Analyst® Software

Peripheral Devices Setup Guide

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Release Date: March 2012

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Contents

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
System Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Supported Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Peripheral Device Software Plug-in Vendors . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Adding AAO-Controlled Devices to the Hardware Profile . . . . . . . . . . . . . . . . . . .7
Chapter 2 Agilent Series Devices Configuration . . . . . . . . . . . . . . . . . . . . . . . . . 9
Configuration of Agilent Devices Through Serial Port Communication . . . . . . . . .9
Configuration of Agilent Devices Through GPIB Communication . . . . . . . . . . . .10
Configuration of Agilent Devices Through LAN (Ethernet) Communication . . . .10
Configuring the Network Interface Card . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
Configuration of Agilent Devices with CAN Cables . . . . . . . . . . . . . . . . . . . . . . .14
Chapter 3 Autosampler Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Agilent Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Connecting the Agilent Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16
CTC PAL Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Connecting the CTC PAL Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Gilson 215 Liquid Handler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Connecting the Gilson 215 Liquid Handler . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Installing the Syringe on the Gilson 215 Liquid Handler . . . . . . . . . . . . . . . . .26
Gilson 233 XL Sampling Injector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26
Connecting the Gilson 233 XL Sampling Injector . . . . . . . . . . . . . . . . . . . . . .26
Installing the Syringe on the Gilson 402 Syringe Pump . . . . . . . . . . . . . . . . .30
PerkinElmer Series 200 Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Connecting the PerkinElmer Series 200 Autosampler . . . . . . . . . . . . . . . . . .31
Spark Holland Endurance Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34
Connecting the Spark Holland Endurance Autosampler . . . . . . . . . . . . . . . . .34
Other Autosamplers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
Chapter 4 Pump Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Agilent Pumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
Connecting the Agilent Pump to the Computer . . . . . . . . . . . . . . . . . . . . . . . .40
Harvard 22 Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
Connecting the Harvard 22 Syringe Pump . . . . . . . . . . . . . . . . . . . . . . . . . . .41
PerkinElmer Series 200 LC Pumps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
Connecting the PerkinElmer Series 200 LC Pumps . . . . . . . . . . . . . . . . . . . .43
Chapter 5 Shimadzu Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Shimadzu LC-30 Series Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Setting Shimadzu Device Communications – SIL-HT (SCL-10Avp) . . . . . . . .46
Setting Shimadzu Device Communications for Use on a Network
– CBM-20A (CBM-20A lite) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
Setting Shimadzu Device Communications for Stand-alone use

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Contents

(Peer-to-peer Network) – CBM-20A (CBM-20A lite) . . . . . . . . . . . . . . . . . . . .47

Configuring the Shimadzu System Controller . . . . . . . . . . . . . . . . . . . . . . . . .48
Shimadzu Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Fault Recovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54
Connecting Shimadzu Devices to the Shimadzu System Controller . . . . . . . .56
Connecting a Shimadzu Valve Interface Unit to the Shimadzu System
Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58
Chapter 6 Column Oven Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Agilent Column Oven . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
Connecting the Column Oven to the Computer . . . . . . . . . . . . . . . . . . . . . . . .60
PerkinElmer Series 200 Column Oven . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Connecting the Column Oven to the Computer . . . . . . . . . . . . . . . . . . . . . . . .61
Chapter 7 Switching Valve Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Valco Two-Position Switching Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63
Initializing the Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .63
Connecting the Valve to the Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .65
Chapter 8 Detector Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Diode Array Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .67
Connecting the Diode Array Detector to the Computer . . . . . . . . . . . . . . . . . .68
Chapter 9 NIDAQ and Terminal Block Installation . . . . . . . . . . . . . . . . . . . . . . . 69
Installing an ADC Card on a New Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . .69
Appendix A Peripheral Device Analog Synchronization . . . . . . . . . . . . . . . . . . .75
API AUX I/O Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
AUX I/O Signal Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
Ready Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
Error Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77
Start Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .77
Wiring Peripheral Devices to the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . .77
Appendix B CTC PAL Autosampler Setup Notes . . . . . . . . . . . . . . . . . . . . . . . .79
Rack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79
Tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .79

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Introduction
1
This guide is intended for customers and FSEs who are responsible for configuring devices to
work with the mass spectrometer. You can control devices automatically during LC/MS/MS data
acquisition through the Analyst® or Analyst TF software. The software supports LC pumps,
autosamplers, column ovens, switching valves, detectors, and analog-to-digital converters from
several manufacturers.
Some hardware setup and configuration is required so that the supported peripheral devices and
the mass spectrometer can communicate properly. Use the procedures in this guide to connect
and configure the peripheral devices and your system.

Related Documentation
The guides and tutorials for the instrument and the Analyst or Analyst TF 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 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 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 www.absciex.com.

System Components
Figure 1-1 is an example of how you can connect peripheral devices to the computer and mass
spectrometer. You do not have to configure your system exactly as shown. In this example, the
pumps, column ovens, autosamplers, and switching valves are controlled from the computer by
means of serial (RS-232) ports. The diode array detector is controlled by LAN (Ethernet) cables.
For more information on how to configure peripheral devices to communicate with the computer,
see the section in this guide specific to each device.

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Introduction

Figure 1-1 Example of system component configuration

Supported Devices
For an up-to-date list of the peripheral devices and firmware supported by the Analyst software,
see the most current Analyst software Installation Guide.

Peripheral Device Software Plug-in Vendors

The Analyst Access Object (AAO) is an interface to the Analyst software that allows peripheral
device vendors to develop device control software that can be plugged into the Analyst software
to enable integrated LC/MS control. The following vendors have released AAO software. See the
vendor documentation or contact the vendors directly for AAO device software information,
including latest releases, installation instructions, and information on device hardware set up and
configuration.
• Advion Biosciences Inc.
• Alcott Chromatography
• Beckman Coulter Inc.
• BioTrove
• Cohesive Technologies
• Dionex Corp.
• Eksigent Technologies
• ESA Inc.
• Flux Instruments
• Hitachi HTA Inc.
• Jasco

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 Introduction

• Leap Technologies
• MassTech Inc.
• Maylab Analytical Instruments
• Micro-Tech Scientific
• PerkinElmer Inc.
• Selerity Technologies
• Shimadzu
• Shiseido Co. Ltd.
• Spark Holland
• Waters Corp.

Adding AAO-Controlled Devices to the Hardware

Profile
You can add AAO-controlled devices to the hardware profile after the AAO software has been
installed.
1. Create or edit a hardware profile. See the Analyst software Help.
2. Click Add Device.

Figure 1-2 Available Devices dialog

3. In the Available Devices dialog, in the Device Type list, click Software
Application.
The list of AAO software applications installed on the computer appears in the
Devices box.
4. Click the AAO software applications you want to add, and then click OK.

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Introduction

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Agilent Series Devices Configuration
2
This section provides information about configuring the Agilent series peripheral devices using a
standard serial (RS-232) port, GPIB (general purpose interface bus), or LAN (Ethernet)
communication, with or without CAN cables. An overview of each type of communication is
provided for the Agilent 1100, 1200, 1260, and 1290 series LC Systems.

Note: Use CAN cables with a RS-232, GPIB, or LAN (Ethernet) cable if configuring
multiple Agilent devices in a stack configuration. See Configuration of Agilent Devices
with CAN Cables on page 14.

Configuration of Agilent Devices Through Serial

Port Communication
Connect the Agilent series autosamplers, pumps, and column oven to the computer with a
standard RS-232 cable (PN WC024736).

Note: You must connect the diode array detector to the computer through GPIB or LAN
(Ethernet) communication.

If you connect an Agilent device (except a DAD) to the computer with a RS-232 cable, set the
DIP switches at the back of the device. The DIP switches configure parameters for the
communication protocol and instrument initialization procedures.
The following table shows the appropriate DIP switch settings for a baud rate of 19 200 bps for
the Agilent 1100, 1200, 1260, and 1290 series devices. If you create a new hardware profile that
includes an Agilent 1100, 1200, 1260, or 1290 series device, or if you add an Agilent device to an
existing hardware profile, set the DIP switches for a baud rate of 19 200, and then set the baud
rate to 19 200 in the Hardware Configuration Editor.

Note: You must restart the devices to apply the new baud rate.

Set the DIP switches as indicated in Table 2-1.

Table 2-1 Agilent 1100, 1200, 1260, and 1290 DIP Switch Settings (19 200 Baud Rate)
For this switch... 1 2 3 4 5 6 7 8
(baud rate 19 200)
Set as... Down Up Up Up Down Up Down Down
(Off) (On) (On) (On) (Off) (On) (Off) (Off)

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Agilent Series Devices Configuration

Configuration of Agilent Devices Through GPIB

Communication
You can connect most Agilent series autosamplers, pumps, and column ovens to the computer
with a GPIB cable (PN WC021365). The exception is the Agilent DAD, which requires a LAN
connection.
Agilent devices, excluding the 1260 and 1290, come with DIP switches preset for GPIB
communication. You need not change the DIP switch settings if you are connecting the device to
the computer with a GPIB cable. To serially connect (daisy chain) multiple Agilent devices with
GPIB cables, make sure that each device is assigned the same Primary Address in the
Hardware Configuration Editor.
Table 2-2 DIP Switch Settings for Autosamplers
For this switch... 1 2 3 4 5 6 7 8
Set as... Down Down Down Up Up Up Down Down
(Off) (Off) (Off) (On) (On) (On) (Off) (Off)

Table 2-3 DIP Switch Settings for Pumps

For this switch... 1 2 3 4 5 6 7 8
Set as... Down Down Down Up Down Up Up Down
(Off) (Off) (Off) (On) (Off) (On) (On) (Off)

Table 2-4 DIP Switch Settings for Diode Array Detectors

For this switch... 1 2 3 4 5 6 7 8
Set as... Down Down Down Up Up Down Up Down
(Off) (Off) (Off) (On) (On) (Off) (On) (Off)

Table 2-5 DIP Switch Settings for Column Compartments

For this switch... 1 2 3 4 5 6 7 8
Set as... Down Down Down Up Up Down Up Up
(Off) (Off) (Off) (On) (On) (Off) (On) (On)

Configuration of Agilent Devices Through LAN

(Ethernet) Communication
You can connect the Agilent series autosamplers, pumps, column oven, and diode array detector
to the computer through LAN (Ethernet) communication. The required LAN (Ethernet) cables are
supplied by Agilent. Use Agilent PN G5183-4649 for a direct connection from the device to the
computer, or use Agilent PN G1530-61485 for hub connections.
Install a network interface card in the Agilent device. (For instructions, see the Agilent
documentation.)

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 Agilent Series Devices Configuration

Note: The 1290 module is shipped with all switches Down (Off). To perform any LAN
configuration, SW1 and SW2 must be Down. For all modules with on-board LAN
(G1315/65C/D, G1314D/E, G4212A, G4220A) the default is all switches Down. For
specific LAN modes, switches 3 to 8 must be set as required. For boot or test modes,
switches 1 and 2 must be Up (On).

Installing the Network Interface Card

1. Install the network interface card in an appropriate free slot in the computer. See the
documentation accompanying the network interface card.
2. Turn on the computer and then log on as an Administrator.
3. Check the driver version.
i. On the Windows desktop, right-click My Computer.
ii. Click Properties.
iii. In the System Properties dialog, click the Hardware tab.
iv. Click Device Manager.
v. Click Network Adaptors.
vi. Right-click one of the following: the 3COM EtherLink, Broadcom NetXtreme
57xx Gigabit Controller, the Intel PRO/1000 PT Dual Port Server Adapter,
or the Intel PRO/1000 PT Dual Port Server Adapter #2.
vii. Click Properties.
viii. In the 3COM EtherLink Properties dialog, click the Driver tab.
4. If the driver is version 4.8.0.0 or later, see Configuring the Network Interface Card on
page 12.
5. Insert the driver installation CD in the CD/DVD drive.
The 3COM EtherCD main menu appears.
6. Click NIC and then select NIC Drivers and Diagnostics.
7. Select Update Drivers and Remove Diagnostics Program.
Various messages appear during the update process.
8. After the driver update process finishes, click OK, and then exit the EtherCD main
menu.
9. Repeat step 3 to check the updated driver version.

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Agilent Series Devices Configuration

Configuring the Network Interface Card

1. On the Windows desktop, right-click My Network Places and then click Properties.

Figure 2-1 Network Connections window

2. Right-click 3COM EtherLink connection and then click Properties.

Figure 2-2 Local Area Connection 2 Properties dialog

3. On the General tab, right-click Internet Protocol and then click Properties.

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 Agilent Series Devices Configuration

Figure 2-3 Internet Protocol (TCP/IP) Properties dialog

4. Select Use the following IP address.
5. If you are using the direct connection method, in the IP address field, type the preset
IP address (192.168.254.10). If you are using BOOTP, use the BOOTP utility to set
up an IP address.

Note: If you are using the BOOTP utility, you need the MAC address from
the label on the module. The MAC address is used to recognize which
device is used in the configuration.

6. Press Enter.
The Subnet mask field is automatically filled.
7. Click OK and then close the Local Area Connection 2 Properties dialog.

Checking the DAD Settings (Direct Connection)

1. At the back of the DAD unit, check the Initializing Mode switches. Set the switches
as follows:
Table 2-6 DIP Switch Settings for Column Compartments
For this switch... 6 7 8
Set as... Down (Off) Up (On) Up (On)

See the Agilent 1200 Series Diode Array and Multiple Wavelength Detector SL User
Manual.

Note: Make sure that the DAD is using the preset LAN settings (IP address
192.168.254.11).

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Agilent Series Devices Configuration

2. To confirm the connection between the computer and the DAD, click Start and then
click Run.
3. In the Open field, type ping 192.168.254.11.
The Ping utility makes four data transmissions to the IP address specified and
reports the reply if successful. If the data transmission fails, the utility reports
“Request timed out.”
4. Using the Analyst® software, add the DAD to a hardware profile. See the Analyst
software Help.

Configuration of Agilent Devices with CAN

Cables
You can use CAN cables in conjunction with a RS-232 cable, GPIB cable, or a LAN (Ethernet)
cable to configure a stack of Agilent devices. In an Agilent stack configuration, a single device is
connected to the computer with a RS-232 cable, a GPIB cable, or a LAN (Ethernet) cable. Any
additional Agilent devices are then connected to each other (in series) with CAN cables. For
serial communication in CAN stacks, set all Agilent CAN-linked devices to the same serial port in
the hardware profile.

Note: The DAD must be connected directly to the PC via Ethernet. It cannot be
connected to other devices via CAN.

To monitor and control the stack manually, you can connect a handheld Agilent series control
module to one of the CAN connections at the back of any Agilent device. The devices connected
by CAN cables in the stack must match the devices in the Analyst software hardware profile. In
the event of a fault in the CAN-linked stack, reboot all the devices in the stack.
For more information on configuring Agilent devices with CAN cables, see the Agilent
documentation.

Note: When configuring devices via CAN, ensure that if the TCC is used, it is at the
end of the CAN chain. The TCC should be the furthest device from the PC.

Note: If you are switching a stack from CAN to another communication mode in the
Analyst software, the CAN cables must be disconnected from the device.

Note: All devices connected by CAN must be at the same level of firmware.

Note: Mixed configurations of differing device series should not be connected via CAN.
For example, if an LC stack contains a 1290 autosampler, a 1260 binary pump, and a
1260 TCC, the two 1260 devices can be connected via CAN, but they cannot be
connected to the 1290 device.

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Autosampler Configuration
3
This section provides information on the required autosampler hardware, how to connect the
autosampler to the computer and the mass spectrometer, and how to configure the most current
autosampler for external control.
The cables for the Agilent and Shimadzu autosamplers, and any other device that does not have
its own AUX I/O cable, are included with the mass spectrometer. The cable for the CTC
autosampler is included with the CTC autosampler.

Note: You can configure autosamplers that are not supported by the Analyst® software
to operate with the mass spectrometer through analog signals or through AAO–type
software. For information on configuring unsupported autosamplers to operate with a
mass spectrometer, see Peripheral Device Analog Synchronization on page 75.

Agilent Autosampler
The following Agilent autosamplers are supported by the Analyst software and are configured the
same way. For the most up-to-date list of supported devices, see the most current Analyst
software Installation Guide.
Table 3-1 Supported Agilent 1100 Series Autosamplers
Autosampler Model number
Standard G1313A
Thermo-enabled standard G1327A
Well-plate G1367A
Thermo-enabled well-plate G1368A
Micro well-plate G1377A
Thermo-enabled micro well-plate sampler G1378A
Micro G1389A
Thermo-enabled micro autosampler G1387A
Thermostat module G1330B

Table 3-2 Supported Agilent 1200 Series Autosamplers

.

Autosampler Model number

Standard autosampler G1329A
Thermostat module G1330B
High performance G1367B
High performance SL G1367C
Micro well-plate G1377A
High performance autosampler SL plus G1367D

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Autosampler Configuration

Table 3-3 Supported Agilent 1260 Series Autosampler

Autosampler Model Number
High Performance G1367E

Table 3-4 Supported Agilent 1290 Series Autosampler

Autosampler Model Number
Standard autosampler G4226A

The following table lists the required hardware. For the latest version of firmware supported, see
the most current Analyst software Installation Guide.
Table 3-5 Required Hardware for the Agilent Autosamplers
Cable Other parts needed
• RS-232 cable (PN WC024736) • Network interface card if using a LAN (Ethernet)
connection
• GPIB cable (PN WC021365)
• Agilent PN G5183-4649 (for a direct LAN connection)
• AUX I/O cable (PN 014474)
• Agilent PN G1530-61485 (for a LAN connection using a
hub)

WARNING! Electrical Shock Hazard: See the Agilent autosampler safety

instructions before configuring any AC mains-powered equipment.

Connecting the Agilent Autosampler

Note: This procedure should be performed only by a trained FSE.

This procedure describes how to connect the Agilent autosampler to the computer through
standard serial port communication. The Agilent autosampler can also be connected to the
computer with a GPIB or LAN (Ethernet) cable.
The autosampler must be wired so that the autosampler injection triggers the mass spectrometer
to begin data acquisition. To do so, connect a pair of wires from the AUX I/O connector at the
back of the mass spectrometer to the remote port of the autosampler.

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1 2 3 4 5

Figure 3-1 Back panel of the Agilent autosampler

B

Item Description
1 Remote port
2 Serial port
3 CAN connectors
4 Agilent GPIB
5 DIP switches

Connecting the Autosampler to the Computer

1. Turn off the Agilent autosampler by pressing the On/Off button on the front of the
device.
2. Shut down the computer.
3. Disconnect all CAN connectors from the module.
4. Set the DIP switches at the back of the autosampler for a baud rate of 19 200. For
more information on setting the DIP switches, see Configuration of Agilent Devices
Through Serial Port Communication on page 9.
For the location of the DIP switches at the back of the autosampler, see Figure 3-1.
5. Connect the RS-232 cable from the serial port at the back of the autosampler to the
desired serial port on the computer, noting the port number.

Connecting the Autosampler to the Mass Spectrometer

1. Connect the 5 V supply wire (red with black stripes) to the anode wire (orange with
black stripes) on the AUX I/O cable and then cover the connection with insulating
tape or heat shrink tubing to prevent shorting to other wires or grounded metal parts.

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Table 3-6 Wiring for the Agilent Autosampler (TTL—Active Low) Injection
Input
Autosampler Mass spectrometer AUX I/O cable
Pin 9 (power 5V) Red with black stripes
Pin 10 (anode) Orange with black
stripes

Remote port (pin 3) White with black stripe Pin 22 (cathode) White with black stripes
0 0
Remote port (pin 1) Green with black stripe Pin 21 (ground) Green with black stripes
0 0
2. Connect the cathode wire (white with black stripes) and the ground wire (green with
black stripes) on the AUX I/O cable to the remote port at the back of the Agilent
autosampler.
3. Connect the cathode wire (white with black stripes) to Pin 3 of the remote port and
connect the ground wire (green with black stripes) to Pin 1 of the remote port.
Polarity is important.

Note: Make the connections to the remote port with a 9-pin DB push-lock
or solder-tail connector. If you use the Agilent remote cable to connect the
remote port to the AUX I/O cable, make the cable as short as possible.

4. Connect the other end of the AUX I/O cable to the mass spectrometer AUX I/O
connector.

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CTC PAL Autosampler

The following CTC PAL autosamplers are supported by the Analyst software: HTS, HTC, and LC.
All are configured the same way. For more information on setting up the CTC PAL autosampler,
see CTC PAL Autosampler Setup Notes on page 79.
The following table lists the required hardware. For the latest version of firmware supported, see
the most current Analyst software Installation Guide.
Table 3-7 Required Hardware for the CTC PAL Autosampler
Cable Other parts needed
• RS-232 cable (PN WC024736) • CTC PAL–ready cable for connecting the instrument
• AUX I/O cable (PN 014474) • DB15 male connector

Connecting the CTC PAL Autosampler

WARNING! Electrical Shock Hazard: See the CTC PAL autosampler safety
instructions before configuring any AC mains-powered equipment.

Note: This procedure should be performed only by a trained FSE.

Wire the autosampler so that the autosampler injection triggers the mass spectrometer to begin
data acquisition. To do so, connect a pair of wires from the AUX I/O connector at the back of the
mass spectrometer to the remote port of the autosampler.

Connecting the Autosampler to the Computer

1. Shut down the computer.
2. Turn off the CTC PAL autosampler by pressing the On/Off button on the power
module.
3. Connect the RS-232 cable from the SER 1 port at the back of the autosampler to the
desired serial port on the computer, noting the port number.

1 2

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Figure 3-2 Connectors at the back of the CTC PAL autosampler

Item Description
1 AUX I/O connector
2 Fast wash station connector

Connecting the Autosampler to the Mass Spectrometer

1. On the free end of the AUX I/O cable, short together the following wires but do not
connect them to anything else:
• Red with black stripe (wire 9)
• Orange with black stripe (wire 10)
The CTC PAL comes with a cable that connects to the mass spectrometer. This
cable has a connector that fits into the 15-pin Interface 1 connector at the back of the
CTC PAL autosampler. The other end has bare wires that you must attach to the
bare wires of the AUX I/O cable.
Table 3-8 Wiring for the CTC PAL Autosampler
.

Autosampler Mass spectrometer AUX I/O cable

Interface 1 Pin 9 (power 5V) Red with black stripes
Pin 10 (anode) Orange with black
stripes

Inject marker (pin 3) White with black stripe Pin 22 (cathode) White with black stripes
0 0
Common (pin 4) Green with black stripe Pin 21 (ground) Green with black stripes
0 0
Caution: Potential Equipment Damage: Cover each connection and then the
entire cable assembly with insulating tape or heat shrink tubing to prevent
shorting to other wires or grounded metal parts.

2. Connect the white with black stripe AUX I/O wire to Pin 3 of the DB15 connector.
3. Connect the green with black stripe AUX I/O wire to Pin 4 of the DB15 connector.
4. Connect the DB15 male connector to the CTC PAL autosampler Interface 1
connector.
5. Connect the other end of the AUX I/O cable into the mass spectrometer AUX I/O
connector.

Configuring the Autosampler to Send and Receive Signals

1. Turn on the CTC PAL autosampler by pressing the On/Off switch on the power
module of the autosampler.
2. Start the computer.
3. On the Home menu of the CTC PAL handheld controller, press F1 to select Menu.

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4. Scroll down and then select Setup.

5. Press F3 and then press ENTER to display the available options.
6. On the next screen, scroll down and then select Objects.
7. Scroll down and then select Sync Signals.
8. Select Start.
9. In the next window that appears, highlight the Source line, and then scroll between
the options. Select Remote and then press ENTER.

Note: Make sure that the tray hardware configured in the system is listed
in the Tray Type and Tray Holder menus. See the manufacturer’s
documentation.

10. Press Esc to return to the previous window and then scroll down to select Inject.
11. In the next window that appears, highlight the Source line and then scroll between
the options. Select Immediate, and then press ENTER.
12. Press Esc twice to move back two windows.
13. Scroll down and then select Out Signals.
14. In the next window that appears, select Injected.
15. Highlight the Destination line, scroll between the options and then select SW-Out1.
16. Press F4 to return to the Home menu.

Gilson 215 Liquid Handler

The Gilson 819 and 841 injectors are supported by the Analyst software for use with the Gilson
215 liquid handler. For the configuration described in this section, the Gilson 215 liquid handler is
paired with the Gilson 819 injection valve actuator. Configuration of the two injectors is similar.
Differences are noted where appropriate.
The following table lists the required hardware. For the latest version of firmware supported, see
the most current Analyst software Installation Guide.
Table 3-9 Required Hardware for the Gilson 215 Liquid Handler
Cable Other parts needed
• RS-232 cable (PN WC024735) GSIOC cable
• AUX I/O cable (PN 014474)

Connecting the Gilson 215 Liquid Handler

WARNING! Electrical Shock Hazard: See the Gilson 215 Liquid Handler and the
Gilson 819 Injection Valve Actuator safety instructions before configuring any AC
mains-powered equipment.

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Note: This procedure should be performed only by a trained FSE.

Wire the autosampler so that the autosampler injection triggers the mass spectrometer to begin
data acquisition. To do so, connect a pair of wires from the AUX I/O connector at the back of the
mass spectrometer to the remote port of the autosampler.

Figure 3-3 I/O connection for the Gilson 215 liquid handler
Item Description
1 Output switch 1 (pins 3 and 4)

Connecting the Autosampler to the Computer

1. Shut down the computer.
2. Connect the 25-pin end of the RS-232 cable from the RS-232 port on the Gilson 215
liquid handler to the desired serial port on the computer, noting the port number.

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4
Figure 3-4 Cable connections for the Gilson 215 liquid handler
Item Description
1 GSIOC cable to the Gilson 819 or 841
2 RS-232 port to computer
3 SW1
4 SW2

Connecting the Autosampler to the Mass Spectrometer

1. Connect the 5V supply wire (red with black stripes) to the anode wire (orange with
black stripes) on the AUX I/O cable and then cover the connection with insulating
tape or heat shrink tubing to prevent shorting to other wires or grounded metal parts.
Table 3-10 Wiring for the Gilson 215 Liquid Handler (Normally Open) Injection
.

Input
Autosampler Mass spectrometer AUX I/O cable
Interface 138 Pin 9 (power 5V) Red with black stripes
Pin 10 (anode) Orange with black
stripes

Output switch (pin 3) White with black stripe Pin 22 (cathode) White with black stripes
0 0
Output switch (pin 4) Green with black stripe Pin 21 (ground) Green with black stripes
0 0

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Note: Polarity is not important.

2. Connect the cathode wire (white with black stripes) and the ground wire (green with
black stripes) on the AUX I/O cable to Output Switch 1 (Pins 3 and 4 of the Output
Port at the back of the Gilson 215 liquid handler) using the green connector supplied
with the liquid handler.
3. Connect the other end of the AUX I/O cable to the mass spectrometer AUX I/O
connector.

Configuring the Autosampler for External Control

WARNING! Electrical Shock Hazard: Disconnect the power cord and wait at least
one minute before removing the cover. See the Gilson Injection Valve Actuator
operator safety manual before removing the cover.

1. Turn off the Gilson 215 liquid handler by pressing the On/Off button.
2. Turn off the Gilson injection valve actuator by pressing the On/Off button.
3. Disconnect the Gilson keypad and any other connections to the Gilson 215 liquid
handler.
4. At the back of the Gilson injection valve actuator, set the UNIT ID so that the white
dot is at position 9. For help locating the UNIT ID, see Figure 3-5 and Figure 3-6.
5. Remove the cover of the injection valve actuator.
6. Do one of the following:
• For the 819 injection valve actuator, set SW 1 so that the white dot is at
Position 0 (External).
• For the 841 injection valve actuator, set the jumper to External.

Note: When viewed from the front of the Gilson 819 injection valve
actuator, the SW1 switch is located on the left side. For the 841 injection
valve actuator, the jumper is located on the right side.

7. Connect the Gilson-supplied GSIOC cable as follows:

i. Attach the end of the cable with the additional RS-232 cable to the GSIOC port
of the Gilson injection valve actuator.
ii. Attach the other end of the cable to the GSIOC port on the autosampler.

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1 2

Figure 3-5 Gilson 819 injection valve actuator

Item Description
1 GSIOC port
2 UNIT ID

Figure 3-6 Gilson 841 injection valve actuator

Item Description
1 GSIOC port
2 UNIT ID

8. At the back of the Gilson 215 liquid handler, do the following:

i. Set the SW 1 switch so that the white dot is at Position 2.
ii. Set the SW 2 switch so that the white dot is at Position 6.

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Installing the Syringe on the Gilson 215 Liquid Handler

Use the 215setup.exe program provided by Gilson to adjust the syringe drive arm position during
syringe installation. See the Gilson documentation. This program is also used to adjust the
vertical arm (z-arm) height.

Gilson 233 XL Sampling Injector

The Gilson 233 XL sampling injector is supported by the Analyst software and is paired with the
Gilson 402 syringe pump.
The following table lists the required hardware. For the latest version of firmware supported, see
the most current Analyst software Installation Guide.
Table 3-11 Required Hardware for the Gilson 233 XL Sampling Injector
Cable Other parts needed
• RS-232 cable (PN WC024735) GSIOC cable
• AUX I/O cable (PN 014474)

Connecting the Gilson 233 XL Sampling Injector

WARNING! Electrical Shock Hazard: See the Gilson 233 XL Sampling Injector
and the Gilson 402 Syringe Pump Safety Instructions before configuring any AC
mains-powered equipment.

Note: This procedure should be performed only by a trained FSE.

Wire the autosampler so that the autosampler injection triggers the mass spectrometer to begin
data acquisition. To do so, connect a pair of wires from the AUX I/O connector at the back of the
mass spectrometer to the remote port of the autosampler.
r

1 2 3 4

Figure 3-7 Back panel on the Gilson 233 XL sampling injector

Item Description
1 Relay output 1
2 DIP switches

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Figure 3-7 Back panel on the Gilson 233 XL sampling injector (Continued)
Item Description
3 GSIOC
4 RS-232 port

Connecting the Autosampler to the Computer

1. Shut down the computer.
2. Connect the 25-pin end of the RS-232 cable from the RS-232 port on the Gilson
233 XL to the desired serial port on the computer, noting the port number.

Connecting the Autosampler to the Mass Spectrometer

1. Connect the 5V supply wire (red with black stripes) to the anode wire (orange with
black stripes) on the AUX I/O cable and then cover the connection with insulating
tape or heat shrink tubing to prevent shorting to other wires or grounded metal parts.
Table 3-12 Wiring for the Gilson 233 XL Sampling Injector (Normally Open)
.

Injection Input
Autosampler Mass spectrometer AUX I/O cable
Pin 9 (power 5V) Red with black stripes
Pin 10 (anode) Orange with black
stripes

Output switch (pin 3) White with black stripe Pin 22 (cathode) White with black stripes
0 0
Output switch (pin 1) Green with black stripe Pin 21 (ground) Green with black stripes
0 0
2. Connect the cathode wire (white with black stripes) and the ground wire (green with
black stripes) of the AUX I/O cable to the Output Switch 1 (Pins 1 and 3 of the Output
Port at the back of the Gilson 233) using the green connector supplied with the liquid
handler.

Note: Polarity is not important.

3. Connect the other end of the AUX I/O cable to the mass spectrometer AUX I/O
connector.

Configuring the Autosampler for External Control

1. Turn off the Gilson 402 syringe pump by pressing the On/Off button at the back of
the device.
2. Turn off the Gilson 233 XL sampling injector by pressing the On/Off button at the
back of the device.

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3. Disconnect the Gilson keypad and any other connections to the Gilson 233 XL
sampling injector and the Gilson 402 syringe pump.
4. Set the Options and ID DIP switches at the back of the Gilson 402 syringe pump as
follows:
Table 3-13 Gilson 402 Pump: Options and ID DIP Switch Settings
For this switch... 8 7 6 5 4 3 2 1
Set as... Left Left Right Left Left Left Left Left
(Off) (Off) (On) (Off) (Off) (Off) (Off) (Off)

5. Set the ID Number DIP switches at the back of the Gilson 233 XL sampling injector
as follows:
Table 3-14 Gilson 233 XL Sampling Injector: ID Number DIP Switch Settings
For this switch... 7 6 5 4 3 2 1 0
Set as... Down Up Up Down Up Down Up Down
(Off) (On) (On) (Off) (On) (Off) (On) (Off)

6. Connect the Gilson-supplied GSIOC cable as follows:

i. Attach the end of the cable with the additional RS-232 cable to the GSIOC port
of the syringe pump.
ii. Attach the other end of the cable to the GSIOC port on the autosampler.

Installing the Rinse Station and Injection Port

Take the following actions depending on the sample rack you are using.
1. If you are using an XL 30 Rack containing vials:
i. Position the rinse station at location A.

Figure 3-8 Rinse station at location A

ii. Position the injection port at location C.

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Figure 3-9 Injection port at location C

2. If you are using a Multiple Microtitre System:
i. Position the rinse station at the near end of the adapter.

Figure 3-10 Rinse station at the near end of the adapter

ii. Position the injection port at the far right end of the adapter, above the
switching valve.

Figure 3-11 Injection port at the far right end of the adapter
3. Turn on the Gilson 402 syringe pump by pressing the On/Off button at the back of
the device.
4. Turn on the Gilson 233 XL sampling injector by pressing the On/Off button at the
back of the device.
5. Restart the computer.

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Installing the Syringe on the Gilson 402 Syringe Pump

Use the 215setup.exe program provided by Gilson to adjust the syringe drive arm position during
syringe installation. See the Gilson documentation. This program is also used to adjust the
vertical arm height (that is, the z-arm height).

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PerkinElmer Series 200 Autosampler

Only the PerkinElmer Series 200 is supported by the Analyst software.
The following table lists the required hardware. For the latest version of firmware supported, see
the most current Analyst software Installation Guide.
Table 3-15 Required Hardware for the PerkinElmer Autosampler
Cable Other parts needed
• RS-232 cable (PN WC024737) N/A
• AUX I/O cable (PN 014474)

Connecting the PerkinElmer Series 200 Autosampler

WARNING! Electrical Shock Hazard: See the PerkinElmer Series 200
Autosampler safety instructions before configuring any AC mains-powered
equipment.

Note: This procedure should be performed only by a trained FSE.

Wire the autosampler so that the autosampler injection triggers the mass spectrometer to begin
data acquisition. To do so, connect a pair of wires from the AUX I/O connector at the back of the
mass spectrometer to the remote port (INJ 1 or INJ 2) signal of the autosampler.

Connecting the Autosampler to the Computer

1. Shut down the computer.
2. Turn off the autosampler by pressing the On/Off button.
3. Connect the RS-232 cable from a serial port at the back of the autosampler to any
available serial port on the computer, noting the port number.

Connecting the Autosampler to the Mass Spectrometer

1. Connect the 5V supply wire (red with black stripes) to the anode wire (orange with
black stripes) on the AUX I/O cable and then cover this connection with insulating
tape or heat shrink tubing to prevent shorting to other wires or grounded metal parts.

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Table 3-16 Wiring for Perkin Elmer Series 200 Autosampler (Normally Open)
Injection Port
Autosampler Mass spectrometer AUX I/O cable
Pin 9 (power 5V) Red with black stripes
Pin 10 (anode) Orange with black
stripes

INJ 1 White with black stripe Pin 22 (cathode) White with black stripes
0 0
Green with black stripe Pin 21 (ground) Green with black stripes
0 0
Note: Polarity is not important; however, use the two middle slots of the
connector.

2. Connect the cathode wire (white with black stripes) and the ground wire (green with
black stripes) to the AUX I/O cable with one of the telephone-style connectors
supplied with the PerkinElmer Series 200 autosampler.

1 2 4
3
Figure 3-12 Wire connections to the telephone-style connector
Item Description
1 Inverted top piece—connector housing
2 AUX I/O cable
3 Bottom piece—connector housing
4 AUX I/O cable
5 Top piece—connector housing
6 Phillips screw

3. Insert the completed connector into the INJ 1 port on the side panel of the
autosampler.

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4. Do one of the following:

• If the autosampler is controlled by the Analyst software only, insert the loop
back connector (see Figure 3-13) into the RDY IN port on the side of the
autosampler.
In this mode, the software directs the autosampler to proceed with injection
when the mass spectrometer is ready.
• If the autosampler is controlled manually, see Peripheral Device Analog
Synchronization on page 75 to set up manual control.
In this mode, the RDY IN signal from the mass spectrometer tells the
autosampler that the mass spectrometer is ready for injection.

Figure 3-13 Loop back connector

5. Connect the other end of the AUX I/O cable to the mass spectrometer AUX I/O
connector.

Configuring the Autosampler for External Control

1. Turn on the autosampler and locate the keypad.
2. Press F7 (CNFG).
The Configure menu appears.
3. Press F2 (COMM).
The Communication menu appears.
4. Press F2 (EXTE) to set External Control.
5. Press Return.
The Configure menu appears.
6. Press Return.
The Main menu appears.

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Spark Holland Endurance Autosampler

The Spark Holland Endurance autosampler device driver is available only from the manufacturer.
Install the device driver before configuring the autosampler in the Analyst software Hardware
Configuration Editor. See the manufacturer’s documentation.
For a list of the required hardware, see Table 3-17. For the latest version of firmware supported,
see the most current Analyst software Installation Guide.
Table 3-17 Required Hardware for the Spark Holland Endurance Autosampler
Cable Other parts needed
AUX I/O cable (PN 014474) • Device driver kit (Spark Holland PN 0920-768). The kit includes
the connection cable.
• DB15 male connector.

Connecting the Spark Holland Endurance Autosampler

WARNING! Electrical Shock Hazard: See the Spark Holland Endurance
Autosampler Safety Instructions before configuring any AC mains-powered
equipment.

Note: This procedure should be performed only by a trained FSE.

Wire the autosampler so that the autosampler injection triggers the mass spectrometer to begin
data acquisition. To do so, connect a pair of wires from the AUX I/O connector at the back of the
mass spectrometer to the remote port of the autosampler.

Connecting the Autosampler to the Computer

1. Shut down the computer.
2. Turn off the autosampler by pressing the On/Off button at the back of the device.

Note: For more information about serial cables, see the autosampler
documentation.

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Figure 3-14 Back panel of the Spark Holland Endurance autosampler

Item Description
1 Communication Interface connectors

3. Connect the serial cable from the serial port on the autosampler to the desired serial
port on the computer, noting the port number. Use any of the following serial cables:
• RS-232
• RS-422
• RS-485

Connecting the Autosampler to the Mass Spectrometer

1. Connect the 5V supply wire (red with black stripes) to the anode wire (orange with
black stripes) on the AUX I/O cable and then cover this connection with insulating
tape or heat shrink tubing to prevent shorting to other wires or grounded metal parts.

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Table 3-18 Wiring for Spark Holland Endurance Autosampler

Autosampler Mass spectrometer AUX I/O cable
P2 vial no. & markers Pin 9 (power 5V) Red with black
(TTL) stripes
Pin 10 (anode) Orange with black
stripes
Inject marker (pin 1) White with black stripe Pin 22 (cathode) White with black
stripes
0 0
Signal ground (pin 13) Green with black stripe Pin 21 (ground) Green with black
0 0 stripes

2. Connect the AUX I/O wire (white with black stripes) to Pin 1 of the DB15 male
connector.
3. Connect the AUX I/O wire (green with black stripes) to Pin 13 of the DB15 male
connector.
4. Insert the DB15 male connector into the P2 connector at the back of the
autosampler.
5. Insert the other end of the AUX I/O cable into the AUX I/O connector on the mass
spectrometer.

To configure the autosampler to accept external control

1. Turn on the autosampler.
2. On the keypad, press the Menu key.
3. Press the Serial key.

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Other Autosamplers
The instructions in this section are required only when AAO or the Analyst software support is not
available. You can synchronize any autosampler with the mass spectrometer for use with the
normally open autosampler contact closure inject signal. The autosampler is connected to the
mass spectrometer by means of an AUX I/O cable.
To synchronize other autosamplers, first create a hardware profile, and then choose the LC
synchronization trigger.

Synchronizing the Autosampler and the Mass Spectrometer

1. Start the Analyst software.
2. Create or edit a hardware profile. See the Analyst software Help.
3. On the Edit Hardware Profile screen, click the mass spectrometer and then click
Setup Device.
The Configuration dialog for the mass spectrometer appears.
4. Click the Configuration tab.
5. Click either Active Low or Active High to set the voltage level at which the mass
spectrometer triggers the autosampler to begin. See the autosampler
documentation.

Note: Active Low is the preset value.

6. Click OK.
The Hardware Configuration Editor dialog appears.
7. Click Activate Profile.
A green check mark appears next to the hardware profile, indicating that the profile
is active.

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4
This section describes the required hardware for each pump, how to connect the pump to the
computer, and how to configure the pump for external control.

Agilent Pumps
The following Agilent pumps are supported by the Analyst® software and all are configured the
same way.
Table 4-1 Supported Agilent 1200 Series Pumps
Pumps Model number 1200
Binary G1312A, G1312B
Quaternary G1311A
Isocratic G1310A
Capillary G1376A
Nano G2226A

Table 4-2 Supported Agilent 1260 Series Pumps

Pumps Model number 1260
Binary G1312B
Isocratic G1310B
Quaternary G1311B

Table 4-3 Supported Agilent 1290 Series Pump

Pumps Model number 1290
Binary G4220A

Note: The Agilent G4220A Binary Pump contains a software-controlled Purge valve.
The Analyst software allows users to control the purge option through the Acquisition
Method. For more information, see the most current Analyst software Release Notes.

The following table lists the required hardware. For the latest version of firmware supported, see
the most current Analyst software Installation Guide. Depending on how the system is
configured, you may not require all of the following cables.

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Table 4-4 Required Hardware for Agilent 1100, 1200, 1260, and 1290 Series Pumps
Cable Other parts needed
• RS-232 cable (PN WC024736) • General purpose cable for Agilent devices (Agilent PN
G1103-61611)
• GPIB cable (PN WC021365)
The following parts are optional. The external relay
• CAN cable (ships with Agilent
contacts board (Agilent PN G1351-68701) is required to
system)
provide timed contact closure events during the LC
program. This option is not required for analog
synchronization of peripheral devices.
• Network interface card (PN 1016082) if using a LAN
(Ethernet) connection
• Agilent PN G5183-4649 (for a direct LAN connection)
• Agilent PN G1530-61485 (for a LAN connection using a
hub)

Connecting the Agilent Pump to the Computer

This procedure describes how to connect the Agilent pump to the computer through standard
serial port communication. You can connect the Agilent pump to the computer with a GPIB or
LAN (Ethernet) cable.

WARNING! Electrical Shock Hazard: See the Agilent Pump Safety Instructions
before configuring any AC mains-powered equipment.

WARNING! Electrical Shock Hazard: Disconnect the power cord and wait at least
one minute before removing the pump cover.

1 2 3 4 5

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Figure 4-1 Agilent pump (back) with external relay contacts board installed
Item Description
1 Remote connector
2 Serial port
3 CAN connectors
4 Agilent GPIB
5 DIP switches

Note: Depending on the firmware version, you may require an access code (300) in
the Agilent Nano Pump (G2226A).

1. Shut down the computer.

2. Turn off the pump by pressing the On/Off button.
3. If you want contact closure functionality, install the relay contact board by performing
the following tasks. Otherwise, go to step 4.
i. Remove the screws that hold the plate.
ii. Insert the new plate with the board into the slot and tighten the screws.
4. Set the DIP switches at the back of the pump (see Figure 4-1). For more information,
see Configuration of Agilent Devices Through Serial Port Communication on page 9.
5. Connect the RS-232 cable from the serial port at the back of the pump to the desired
serial port on the computer, noting the port number.

Harvard 22 Syringe Pump

Only the Harvard 22 syringe pump (model number G1312) is supported by the Analyst software.

The following table lists the required hardware. For the latest version of supported firmware, see
the most current Analyst software Installation Guide.
Table 4-5 Required Hardware for the Syringe Pump
Cable Other parts needed
RS-232 cable (PN WC024735) N/A

Connecting the Harvard 22 Syringe Pump

WARNING! Electrical Shock Hazard: See the Harvard 22 Syringe Pump Safety
Instructions before configuring any AC mains-powered equipment.

Connecting the Pump to the Computer

1. Shut down the computer.

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2. Turn off the pump by pressing the On/Off button.

3. Connect the 25-pin end of the RS-232 cable from the serial port at the back of the
pump to the desired serial port on the computer, noting the port number.

Setting the Baud Rate

1. Turn on the pump and press the ENTER key.
2. Press the SET key while pressing the STOP/START key.
Table 4-6 Current Baud Rate LED Displays
LED Baud rate
300 300 baud
1200 1200 baud
24 2400 baud
96 9600 baud

3. Press the STOP/START key until 96 is displayed and then press the ENTER key.
The baud rate is set to 9600.

Setting the Device Address

1. Hold the SET key and then press the 0 key.
The LED displays the current address using the format AD.n, where n is the address
number.
2. Press the 0 key and then press the ENTER key.

PerkinElmer Series 200 LC Pumps

The following PerkinElmer Series 200 pumps are supported by the Analyst software and all are
configured the same way.
Table 4-7 Supported PerkinElmer Pumps
Pumps Model number
Micro 200
Quaternary 200

Note: To run a gradient with two PerkinElmer Series 200 micro pumps, you need two
cables and two serial ports.

The following table lists the required hardware. For the latest version of supported firmware, see
the most current Analyst software Installation Guide.

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Table 4-8 Required Hardware for the PerkinElmer Pumps

Cable Other parts needed
• RS-232 cable (PN WC024736) N/A

Note: One cable is needed for each micro

pump.

Connecting the PerkinElmer Series 200 LC Pumps

WARNING! Electrical Shock Hazard: See the PerkinElmer Series 200 LC Pump
Safety Instructions before configuring any AC mains-powered equipment.

Connecting the Pump to the Computer

1. Shut down the computer.
2. Turn off the pump by pressing the On/Off button.
3. Connect the RS-232 cable from the serial port at the back of the pump to the desired
serial port on the computer, noting the port number.
If you are using the micro pumps, the two RS-232 cables from the pumps must be
connected to the computer. The pump that was configured first in the Analyst
software Hardware Profile is pump A, followed by pump B.

Configuring the Pump for External Control

1. Turn on the pump.
2. Press F7 (CNFG).
The Configure menu appears.
3. Press F2 (COMM).
The Communication menu appears.
4. Press F3 (EXTE) to set External Control.
5. Press Return.
The Configure menu appears.
6. Press Return.
The Main menu appears.

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5
You can use the following three system controllers to connect to and control a Shimadzu HPLC
system using the Analyst® software:
• CBM-20A
• CBM-20A lite
• SIL-HT (SCL-10Avp)
Communications settings are similar for all three.
The CBM or SCL is required for the Analyst software to communicate with and control any
Shimadzu device. For the SCL, the only way to connect to the computer is using a RS-232
(serial) cable. The CBM uses serial or TCP/IP (Ethernet) connectivity, with TCP/IP being the
preferred mode of communication. For more information on controlling Prominence devices
using the Analyst software, contact your AB SCIEX FSE.

Shimadzu LC-30 Series Devices

In addition to the earlier Shimadzu HPLC series, the Analyst software also supports the following
Shimadzu LC-30 series devices:
• SIL-30ACMP autosampler
• SIL-30AC autosampler
• CTO-30AS column oven
• CTO-30A column oven
• LC-30AD pump
The CBM-20A system controller with a new ROM is used to connect to Shimadzu LC-30 series
devices.
The following table lists the required hardware. For the latest version of supported firmware, see
the most current Analyst software Installation Guide.
Table 5-1 Required Hardware for Shimadzu Devices
Cable Other parts needed
RS-232 cable (PN WC24736) or • Shimadzu fiber optic cables (one for each device
LAN cable (with Prominence connected)
devices)
• Shimadzu event cable

WARNING! Electrical Shock Hazard: See the Shimadzu CBM System Controller
Safety Instructions before configuring any AC mains-powered equipment.

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Setting Shimadzu Device Communications – SIL-HT

(SCL-10Avp)
ROM version 5.33 or later is acceptable.
1. Press 4 (System).
2. Using the arrow keys, navigate to RELAY 1 and then select START.
3. Press F3 (NEXT).
4. Use the arrow keys to set the following:
• Communication CLASSvp 5 or 6
• Interface RS-232C
• Baud Rate 19200
• Level Enhanced
5. POWER CYCLE the unit to accept and save the changes.

Setting Shimadzu Device Communications for Use on a

Network – CBM-20A (CBM-20A lite)
From the front panel of the autosampler or any other pump that is properly connected (fiber optic
cable installed, proper address set, and REMOTE LED lit) to the CBM, or from the front panel of
the unit in which the CBM lite is installed, follow this procedure to set the communications for use
on a network.
1. Press the VP key four times to display CALIBRATION.
2. Press FUNC to display INPUT PASSWORD.
3. Type 00000 (five zeros) and then press ENTER to display FLOW COMM.
4. Press BACK to display CBM PARAMETER.
5. Press ENTER and the Serial Number is displayed (or serial number of the installed
CBM lite).
6. Press the FUNC key twice to display INTERFACE and then type the following
parameters:
a. Interface:
• Press 1 for RS-232C and then press ENTER.
• Press 2 for Ethernet (preferred) and then press ENTER.
b. Ethernet Speed:
• Press 0 (zero) for auto-detect and then press ENTER.
7. The next four parameters require information from the Network Administrator (IT
group) if the system is installed on the laboratory network for remote HPLC
monitoring:
• USE GATEWAY: 0 (zero) for NO; 1 for YES – and then press ENTER.
• IP ADDRESS: Type the static IP address assigned to the unit by the Network
Administrator, and then press ENTER.

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• SUBNET MASK: Type the number supplied by the Network Administrator, and
then press ENTER.
• DEFAULT GATEWAY: Type the value supplied by the Network Administrator,
and then press ENTER.
8. TRS MODE sets the communications protocol parameters. Press 2 and then press
ENTER.
9. POWER CYCLE the unit to accept and save the changes.

Setting Shimadzu Device Communications for Stand-alone

use (Peer-to-peer Network) – CBM-20A (CBM-20A lite)
This method is the most reliable way to communicate with the Shimadzu system. If you also want
to have network access with the computer for data back-up, then install a second network card
into the computer. This additional network card is then configured to communicate exclusively
with the Shimadzu CBM interface.
From the front panel of the autosampler or any pump that is properly connected (fiber optic cable
installed, proper address set, and REMOTE LED lit) to the CBM or from the front panel of the unit
in which the CBM lite is installed, do the following:
1. Press the VP key four times to display CALIBRATION.
2. Press FUNC to display INPUT PASSWORD.
3. Type 00000 (five zeros) and then press ENTER to display FLOW COMP.
4. Press BACK to display CBM PARAMETER.
5. Press ENTER and the Serial Number is displayed (or serial number of the installed
CBM lite).
6. Press the FUNC key twice to display INTERFACE and then type the following
parameters:
a. Interface:
• Press 1 for RS-232C and then press ENTER.
• Press 2 for Ethernet (preferred) and then press ENTER.
b. Ethernet Speed:
• Press 0 (zero) for auto-detect and then press ENTER.
7. The next four parameters are needed to set up the peer-to-peer network with the
computer:
• USE GATEWAY: 0 (zero) for NO and then press ENTER.
• IP ADDRESS: 192.168.200.99 (default) and then press ENTER.
• SUBNET MASK: 255.255.255.0 (default) and then press ENTER.
• DEFAULT GATEWAY: ---.---.---.--- (default) and then press ENTER.
8. TRS MODE sets the communications protocol parameters. Press 2 and then press
ENTER.
9. POWER OFF the unit to accept and save the changes.
10. On the computer desktop, right-click My Network Places and then click Properties.

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11. Right-click the network connection that you want to dedicate to the Shimadzu CBM
communications and then click Properties.
12. Click Internet Protocol (TCP/IP) and then click Properties.
13. Click Use the following IP address and then type the following:
• IP ADDRESS: 192.168.200.99
• SUBNET MASK: 255.255.255.0
• DEFAULT GATEWAY: Leave blank
14. Click OK to accept the changes.
15. Click CLOSE.
16. Shut down the computer.
17. Using a CAT 5 network cable, connect the Shimadzu CBM (lite) to the supplied
(Shimadzu) network switch.

Note: You can use a CAT 5 crossover cable instead of the network switch
to directly connect the computer to the Shimadzu CBM (lite).

18. Connect the computer to the network switch using the network card that was
configured for use with the Shimadzu system.

19. Turn on the computer and the CBM (lite) and wait for them to complete their
respective boot-up routines.
20. To determine whether proper communications have been established between the
computer and CBM (lite), start Microsoft Internet Explorer (other browsers may not
display properly), type the CBM (lite) IP address in the address bar
(192.168.200.99), and then click GO.

Note: Make sure that all pop-up blockers are turned off.

The Shimadzu Prominence LC CBM-20A screen appears for a few seconds followed
by the Status screen.
21. Make sure that the Serial number listed for the HPLC system under System Name
matches that of the unit to which you are connected and that its status is Ready.
22. Close Internet Explorer.
23. Start the Analyst software and then configure the HPLC system.

Configuring the Shimadzu System Controller

Use the following procedures to configure the Shimadzu system controller.

Connecting the Shimadzu System Controller to the Computer

1. Shut down the computer.
2. Turn off the Shimadzu system controller by pressing the On/Off button.

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3. Connect the RS-232 cable from the serial port at the back of the system controller to
any available serial port on the computer, noting the port number. See Figure 5-1
Back of the Shimadzu SCL system controller or Figure 5-2 Back of the Shimadzu
CBM system controller.

1
2 3
4

5 6 7
5

10 10 8
9

Figure 5-1 Back of the Shimadzu SCL system controller

Item Description
1 Remote Connector Channels 1 to 8 (fiber optic ports)
2 RS-232C connector
3 OPT LINK connector
4 AC REMOTE connector
5 EVENT OUT connectors
6 MAN. INJ. IN connector
7 ALARM IN connector
8 Power connector
9 Fuse holder
10 AC OUT connectors

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3
8 6 3

5 5 4

Figure 5-2 Back of the Shimadzu CBM system controller

Item Description
1 Ethernet port
2 Remote Connector Channels 1 to 8 (fiber optic ports)
3 External I/O connectors
4 Power connector (AC IN)
5 AC output connectors (AC OUT)
6 RS-232 connector
7 Network indicators (100M/ACT/LINK)
8 Initialization button (INIT)

Configuring the System Controller for External Control (Analyst Software Version
1.3 or Later)
1. Turn on the Shimadzu SCL system controller.
The System Configuration window appears.
2. If the word FIXED appears in the upper right corner of the System Configuration
screen, press the F2 key (screen name FIX) to deselect FIX.
3. Press the F5 key (screen name MENU).
The Menu window appears.
4. Press the number 4 key.
The System screen appears.
5. Press the F3 key (screen name NEXT).
6. Set the Class VP to 5.x: Use the up and down arrow keys to select Class VP and
then use the left and right arrow keys to select 5.x.

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7. Set the Interface to RS-232C: Use the up and down arrow keys to select Interface
and then use the left and right arrow keys to select RS-232C.
8. Set the Baud Rate to 9600: Use the up and down arrow keys to select Baud Rate
and then use the left and right arrows to select 9600.
9. Set the Level to Enhanced: Use the up and down arrow keys to select Level and
then use the level and right arrows to select Enhanced.
10. Press the F5 key (screen name MENU).
11. Turn off the Shimadzu SCL System Controller.
12. Turn on the Shimadzu SCL System Controller.
The System Configuration screen loads.
13. Connect and configure individual devices to the system controller, following the
instructions in their respective guides.
14. Verify that each connected device is listed on the System Configuration screen on
the system controller.

Configuring the System Controller for External Control (Analyst Software Version
1.2 or Earlier)
1. Turn on the Shimadzu SCL System Controller.
The System Configuration window appears.
2. If the word FIXED appears in the upper right corner of the System Configuration
screen, press the F2 key (screen name FIX) to deselect FIX.
3. Press the F5 key (screen name MENU).
The Menu window appears.
4. Press the number 4 key - Response.
The System screen appears.
5. Press the F3 key (screen name NEXT).
6. Set the Class VP to 4.x: Use the up and down arrow keys to select Class VP and
then use the left and right arrow keys to select 4.x.
7. Set the Interface to RS-232C: Use the up and down arrow keys to select Interface:
8. Set the Baud Rate to 9600: use the up and down arrow keys to select Baud Rate.
9. Press the F5 key (screen name MENU).
10. Turn off the Shimadzu SCL System Controller.
11. Turn on the Shimadzu SCL System Controller.
The System Configuration screen loads.
12. Connect and configure individual devices to the system controller, following the
instructions in their respective guides.
13. Verify that each connected device is listed in the System Configuration window on
the system controller.

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Connecting the Shimadzu SCL System Controller to the Mass Spectrometer

The AUX I/O cable (PN 014474) is used to connect the Shimadzu SCL system controller to the
mass spectrometer.

Note: This procedure should only be performed by a trained FSE.

1. Connect the Shimadzu Event Cable to the Event1–3 Out connector, shown in
Figure 5-1 Back of the Shimadzu SCL system controller on page 49, to the back of
the SIL-HT/SCL-10Avp system controller.
2. Connect the wires from the free end of the AUX I/O cable to the two wires from the
free end of the Event Cable as follows:
Table 5-2 Wire Connections
Use this AUX I/O wire... And connect to Event Cable...
White with black stripe (wire 22) Orange wire
Green with black stripe (wire 21) Brown wire

Table 5-3 Wiring for the Shimadzu SIL-HT/SCL-10Avp System Controller

SIL/HT/SCL Mass spectrometer AUX 1/O cable
Event cable Pin 9 (power 5V) Red with black stripes
Pin 10 Orange with black stripes

Orange wire White with black stripe Pin 22 (cathode) White with black stripes
0 0
Brown wire Green with black stripe Pin 21 (ground) Green with black stripes
0 0
Note: Isolate these wires so they do not contact any other wires or metal.

3. On the free end of the AUX I/O cable, short together the following wires but do not
connect them to anything else:
• Red with black stripe (wire 9)
• Orange with black stripe (wire 10)
4. Connect the other end of the AUX I/O cable to the mass spectrometer AUX I/O
connector.
5. Verify that RELAY 1 in the SIL-HT (SCL-10Avp) is set to START while you are
configuring the Shimadzu system controller in the Analyst software.

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Note: Shimadzu firmware versions of 9.XX are provisional ROMs that

impart special functionality to the device. Before configuring the hardware in
the Analyst software, determine which features may have been added or
deleted and their impact on communications. Due to programming delays
and limited application, the Analyst software may not be updated for control
of such features.

Connecting the Shimadzu CBM (lite) System Controller to the Mass Spectrometer

Note: This procedure should only be performed by a trained FSE.

The AUX I/O cable (PN 014474) is used to connect the Shimadzu CBM (lite) system controller to
the mass spectrometer.
1. Connect the Shimadzu Event cable to Out 1 at the back of the CBM, shown in
Figure 5-2 Back of the Shimadzu CBM system controller on page 50, by pressing the
button above the terminal with a flat-head screwdriver and pushing the wire inside.
Make sure the wire is held securely inside the terminal.

Note: Polarity does not matter.

2. Connect the wires from the free end of the AUX I/O cable as follows:
Table 5-4 Wire Connections
Use this AUX I/O wire... And connect to Event Cable...
White with black stripe (wire 22) Black wire
Green with black stripe (wire 21) White wire

Table 5-5 Wiring for the Shimadzu CBM (lite) System Controller
CBM Mass spectrometer AUX 1/O cable
Event Pin 9 (power 5V) Red with black stripes
cable Pin 10 Orange with black stripes

Black wire White with black stripe Pin 22 (cathode) White with black stripes
0 0
White wire Green with black stripe Pin 21 (ground) Green with black stripes
0 0
3. On the free end of the AUX I/O cable, short together the following wires but do not
connect them to anything else:
• Red with black stripe (wire 9)
• Orange with black stripe (wire 10)

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4. Connect the other end of the AUX I/O cable to the mass spectrometer AUX I/O
connector.
5. Make sure that RELAY 1 in the CBM-20A lite is set to START while you are
configuring the Shimadzu system controller in the Analyst software.

Shimadzu Devices
Shimadzu recommends that the devices attached to the CBM system controller be identical to
those configured in the Analyst software hardware profile. Differences between the two
configurations can result in communication problems between the Analyst software, the
Shimadzu system controller, and the attached devices.
If the vial detection sensor is ON, then missing autosampler vials or aborting a run during an
autosampler rinse creates Shimadzu device fault conditions. To correct these errors you will have
to intervene manually before the Analyst software can continue functioning normally. To recover
Analyst software control, perform the task indicated on the device display. Alternatively, follow the
Fault Recovery procedure to clear all conditions.
The Shimadzu preset run time is set at 90 minutes. If required, change the duration in the
method.

Note: The needle height in the method must match that of the current tray. The preset
value is not valid for all trays.

Fault Recovery
The Shimadzu HPLC equipment can generate three different error conditions that cause the
Analyst software to stop: warning, error, and fatal error.

Warnings
A warning is an informational notification of conditions such as a door open on a temperature
controlled module, solvent level, or temperature not ready. These conditions do not prevent the
Shimadzu system from operating properly; however, the Analyst software does not recognize
these warnings, generates an error, and then stops the sequence. Contact your local Shimadzu
Technical Support specialist for more information on how to minimize these conditions.

Errors
Any error condition on the Shimadzu system stops the Analyst sequence. The Shimadzu system
typically sounds an audible alarm in the event of an error until you acknowledge the error. Some
errors that may be encountered and the Shimadzu suggested action include the following:
• LEAK DETECT: Press CE to stop the alarm. Find and address the problem.
Thoroughly dry the area around the leak sensor of the affected module (and possibly
any module below it in the stack due to the internal drain system). Recover
according to the procedures below.

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• PRESSURE OVER PMAX: Press CE to stop the alarm. Correct the problem.
Recover with one of the following procedures: To recover from a fault for systems
equipped with a CBM-20A lite system controller, ROM 1.11 or higher on page 55 or
To recover from a fault for systems equipped with a SCL-10Avp (SIL-HT) system
controller on page 56.
• MISSING VIAL: This error appears on the autosampler if it does not find a vial it is
asked to inject. The result of this condition can be dealt with in one of two ways
through the Analyst software in the Shimadzu Hardware configuration settings.
Select the autosampler model from the list and then click Configuration to display
the Autosampler Configuration dialog.

Figure 5-3 Autosampler configuration dialog box

Select the Skip sequence line if vial is missing check box and click OK. The
Analyst software skips that vial and continues running. If the check box is not
selected, then the Analyst software reports an error and stops the sequence.
The Skipped Vial notification appears on the SIL front panel display and the vial
number skipped is shown. Be sure to reconcile the data obtained in subsequent
runs.

Fatal Errors
The final level of error generated by Shimadzu equipment is a fatal error. Fatal errors are
normally generated by a mechanical failure and are generally associated with the autosampler
injection mechanism. The only way to recover from a fatal error is to power cycle the entire
system. If, after power cycling, the error occurs again, contact your local Shimadzu Service
Engineer for assistance.

To recover from a fault for systems equipped with a CBM-20A lite system
controller, ROM 1.11 or higher
For warnings and typical errors, the module experiencing the problem displays the condition on
its front panel display and the module and CBM display a RED status LED bar. The connect LED
on the CBM is no longer lit. The CBM-20A lite system controller works in the same way but has
no indication of the error because it is installed in a module.
1. Press CE to stop the alarm and clear the error.

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2. Correct the cause of the error.

3. Press the black INIT button at the back of the CBM-20A lite for no longer than five
seconds. See Figure 5-2 Back of the Shimadzu CBM system controller on page 50.
The CBM status LED bar changes to green and the connect LED illuminates, thus
confirming that communication with the Analyst software has been restored.
4. If either the status LED does not change to green or the connect LED fails to
illuminate, continue with To recover from a fault for systems equipped with a SCL-
10Avp (SIL-HT) system controller on page 56.

To recover from a fault for systems equipped with a SCL-10Avp (SIL-HT) system
controller

Note: In the event of a device fault, either within the Analyst software or at the device
itself, it may be difficult to reactivate or run the devices. If this occurs, perform the
following reboot sequence to regain control.

1. Deactivate the hardware profile in the Analyst software.

2. Turn off all Shimadzu devices, including the system controller.
3. Turn on all devices attached to the system controller and allow them to finish
initialization.
4. Turn on the system controller.
5. Make sure that all devices shown in the system controller System Configuration
screen are the same devices configured in the Analyst software hardware profile for
Shimadzu. If not, clear and select F2 (screen name FIXED) on the system controller
until both configurations match. If necessary, restart the system controller.
6. Activate the hardware profile in the Analyst software.

Connecting Shimadzu Devices to the Shimadzu System

Controller
You can connect the Shimadzu autosampler, UV detector, column oven, or pump to the
Shimadzu system controller.

Note: You can control up to four pumps using the Shimadzu CBM system controller. A
provisional ROM is available for four-pump control through the SIL-HT (SCL-10Avp).
For more information, contact your local Shimadzu Representative.

Connecting the Devices

1. Turn off the Shimadzu device by pressing the On/Off button.
2. Turn off the Shimadzu system controller by pressing the On/Off button.
3. Connect the fiber optic cable from the device to an appropriate connection at the
back of the CBM-20A lite or SIL-HT (SCL-10Avp).
• Connect the SIL-XX to fiber optic port 1/SIL.

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• Connect pumps to any fiber optic port from 3 to 8 ensuring that Pump A is
connected to a lower numbered port than Pump B.
• Connect detectors to any fiber optic ports 3 to 8.
• Connect any other accessories to any fiber optic ports 3 to 8.

Configuring the LC-10ADvp Pump to Operate through the System Controller

1. Turn the pump on by pressing the On/Off button.
2. Press Func until the LED displays ADRS.
3. Press the number that corresponds to the address connection of the pump to the
system controller, and then press ENTER.
4. Press Func until the LED displays Local.
5. Press 0 to select Remote mode, and then press ENTER.
6. Press VP until Calibration appears.
7. Press Func and enter the password. The password is 00000.
8. Press Func until OP Mode appears.
9. Select 0 to indicate control by a VP series system controller.
10. Repeat the procedure for each additional pump to be configured.

Configuring the LC-8Ap Pump to Operate through the System Controller

1. Turn on the pump by pressing the On/Off button.
2. Press the – (dash) key until the LED displays ADRS.
3. Press the number that corresponds to the address connection of the pump to the
system controller, and then press ENTER.
4. Press the – (dash) key until the LED displays Local.
5. Press 0 and then press ENTER.
6. Press the – (dash) key until the LED displays SYS.
7. Press 1 and then press ENTER.
8. Turn off the system controller and pump, wait two seconds, and then restart first the
pump and then the system controller.
9. Repeat the procedure for each additional pump to be configured.

Note: For more information on setting up the system controller for other
pumps, see the appropriate Shimadzu manual.

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Connecting a Shimadzu Valve Interface Unit to the Shimadzu

System Controller
Follow the procedures in this section in the order given.

Connecting the Valve Interface Unit to the System Controller

1. Turn off the system controller by pressing the On/Off button.
2. Connect the valves to the valve interface unit (Option Box-L, or Subcontroller VP).
3. Connect the fiber optic cable from the valve interface unit to an address connector at
the back of the system controller.
You can use Address Connectors 3 through 8.
4. Set the DIP switches at the back of the valve interface unit according to the
information provided at the back of the unit. The DIP switch setting must match the
pump address number used to connect the valve interface unit to the system
controller.

Configuring the System Controller for the Valve Interface Unit

• If the system controller is not already turned on, turn it on by pressing the On/Off
button.

Note: The model number for each connected device appears on the
System Configuration screen. The message Remote appears on any
connected valve.

Configuring the System Controller for a Newly Attached Shimadzu Device

• Turn off the system controller and other devices, wait two seconds, and then restart
all devices, turning on the system controller last.

Note: The model number for each connected device appears on the
System Configuration screen. The message Remote appears on any
connected pump.

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Column Oven Configuration
6
This section provides information about the required hardware and how to connect a column
oven to the computer.
The Analyst® software supports the following column ovens:
• Agilent column oven.
• PerkinElmer Series 200 column oven.
• Shimadzu column ovens via the Shimadzu SCL-10Avp, CBM20A, or CBM20A lite
system controllers. See Shimadzu Devices on page 45.

Agilent Column Oven

The Analyst software supports the following Agilent column oven models and switching valves:
Table 6-1 Supported Agilent Models and Switching Valves
Models Valves
G1316A (1100, 1200, and 1260 series) • 6-port/2-position valve
• 10-port/2-position valve
G1316C (1290 series) • 6-port/2-position valve
• 9-port/8-position valve
• 10-port/2-position valve

Note: To determine whether a specific switching valve is supported by the Analyst

software, contact [email protected].

The following table lists the required hardware. For the latest version of supported firmware, see
the most current Analyst software Installation Guide.
Table 6-2 Required Hardware for the Agilent Column Ovens
Cable Other parts needed
• RS-232 cable (PN WC024736) • Network interface card (PN 1016082) if using a LAN
(Ethernet) connection
• GPIB cable (PN WC021365)
• Agilent PN G5183-4649 (for a direct LAN [Ethernet]
connection)
• Agilent PN G1530-61485 (for a LAN [Ethernet]
connection using a hub)
• CAN cable (ships with Agilent system)

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Column Oven Configuration

Connecting the Column Oven to the Computer

WARNING! Electrical Shock Hazard: See the Agilent Column Oven safety
instructions before configuring any AC mains-powered equipment.

This procedure describes how to connect an Agilent column oven to the computer through
standard serial port communication.
1. Turn off the column oven.
2. Set the DIP switches at the back of the column oven. Make sure that the switches
are set for a baud rate of 19 200. For specific instructions on setting the DIP
switches, see Configuration of Agilent Devices Through Serial Port Communication
on page 9.
For the location of the DIP switches at the back of the column oven, see Figure 6-1.

1 2 3

Figure 6-1 Back panel of the Agilent column oven

Ba

Item Description
1 Serial connector
2 CAN connectors
3 DIP switches

3. Connect the RS-232 cable from the serial port at the back of the column oven to the
desired serial port on the computer, noting the port number.

Note: For instructions on connecting an Agilent column oven to a

computer using the LAN (Ethernet) connection, see the Agilent
documentation.

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PerkinElmer Series 200 Column Oven

The following table lists the required hardware. For the latest version of firmware supported, see
the most current Analyst software Installation Guide.
Table 6-3 Required Hardware for the PerkinElmer Column Oven
Cable Other parts needed
RS-232 cable (PN WC024735) N/A

WARNING! See the PerkinElmer Series 200 Column Oven safety instructions
before configuring any AC mains-powered equipment.

Connecting the Column Oven to the Computer

1. Turn off the column oven.
2. Connect the 25-pin end of the RS-232 cable to the serial port at the back of the
column oven.
3. Connect the other end to the desired 9-pin serial port on the computer, noting the
port number.

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Switching Valve Configuration
7
The Analyst® software supports the following switching valves:
• Valco two-position switching valve.
• Agilent switching valves. See Agilent Column Oven on page 59.
• Shimadzu internal valves using the Shimadzu CBM controller. See Shimadzu
Devices on page 45.
The following table lists the required hardware. For the latest version of firmware supported, see
the most current Analyst software Installation Guide.
Table 7-1 Required Hardware for the Valco Valve
Cable Other parts needed
RS-232 cable (PN WC024740) WC027522 Valve kit and all accessories

WARNING! See the Valco Two-Position Switching Valve safety instructions

before configuring any AC mains-powered equipment.

Valco Two-Position Switching Valve

Initialize the Valco two-position switching valve when electrical power to the valve is interrupted.
To initialize the valve, use the Valco manual controller, which is disconnected for routine use of
the switching valve. The manual controller is included in the valve kit. Follow the procedures in
this section in the order given.

Initializing the Valve

If electrical power to the Valco valve is interrupted, follow this procedure to initialize the valve.
1. Insert the four-wire connector from the Valco power supply into the receptacle at the
rear right of the Valco two-position actuator control module.

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Switching Valve Configuration

Figure 7-1 Valco switching valve configuration for initialization

Caution: Do not connect the round connector on this cable to the valve and
motor assembly at this time, as it will damage the valve setting.

2. Insert the five-wire connector of the Valco motor output cable into the receptacle at
the rear left of the Valco two-position actuator control module.
3. Connect the 10-wire Valco manual controller cable from the receptacle on the front
right of the Valco two-position actuator control module to the receptacle on the front
of the Valco manual controller.
The 10-wire cable should have a 10-wire connector on each end.
4. Connect the Valco power supply to the mains power.
5. On the Valco manual controller, cycle the actuator at least two times by pressing
Position A followed by Position B and so on.
Initialization is achieved when the position indicator lights on the actuator change
according to the position button pressed on the manual controller.
6. Insert the round connector of the motor driver output cable into the receptacle at the
rear underside of the valve and motor assembly.
7. Check the operation of the Valco kit by using the manual controller to change valve
positions several times.

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8. Disconnect the Valco manual controller cable from the receptacle on the front of the
Valco two-position actuator control module. Store the manual controller and cable
until the next time it is needed.

Connecting the Valve to the Computer

1. Shut down the computer.
L

Figure 7-2 Valco switching valve integration for serial control

2. Connect the 3-pin end of the RS-232 cable to the receptacle on the Valco two-
position actuator control module.
3. Connect the other end of the RS-232 cable to the desired 9-pin serial port on the
computer, noting the port number.

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Detector Configuration
8
The Analyst® software supports the following detectors:
• Agilent diode array detectors (DADs).
• Shimadzu UV-VIS detector (see Shimadzu Devices on page 45).
The following types of Agilent diode array detectors are supported by the Analyst software.
Table 8-1 Supported Detectors
Detector Model Number
Agilent DAD G1315 A, B, C, D
Agilent 1260 DAD G4212B
Agilent 1290 DAD G4212A

The Agilent G4212A and G4212B DADs have one lamp source instead of two, as in previous
DADs. As a result, the usable wavelength range has been changed to 190 nm to 640 nm.
The G4212A DAD supports slit widths up to 8 nm, and the G4212B DAD has a fixed slit width of
4 nm.
The following table lists the required hardware. For the latest version of supported firmware, see
the most current Analyst software Installation Guide.
Table 8-2 Required Hardware for the Agilent Detector
Cable Other parts needed
WC021365 (for GPIB connection) • Network interface card if using a LAN (Ethernet)
connection
Note: This cable is not required for
models that use a LAN (Ethernet) • Agilent PN G5183-4649 (for a direct LAN connection)
connection. • Agilent PN G1530-61485 (for a LAN connection using a
hub)

WARNING! Electrical Shock Hazard: See the Agilent Diode Array Detector safety
instructions before configuring any mains-powered equipment.

Diode Array Detector

The Agilent 1200, 1260, and 1290 DADs are shipped with an on-board LAN interface. Connect
them to the computer with a LAN (Ethernet) cable.
The Agilent 1100 DAD can communicate using either a GPIB or LAN interface. To use the LAN
interface, install a network interface card in the DAD. For instructions, see the Agilent
documentation.
See Configuration of Agilent Devices Through LAN (Ethernet) Communication on page 10.

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Detector Configuration

Connecting the Diode Array Detector to the Computer

1. Shut down the computer.
2. Turn off the Agilent diode array detector by pressing the On/Off button.
3. Connect either the GPIB cable or a LAN cable to the back of the Agilent diode array
detector. If you are using a LAN cable, use Agilent PN G5183-4649 for a direct
connection from the diode array detector to the computer; if you are setting up a hub
connection, use Agilent PN G1530-61485.
r

1 2

Figure 8-1 Back of the Agilent diode array detector

Item Description
1 LAN port
2 GPIB port

4. Connect the other end of the cable (GPIB or LAN) to the computer.

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NIDAQ and Terminal Block Installation
9
Installing an ADC Card on a New Instrument
Current systems have the correct drivers installed. The list of supported devices may change.
See the most current Analyst® software Installation Guide. The following are requirements for
earlier Analyst software versions:
• Analyst TF 1.5 software requires driver version 8.3 or higher
• Analyst 1.5 software requires driver version 8.3
• Analyst 1.4.1 software requires driver version 7.1 of the appropriate driver
• Analyst 1.4 software requires driver version 6.9.3
• All previous versions of the Analyst software require driver version 6.7
The current systems include the Measurement and Automation Explorer software. This software
is also installed on systems that had a GPIB board previously installed.
1. Insert the NIDAQ PCI board in the computer.
2. Open the Measurement and Automation Explorer software.
The left pane displays a list of available devices.
3. Expand the list to view the PCI 6032E ADC card.
If this card is in the list, then it is installed on the computer. There are some useful
tools within this software that you can use to monitor the input to the terminal block
without having to use the Analyst software. You can use an AA battery to supply a
test signal.
4. Attach the ADC terminal box.
The block is marked as having 16 analog channels mixed in with earthed channels
(marked as A1 1 to A1 16).

Note: Because the system uses Differential mode, the software has to
distinguish the voltage difference between the anode and cathode of the
variable wavelength detector, as opposed to grounding the cathode and
monitoring only the anode.

5. Connect to ACH0 1 and ACH0 9.

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NIDAQ and Terminal Block Installation

Figure 9-1 Cable polarity locations

Figure 9-1 shows the polarity of the two cables: the positive polarity is channel 33
(A1 1) and the negative polarity is channel 66 (A1 9).

Figure 9-2 Cable connections

6. Make sure the DIP switches are set to Differential mode, as shown in Figure 9-2.

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7. In the Analyst software, add the ADC card to the hardware profile as shown in
Figure 9-3. Make sure the settings are exactly as shown.

Figure 9-3 ADC configuration

Note: The ADC channel must be set to channel 2. This equates to channel
1 on the terminal block.

8. Check the settings on the UV detector.

9. Using the handheld controller, from the main analysis screen, go to the System
page and then select VW Detector. The settings shown in Figure 9-4 to Figure 9-7
work well.

Figure 9-4 Wavelength

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Note the polarity and response times as shown in Figure 9-4.

Figure 9-5 Auto Balance

The Margin for Negative Absorbance field, shown in Figure 9-5, is variable. Adjust
it according to requirements.

Figure 9-6 Parameters

All three parameters here are important.

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Figure 9-7 Configuration screen

10. Test the system by following these steps:
i. Set up an LC system with methanol:water.
ii. Add acetone, which is highly fluorescent under UV, to an HPLC vial.
iii. Run a basic method at a flow rate of 20 µl/min.
iv. Perform a 5 µl injection.
The Analyst software acquires the data with the MS data.
11. To access the data, open the data file in Explore mode, right-click in the window, and
then select Open ADC data.

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Peripheral Device Analog Synchronization
A
The preferred method of synchronizing peripheral devices is through the Analyst® software
control. For devices that cannot be controlled through the Analyst software, synchronize through
the use of analog signals (contact closure).

API AUX I/O Interface

The mass spectrometer provides an analog interface through the AUX I/O port located at the rear
of the instrument. Figure A-1 and Figure A-2 are schematic representations of the AUX I/O
interface and the AUX I/O cable provided with the mass spectrometer.
In both figures, on the left side, wire colors are indicated as background/stripe. Mass
spectrometer signals are shown in NOT READY and NO ERROR states.

Figure A-1 Schematic of the AUX I/O interface and cable on AB SCIEX TripleTOF™ 5600,
triple quadrupole, and LIT instruments.

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Peripheral Device Analog Synchronization

Figure A-2 Schematic of the AUX I/O interface and cable on the 5500 series of
instruments.

AUX I/O Signal Details

The mass spectrometer displays three types of signals.

Ready Signal
The Ready signal is an autosampler Inject signal that is generated using a DPST (Double-Pole,
Single-Throw) relay. It provides either an NO (Normally Open) or NC (Normally Closed) contact
closure.

Note: The Ready signal is active only when the mass spectrometer is operated in LC
Synch mode. For more information on operating modes, see the Analyst software Help.

The Ready signal is activated when the LC/MS devices are ready to acquire data and are waiting
for an injection. As soon as the MS acquisition is started (by the START signal), READY is
deactivated. Do not confuse READY with the MS Ready status, which is not specific to the LC
Sync mode.

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Error Signal
The Error signal is used as an External Stop signal for any LC pumps connected to the ion
source to prevent accidental overflow of the source. An error is generated using a DPST relay
and provides either a NO or NC contact closure. The Error signal is active regardless of the MS
synchronization mode. The Error signal is activated for approximately five seconds when an MS
error occurs. The error type is non-specific and may include source, electronic, or vacuum
system failures.

Start Signal
The Start signal is given to the mass spectrometer to initiate data acquisition. This signal is
passed to the MS electronics through an optocoupler (a device that couples a light-emitting-diode
and a phototransistor to provide an isolated digital connection between the sender and receiver).
The Start signal may be any signal that creates a potential of between 2 to 8 volts across Pins 10
and 22. For example, a voltage pulse in the normal TTL range (2 to 5 volts) would be a START
signal.
By setting the MS synchronization trigger level, you can configure the Start signal as either Active
High or Active Low, as required. See Autosampler Configuration on page 15.

Use the biased +5V and ground signals provided on the AUX I/O port to:
• Generate the appropriate START using a contact closure.
• Generate TTL-level READY and ERROR signals.

Wiring Peripheral Devices to the Mass

Spectrometer
Figure A-3 shows a general scheme for connecting peripheral devices to the mass spectrometer.
The signals available on your peripheral devices indicate to what extent the scheme presented
here can be used.

Figure A-3 General scheme for analog synchronization of peripheral devices and the
mass spectrometer

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Peripheral Device Analog Synchronization

Note: Set the mass spectrometer Sync Mode to LC Sync in the acquisition method to
provide analog synchronization between the peripheral devices and the mass
spectrometer.

The following examples are used as guidelines for developing an analog synchronization
scheme for your peripheral devices. For more information about the types of signals generated
and required by the peripheral device, see the appropriate peripheral device documentation.
In both figures, in the center, wire colors are indicated as background/stripe.

Figure A-4 Analog synchronization scheme using contact closure signals

Figure A-5 Analog synchronization scheme using TTL signals

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CTC PAL Autosampler Setup Notes
B
This section provides an overview of the setup for the CTC PAL autosampler. With all versions of
the PAL autosampler, the only differences are in the frame size and the tray holders (or stacks)
bolted to the autosampler frame. In some cases, additional valves and accessories can be
attached.
The Analyst® software uses a software driver developed by CTC Analytics. The driver is
essentially the same as that used by the CTC software, Cycle Composer.

Note: The firmware required to operate the different models of autosampler is exactly
the same for all models when used with the Analyst software.

An FSE must configure the CTC autosampler firmware to indicate where the trays can be placed
and where everything is located in the X, Y, and Z dimensions. Use the handheld controller for
the autosampler to configure the PAL or use a separate utility from CTC to write the configuration
information into the autosampler's non-volatile memory.
The following terms are used to describe the Analyst software Batch Editor elements in relation
to the CTC.

Rack
CTC defines a rack as a drawer or tray that holds microtitre or vial plates. The Rack Position
designates where the rack is placed, and the Rack Code designates the type of rack.

Plate
CTC defines a plate as a microtitre plate or tray that holds vials. The Plate Code specifies the
type of plate and the plate position indicates where the plate sits on the rack.

Note: There is not a one-to-one mapping between a rack and the tray in CTC
terminology.

Tray
In the Analyst software, the term tray is used to define a physical location. A tray is a placeholder
for a location in which you can place different types of trays. The tray group indicates the tray
types you can use in each tray location.
The Analyst software imposes no restrictions on the number of tray types used in each location.
You can use all defined tray types in all tray locations, if required. With the Analyst software,
duplicate tray definitions are not required.
For every tray location on the autosampler, use the handheld controller for the autosampler to
verify and correct the position of each tray type. If any trays are incorrectly defined on the X, Y, or
Z dimension, the CTC driver cannot find the correct layout of the trays in the autosampler. This

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either causes the Analyst software to load the tray configuration incorrectly, which results in the
Batch Editor Locations tab displaying 6 tray locations, or it causes the Analyst software to not
indicate the trays that should be present.

Note: The AUX I/O triggers the mass spectrometer to start scanning through the
contact closure. If the mass spectrometer does not start scanning, it may be because
the CTC autosampler Sync Signal is not set to Immediate. This situation typically occurs
when the autosampler is being used as a standalone device without any controlling
software. The CTC autosampler has a handheld controller for the user to configure
settings in the autosampler. One of these settings is the Sync Signal. If you use the
autosampler by itself with no computer control, you may set this to wait for an external
ready signal. Under the Analyst software control, however, typically this is not needed.
Therefore, if the autosampler is configured incorrectly, it will sit and wait and not inject.

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