Agilent Technologies G1978B User manual

Agilent Technologies
Agilent G1978B
Multimode Source for
6410 Triple Quad LC/MS
User Guide

2 Multimode Source for 6410 Triple Quad LC/MS User Guide
Notices
© Agilent Technologies, Inc. 2006
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Manual Part Number
G1978-90010
Edition
First Edition, October 2006
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Blvd.
Santa Clara, CA 95051 USA
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Multimode Source for 6410 Triple Quad LC/MS User Guide 3
In This Guide
This guide explains how to install, maintain and troubleshoot your multimode
ion source.
1Basic Operation and Maintenance
This chapter describes basic operation and maintenance for the multimode
source.
2Installation
This chapter tells you how to install the multimode source.
3Reference
This chapter contains an overview of the multimode source, safety
precautions, and technical specifications.

4 Multimode Source for 6410 Triple Quad LC/MS User Guide

Contents
Multimode Source for 6410 Triple Quad LC/MS User Guide 5
Content
1 Basic Operation and Maintenance 7
To set up a method to use the multimode source 8
To open the multimode source 10
To clean the multimode source daily 11
To clean the multimode source weekly 13
To check tuning with the multimode source 15
2 Installation 17
Step 1. Prepare to install 18
Step 2. Install the HV control PCA and cables 19
To remove the multimode source 23
To convert from multimode to ESI or APCI 24
To convert from ESI or APCI to the multimode source 25
3 Reference 31
Safety and Specifications 32
Safety 32
Safety Symbols 36
Technical Specifications 37
Overview 38
Benefits of a multimode source 38
Mobile phase considerations when using the multimode source 46
Source comparison in positive ion mode 48
Source comparison in negative ion mode 49
Guidelines 50
Guidelines for multimode source settings in MM-ES mode 50
Guidelines for multimode source settings in MM-APCI mode 51
Guidelines for multimode source settings in MM-ES+APCI mode 52
Empirical Formulas for high resolution MS 53

6 Multimode Source for 6410 Triple Quad LC/MS User Guide
Contents
G2421A MM-ES Calibration Ions 53
G2432A MM-APCI Calibration Ions 54
Tuning Mix and Test Mix 55
G2421A ES Tuning Mix (100mL) 55
G2432A APCI Tuning Mix (100mL) 56
Chemical structures in the multimode test mix 57

7
Agilent G1978B Multimode Source for 6410 Triple Quad LC/MS
User Guide
Agilent Technologies
1
Basic Operation and Maintenance
To set up a method to use the multimode source 8
To open the multimode source 10
To clean the multimode source daily 11
To clean the multimode source weekly 13
To check tuning with the multimode source 15
This chapter describes the tasks that you need to operate and maintain the
multimode source.
s

8 Multimode Source for 6410 Triple Quad LC/MS User Guide
1 Basic Operation and Maintenance
To set up a method to use the multimode source
To set up a method to use the multimode source
1In the MassHunter software, change the Context to Acquisition.
2In the MS QQQ tab, set Ion source to MMI (see Figure 1 on page 9).
3In the Time Segments table, chose an ionization mode from the Ion Mode
list. You may set the ionization mode to one of the following:
•ESI
•APCI
•ESI+APCI
The Ion Mode selection ESI + APCI will specify a method for alternating ESI
and APCI operation.
Note that the Ion Mode selection is only visible if Ion source is set to MMI.
4In the Source tab, set the desired source conditions. See the
“Guidelines” on page 50 for suggested source conditions for the multimode
source for the different ionization modes.
5Make any other changes that are necessary for your method.
6Save the method.

Multimode Source for 6410 Triple Quad LC/MS User Guide 9
Basic Operation and Maintenance 1
To set up a method to use the multimode source
Figure 1 Multimode acquisition settings
WARNING The LC/MS diverter valve is an integral part of the G1978B safety system. The LC
mobile phase flow must always be connected to the diverter valve inlet filter. Never
bypass the diverter valve and connect directly to the nebulizer. If the diverter valve is
used in a manner not specified by Agilent Technologies, the protections provided by
the diverter valve may be impaired and the system may catch fire.

10 Multimode Source for 6410 Triple Quad LC/MS User Guide
1 Basic Operation and Maintenance
To open the multimode source
To open the multimode source
Open the multimode source to access the end cap and the capillary cap for
cleaning and inspection.
1Turn off the multimode source temperatures and flows:
aChange the Context view to Acquisition.
bClick the MS QQQ tab.
cTurn off all voltages and temperatures in the Source tab.
dWait approximately 20 minutes for the source to cool down.
2Open the spray chamber cover by pulling the latch.
The high voltage automatically turns off when the chamber door is opened
so that no high voltages are present within the chamber.
3Check that the vaporizer temperature sensor is straight and extends 15mm
from back of chamber.
4Check that the separator is aligned vertically.
5Check that the APCI corona needle is in and extends approximately 3mm
from the corona guide.
6Check that the source is clean.
WARNING Do not touch the multimode source or the capillary cap. They may be very hot. Let the
parts cool before you handle them.
WARNING Never touch the source surfaces, especially when you analyze toxic substances or
when you use toxic solvents. The source has several sharp pieces which can pierce
your skin including the APCI corona needle, vaporizer sensor and counter current
electrode.
WARNING Do not insert fingers or tools through the openings on the multimode chamber. When
in use, the capillary and capillary cap are at high voltages up to 4 kV.

Multimode Source for 6410 Triple Quad LC/MS User Guide 11
Basic Operation and Maintenance 1
To clean the multimode source daily
To clean the multimode source daily
You should clean the multimode source daily or any time you suspect
carryover (contamination) from one sample or analysis to another. The
multimode source spray chamber is made of 316 stainless steel which is the
same material used to make the spray shield.
Before you begin, check that you have:
•Abrasive paper, 8000 grit (p/n 8660-0852)
•Cloths, clean, lint-free (p/n 05980-60051)
•Cotton swabs (p/n 5080-5400)
•Gloves
•Mobile phase from the current method or clean isopropanol, reagent
grade or better
•Wash bottle
•Water, reagent-grade or better
1Turn off the spray chamber.
2Remover the nebulizer and APCI corona needle.
3Remove the cosmetic cover. The thermocouple probe will need to be
removed if any wiping of the spray chamber will be done. Then, open the
spray chamber.
4Rinse the interior of the spray chamber using the wash bottle filled with the
current mobile phase or with a mixture of isopropanol and water.
.
WARNING Do not touch the multimode source or the capillary cap. They may be very hot. Let the
parts cool before you handle them.
NOTE Recent residue should be soluble in the mobile phase. If you are not sure what mobile
phase was used recently, a mixture of 50% isopropanol and 50% water works well as a
general cleaning solution.
WARNING Some mobile phases are hazardous chemicals. Use caution that is appropriate for
the current mobile phase.

12 Multimode Source for 6410 Triple Quad LC/MS User Guide
1 Basic Operation and Maintenance
To clean the multimode source daily
5Wipe the interior of the spray chamber with a clean, lint-free cloth.
6Rinse the area around the spray shield. Do not spray directly at the end of
the capillary. This can cause pressure surges in the vacuum system.
7Dampen a clean cloth with the mobile phase. Wipe the spray shield, field
shaping electrodes and the area around the spray shield.
8Replace the nebulizer and the APCI corona needle.
9Install the thermocouple probe and adjust it so that it protrudes 15 mm
from the inner spray chamber wall. See Figure 2.
Figure 2 Installing the thermocouple probe and 15 mm adjustment
10 Replace the cosmetic cover.
11 Close the spray chamber.
WARNING There are sharp edges inside the spray chamber such as the separator. Pay close
attention when wiping the interior of the spray chamber.
Thermocouple probe
NOTE If symptoms of contamination persist, or if the spray shield or capillary cap show significant
discoloration that cannot be removed by the regular, daily cleaning, use the weekly
cleaning procedure.

Multimode Source for 6410 Triple Quad LC/MS User Guide 13
Basic Operation and Maintenance 1
To clean the multimode source weekly
To clean the multimode source weekly
The cleaning procedure for cleaning the multimode source weekly is similar to
the procedure for cleaning the source daily. The main difference is that the
multimode source is removed from the instrument.
Before you begin, check that you have:
•Abrasive paper, 8000 grit (p/n 8660-0852)
•Cloths, clean, lint-free (p/n 05980-60051)
•Cotton swabs (p/n 5080-5400)
•Gloves
•Mobile phase from the current method, or clean isopropanol, reagent
grade or better
•Wash bottle
•Water, reagent-grade or better
1Do the steps in “To remove the multimode source” on page 23.
2Fill the spray chamber with clean mobile phase, or with a mixture of
isopropanol and water.
3Scrub the corona insulator and the interior of the spray chamber with a
clean cotton swab.
4Empty the spray chamber.
5Wipe the interior of the spray chamber with a clean, lint-free cloth.
NOTE Recent residue should be soluble in the mobile phase. If you are not sure what mobile
phase was used recently, a mixture of 50% isopropanol and 50% water works well as a
general cleaning solution.
WARNING Some mobile phases are hazardous chemicals. Use caution that is appropriate for
the current mobile phase.
WARNING The inside of the spray chamber has sharp edges, such as on the separator. Pay
close attention when you wipe the interior of the spray chamber.

14 Multimode Source for 6410 Triple Quad LC/MS User Guide
1 Basic Operation and Maintenance
To clean the multimode source weekly
6Remove the spray shield. Use abrasive paper to gently clean the end of the
capillary cap.
7Dampen a clean cloth and wipe the end of the capillary cap.
8Reinstall the spray shield.
9Use abrasive paper to gently clean the spray shield. Dampen a clean cloth
and wipe the spray shield.
10 Rinse the area around the spray shield. Then wipe the area around the
spray shield.
11 Reinstall the spray chamber on the instrument.
12 Replace the nebulizer and APCI corona needle.
13 Install the thermocouple probe and adjust it so that it protrudes 15 mm
from the inner spray chamber wall. See Figure 2 on page 12.
14 Replace the cosmetic cover.
15 Close the spray chamber.

Multimode Source for 6410 Triple Quad LC/MS User Guide 15
Basic Operation and Maintenance 1
To check tuning with the multimode source
To check tuning with the multimode source
Autotune is currently available for the G1948B Electrospray source only. To
check tuning with the multimode source, do these steps.
1Run an Autotune with the G1948B Electrospray source installed.
2Remove the G1948B Electrospray source and install the G1978B multimode
source.
3Pour the Electrospray calibrant back into its original bottle or another
suitable container, rinse the calibrant bottle with acetonitrile, pour the
APCI calibrant into the calibrant bottle, and attach the calibrant bottle back
onto the CDS.
4Set the Context view to Tune in the MassHunter Workstation program.
aLoad the autotune file that was generated with the G1948B Electrospray
source.
bAdjust the lens voltages and other tune parameters as required.
cVerify that you have sufficient abundance for the tune peaks, that the
tune peaks have peak widths of 0.7 ±0.05 amu, and that mass
assignments are within ±0.15 amu of the target mass assignments.
5Save the tune file.

16 Multimode Source for 6410 Triple Quad LC/MS User Guide
1 Basic Operation and Maintenance
To check tuning with the multimode source

17
Agilent G1978B Multimode Source for 6410 Triple Quad LC/MS
User Guide
Agilent Technologies
2
Installation
Step 1. Prepare to install 18
Step 2. Install the HV control PCA and cables 19
To remove the multimode source 23
To convert from multimode to ESI or APCI 24
To convert from ESI or APCI to the multimode source 25
This chapter contains instructions to install the multimode source on a 6400
Series Triple Quad LC/MS system, and also to remove and replace the source.

18 Multimode Source for 6410 Triple Quad LC/MS User Guide
2 Installation
Step 1. Prepare to install
Step 1. Prepare to install
The Multimode Enablement Kit, G1978-60451, is shipped with the multimode
source. This kit needs to be installed before the multimode source is used.
Note that the multimode source and its accessories are to be installed by an
Agilent Customer Engineer.
1Check that the Multimode Enablement Kit contains the following parts:
•Multimode Bd HV Cable, p/n G1960-60858
•Multimode HV PCA, p/n G1960-61015
•Multimode Bd Power/Data Cable, p/n G1960-60873
Figure 3 From left to right: G1960-60858, G1960-61015 and G1960-60873
2Install the APCI Enablement Kit, G1947-60451, which is shipped with the
multimode source.
The APCI Enablement kit contains the following parts:
•Fast APCI HV Supply, p/n G1946-80058
•Valve BD-APCI Supply Cable, p/nG1960-60802
•Valve BD-APCI Needle Interlock Cable, p/n G1960-60856
Figure 4 From left to right: G1946-80058, G1960-60802 and G1960-60856

Multimode Source for 6410 Triple Quad LC/MS User Guide 19
Installation 2
Step 2. Install the HV control PCA and cables
Step 2. Install the HV control PCA and cables
1Turn off the system power and remove the system power cord.
The power cord should be kept intact if the vacuum control switch box is
used. The switch box is intended to keep the vacuum on while a service
engineer works on the electronics. The switch box is for service engineer
use only.
2Remove the CDS cover, top, side, front, and the Aux Module cover.
3Disconnect the ribbon cable that connects the valve PCA to the
Vcap/Vchamber power supply. Then disconnect the Vcap and Vchamber
cable from the power supply.
Figure 5 Disconnecting the Vcap/Vchamber power supply from the valve PCA (left) and the Vcap/Vchamber.
4Place the MM HV power supply PCA in the slot between the valve PCA and
the Vcap/Vchamber power supply. Secure the board by pressing it down
into its slot and then attach it with two screws.
5Connect the short gray cable from the valve PCA to the multimode HV
power supply.
Figure 6 Connecting the valve PCA to the multimode HV power supply.

20 Multimode Source for 6410 Triple Quad LC/MS User Guide
2 Installation
Step 2. Install the HV control PCA and cables
6Install the APCI HV power supply. The APCI HV power supply is located at
the end of the AUX Module.
7Connect ribbon cable between the valve PCA and Vcap/Vchamber power
supply.
Figure 7 Connecting the valve PCA to the Vcap/Vchamber power supply.
8Connect the Vcap and Vchamber cables to the Vcap/Vchamber power
supply.
Figure 8 Connecting the Vcap and Vchamber cables to the power supply.
9Connect the long ribbon cable, p/n G1960-60802, from the APCI HV power
supply to the valve PCA.