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
Agilent Technologies, Inc.
5301 Stevens Creek Blvd.
Santa Clara, CA 95051
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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