight tube is filled with nitrogen. This protects the detector from
moisture damage.
5Turn off the front switch located in the lower left front corner of the
instrument.
CAUTION
When you click Vent in the Q-TOF shortcut menu, the Q-TOF LC/MS does not turn off.
You must follow the entire shutdown procedure.
WARNING
The spray shield and related spray chamber components are likely to be hot. Do not
touch them!

20 Agilent 6500 Series Q-TOF LC/MS Maintenance Guide
1 Basic Operation
To shut down the instrument
6Unplug the main power cable behind the service panel. This action prevents
the turbo pump components from overheating.
7At this point, you can also shut down the Data Acquisition program and
computer. The system is now shut down.