PerkinElmer CLARUS 680 GC, CLARUS 600 GC User Manual

CLARUS 600/680 GC

User’s Guide

GAS CHROMATOGRAPHY



Clarus 600/680 GC

User’s Guide

ii

Release History

Part Number Release Publication Date

09936780 C February 2010

Any comments about the documentation for this product should be addressed to:

User Assistance
PerkinElmer, Inc.
710 Bridgeport Avenue
Shelton, Connecticut 06484-4794
U.S.A.

Or emailed to: [e-mail]

Notices

The information contained in this document is subject to change without notice.

Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes no
warranty of any kind with regard to this document, including, but not limited to, the implied
warranties of merchantability and fitness for a particular purpose.

PerkinElmer shall not be liable for errors contained herein for incidental consequential damages in
connection with furnishing, performance or use of this material.

Copyright Information

This document contains proprietary information that is protected by copyright.
All rights are reserved. No part of this publication may be reproduced in any form whatsoever or
translated into any language without the prior, written permission of PerkinElmer, Inc.

Copyright © 2010 PerkinElmer, Inc.

Trademarks

Registered names, trademarks, etc. used in this document, even when not specifically marked as such,
are protected by law.

PerkinElmer is a registered trademark of PerkinElmer, Inc.

iii

Table of Contents

Introduction .................................................................................................................... 1-1

About This Manual .......................................................................................................... 1-3

Conventions Used in this Manual .................................................................................... 1-4

Notes, cautions and warnings ................................................................................... 1-4

Warning Signs on the Instrument..................................................................................... 1-5

Screen Abbreviations ....................................................................................................... 1-6

Glossary of Clarus GC Terms .......................................................................................... 1-7

Autosampler Terms .......................................................................................................... 1-7

Instrument-Specific Terms ............................................................................................... 1-8

Glossary of Chromatographic Terms ............................................................................. 1-10

Touch Screen Navigation .............................................................................................. 2-1

Chapter Overview ............................................................................................................ 2-3

Touch Screen ................................................................................................................... 2-4

Tabs........................................................................................................................... 2-6

Non-Configured Devices .......................................................................................... 2-6

Non-installed Devices ............................................................................................... 2-7

Run Button ................................................................................................................ 2-8

Stop Menu ............................................................................................................... 2-11

Signal Button .......................................................................................................... 2-11

Heated Zones .......................................................................................................... 2-13

Navigation Bar ............................................................................................................... 2-16

Injectors ......................................................................................................................... 2-17

Program Buttons ..................................................................................................... 2-18

Display Text ............................................................................................................ 2-18

PSS .......................................................................................................................... 2-18

Packed (Pkd) ........................................................................................................... 2-24

POC......................................................................................................................... 2-28

Capillary (Cap) Injector .......................................................................................... 2-29

Oven ............................................................................................................................... 2-30

Aux Zone ....................................................................................................................... 2-31

Detectors ........................................................................................................................ 2-32

FID .......................................................................................................................... 2-32

TCD ........................................................................................................................ 2-36

ECD ........................................................................................................................ 2-37

PID .......................................................................................................................... 2-39

NPD ........................................................................................................................ 2-40

FPD ......................................................................................................................... 2-41

Timed Events ................................................................................................................. 2-42

iv

Events Tab .............................................................................................................. 2-42

Timed Events Table ................................................................................................ 2-43

Using the Active Method ............................................................................................... 3-1

Overview .......................................................................................................................... 3-3

Editing the Active Method ............................................................................................... 3-4

Getting Ready to Edit the Active Method ........................................................................ 3-5

Setting Up Oven and Inlet Temperature Programs .......................................................... 3-6

Configuring the Equilibration Time (Init) ................................................................ 3-7

Setting a Coolant Timeout Value .............................................................................. 3-7

Setting a Coolant Cut-In Temperature ...................................................................... 3-8

Setting Up an Isothermal Program ............................................................................ 3-8

Setting Up a One-Ramp Temperature Program ...................................................... 3-10

Holding an Oven Temperature ............................................................................... 3-11

Setting Injector Temperatures ........................................................................................ 3-14

Displaying Injector Temperature Screens ............................................................... 3-14

Turning Injector Heaters On or Off ........................................................................ 3-16

Changing Injector Temperatures ............................................................................ 3-16

Oven Temperature Programming Mode ................................................................. 3-17

Inlet Temperature Programming Mode .................................................................. 3-18

Setting Up a One-Ramp Injector Program .............................................................. 3-19

Viewing/Setting Carrier Gas Pressure/Flow/Velocity ................................................... 3-21

Setting Carrier Gas Pressure ................................................................................... 3-23

Setting Carrier Gas Flow using PPC ....................................................................... 3-25

Viewing/Setting Carrier Gas Velocity .................................................................... 3-27

Setting the Septum Purge Mode and Offset ................................................................... 3-29

Setting Up Valves .......................................................................................................... 3-37

Setting the Split Mode Using PPC .......................................................................... 3-37

Set up the Splitless Mode for a CAP or PSS Injector .................................................... 3-41

Splitless Injection with Pressure Pulse (Flow Pulse, Velocity Pulse) Technique ... 3-41

Contolling the Autosampler ........................................................................................... 3-51

Autosampler Trays and Carousel ............................................................................ 3-51

Autosampler Touch Screen ..................................................................................... 3-53

Start Button ............................................................................................................. 3-54

Stop Button ................................

............................................................................. 3-55

About Waste and Wash Vials ................................................................................. 3-62

Multi-Program Mode .............................................................................................. 3-62

About Sample Vials ................................................................................................ 3-63

Using a TCD with the Autosampler ....................................................................... 3-63

Available Syringes .................................................................................................. 3-64

Setting Up the Detectors ................................................................................................ 4-1

Overview .......................................................................................................................... 4-3

v

FID Overview .................................................................................................................. 4-5

Setting Up an FID ..................................................................................................... 4-6

Automatically Ignite the Flame .............................................................................. 4-11

Manually Ignite the Flame ...................................................................................... 4-13

Using the FID in Corrosive Environments ............................................................. 4-15

Setting up an ECD ......................................................................................................... 4-17

United States Government Regulations for ECDs .................................................. 4-17

Special Instructions for ECD Cell Purchasers ........................................................ 4-18

United Kingdom Regulations ................................................................................. 4-20

ECD Overview ........................................................................................................ 4-20

ECD Set Up ............................................................................................................ 4-22

Setting up a TCD ........................................................................................................... 4-28

TCD Setup .............................................................................................................. 4-29

TCD Setup Summary .............................................................................................. 4-29

Using a TCD with the Autosampler or GSV .......................................................... 4-35

Setting up a PID ............................................................................................................. 4-36

PID Overview ......................................................................................................... 4-36

PID Setup ................................................................................................................ 4-37

Setting Up a NPD........................................................................................................... 4-43

NPD Overview ........................................................................................................ 4-44

Setting Up a NPD ................................................................................................... 4-45

NPD Bead Activation Procedure ............................................................................ 4-48

Setting up an FPD .......................................................................................................... 4-55

FPD Overview ........................................................................................................ 4-55

Setting Up the FPD ................................................................................................. 4-57

FPD Setup Summary .............................................................................................. 4-57

Configure the Linearizer and Signal Filter ............................................................. 4-57

Set the FPD Temperature ........................................................................................ 4-61

Detector Temperatures ................................................................................................... 4-72

Setting the Range ........................................................................................................... 4-74

Setting the FID, PID, or NPD Range ...................................................................... 4-74

Changing the FID, PID, or NPD Range During a Run .................................................. 4-75

Setting the TCD Current (Filament Current) ................................

................................. 4-78

Changing TCD Polarity During a Run ........................................................................... 4-80

Routing Detector Output ................................................................................................ 4-83

Rerouting Output .................................................................................................... 4-83

Attenuating Detector Signals Going to a Recorder ........................................................ 4-87

Optimizing a Detector Signal to an Integrator for Maximum Sample Dynamic Range 4-89

Matching Detector Signals with Your Integrator ........................................................... 4-90

Autozeroing a Detector .................................................................................................. 4-93

Using the Method Editor ............................................................................................... 5-1

vi

Method Editor .................................................................................................................. 5-3

Method Edit Mode ........................................................................................................... 5-5

Oven Settings ............................................................................................................ 5-7

Managing Methods .......................................................................................................... 5-9

File Menu .................................................................................................................. 5-9

Using the Tools Menu .................................................................................................... 6-1

Tools Menu ...................................................................................................................... 6-3

Method Editor .................................................................................................................. 6-4

Event Log ......................................................................................................................... 6-5

Maintenance ..................................................................................................................... 6-6

Configuration ................................................................................................................. 6-10

Injectors (Deconfiguring and Configuring Injectors) ............................................. 6-10

Oven ............................................................................................................................... 6-18

Detectors ........................................................................................................................ 6-20

Run/AutoSampler ................................................................................................... 6-26

Setup ....................................................................................................................... 6-28

Pneumatics .............................................................................................................. 6-33

Connecting the PPC Modules ........................................................................................ 6-35

Reference Settings .................................................................................................. 6-48

Relays ..................................................................................................................... 6-48

Zeroing and Calibrating the PPC Modules ............................................................. 6-49

Zeroing the PPC Gas Modules................................................................................ 6-49

Setting the Reference Temperature and Pressure ................................................... 6-53

Calibrating the Carrier Gas Modules ...................................................................... 6-54

Calibrating the Detector Gas Modules .................................................................... 6-57

Calibrating the Oven Temperature ................................................................................. 6-60

Calibrate the Reference Thermometer .................................................................... 6-60

Place the Thermometer Probe in the Oven ............................................................. 6-61

Equilibrate the Oven Temperature .......................................................................... 6-62

Enter the Required Offset Value ............................................................................. 6-65

Remove the Thermometer Probe ............................................................................ 6-65

Utilities ........................................................................................................................... 6-66

Column Flow Calculator ................................

......................................................... 6-67

Split Flow Calculations Screen ............................................................................... 6-71

Column Length Calculator...................................................................................... 6-73

Background Compensation ..................................................................................... 6-74

Stopwatch ............................................................................................................... 6-76

Program (Max Oven Program Rates) ............................................................................. 6-77

Release… ....................................................................................................................... 6-78

Logout… ........................................................................................................................ 6-79

About ............................................................................................................................. 6-80

vii

Setting up a Typical Analysis ........................................................................................ 7-1

System Status Screen ....................................................................................................... 7-4

Injector Settings ............................................................................................................... 7-6

Packed Column (PKD) Injector ................................................................................ 7-6

Programmed Split/Splitless (PSS) Injector ............................................................... 7-8

Detector Settings ............................................................................................................ 7-11

Flame Ionization Detector (FID) ............................................................................ 7-11

Detector .......................................................................................................................... 7-16

Thermal Conductivity Detector (TCD) ................................................................... 7-16

Autosampler ................................................................................................................... 7-22

Index

viii

Introduction

1

Introduction

1-2

Clarus 600/680 GC User’s Guide

1-3

About This Manual

This guide is divided into following chapters:

Chapter 1 Introduction

This chapter contains a brief introduction to the Clarus GC, the conventions and
warnings used in the manual.

Chapter 2 Touch Screen Navigation

This chapter contains information that introduces you to the look and feel of the
touch screen. It shows you how to turn on the GC, check the status, and perform
fundamental operations such as changing parameters, selecting options, using the
tools menus, etc.

Chapter 3 Active Method

This chapter contains step by step explanation of the active method. Detailed
information on setting up the autosampler is contained in this chapter.

Chapter 4 Setting Up the Detectors

This chapter contains detailed information on setting up the detectors.

Chapter 5 Using the Method Editor

This chapter describes how to modify, save and use the method editor.

Chapter 6 Using the Tools Menu

The chapter contains detailed information on the tools menu section of the touch
screen.

Chapter 7 Setting Up a Typical Analysis

This chapter describes how to run a typical analysis on the Clarus GC using the
most common configuration.

Introduction

1-4

Conventions Used in this Manual

Normal text is used to provide information and instructions.

Bold text refers to text that is displayed on the screen.

All eight-digit numbers are PerkinElmer part numbers unless stated otherwise.

Notes, cautions and warnings

Three terms, in the following standard formats, are also used to highlight special
circumstances and warnings.

NOTE: A note indicates additional, significant information that is provided with some

procedures.

CAUTION

We use the term CAUTION to inform you about situations that
could result in serious damage to the instrument or other
equipment. Details about these circumstances are in a box like this
one.

WARNING

We use the term WARNING to inform you about situations that
could result in personal injury to yourself or other persons. Details
about these circumstances are in a box like this one.

Clarus 600/680 GC User’s Guide

1-5

Warning Signs on the Instrument

For detailed safety information see the Safety Practices chapter in the Clarus
600/680 GC Customer Hardware and Service Guide (P/N 09936781).

Caution, hot surface.

Caution, risk of electric shock.

Caution, laser radiation hazard.

Caution (refer to accompanying documents).

Introduction

1-6

Screen Abbreviations

AUX – Auxiliary zone

Cap – capillary split/splitless injector

Cmptr – computer

Ctrl – syringe control parameters

ECD – Electron Capture Detector

FID – Flame Ionization Detector

FPD – Flame Photometric Detector

Gen – generate

Inj/Vial – injections per vial

Int – integrator

kPa – kilopascals

NPD – Nitrogen Phosphorus Detector

PID – Photoionization Detector

Pkd – packed injector

POC – Programmed On-Column Injector

PPC – programmed pneumatic control

Pre – # of preinjection syringe washes

Psi or psig – pounds per square inch (gauge)

PSS – Programmed Split/Splitless Capillary Injector

TCD – Thermal Conductivity Detector

Clarus 600/680 GC User’s Guide

1-7

Glossary of Clarus GC Terms

The glossary of Clarus GC terms are divided into two types:

• Autosampler Terms

• Instrument-Specific Terms

Autosampler Terms

Term

Description

Washes Washing the syringe.

Pre-Wash The number of prewashes of sample to prime the syringe

(no pumping).

Pre-Inject The number of pre-injection syringe washes with a solvent.

Post-Inject The number of post injection syringe washes with a

solvent.

Pumps The number of times the syringe draws up sample and

evacuates it before acquiring the volume. This is done to
eliminate bubbles.

Mode The style of injection.

Fast Fast speed of the syringe during sample injection. This is

used to eliminate discrimination in the needle.

Normal Normal speed of the syringe during sample injection.

Slow Slow speed of the syringe during sample injection in order

to inject directly into a wide-bore capillary column, in hot
injection port.

Introduction

1-8

Instrument-Specific Terms

Term

Description

Attenuation The amplification of the detector output signal.

Background
compensation

A routine that automatically subtracts a stored calibrated
baseline profile from the signal generated during a GC run.

Ballistically Changing the oven temperature as quickly as possible to

reach a set point.

Soft Cooling Soft-cooling is a technique whereby, the cooling rate of the

GC oven is initially limited by controlling (throttling) the intake
of the ambient (cold) air used to cool the oven.

Detector
background

The detector output signal when no components are being
eluted.

Equilibration The delay time after the method set points have been

reached before the system becomes READY.

Flameout Detects if the flame is on to prevent injection into a

nonfunctioning system and subsequent loss of sample.

Isothermal
method

A method in which the oven temperature remains constant
throughout a GC run.

Method A collection of parameters that control the GC.

Negative-time
event

A timed event that you set to occur before the instrument
becomes READY.

Clarus 600/680 GC User’s Guide

1-9

Term Description

Parameter An independent variable used to specify a condition to be

met.

PPC

Programmable Pneumatic Control

Pre-run The time after equilibration during which negative-time events

are executed.

PreVent

PPC version only. Sample management system.

Range For a Flame Ionization Detector, range means sensitivity of

the detector output signal.

Ready Indicates that all method parameters have reached their set

points and that you can start your analysis.

Run The time from sample injection to the end of the oven

temperature program.

Sleep mode The GC can be set to a predefined method for gas savings.

Temperature
program

PPC version only. A program that specifies the rate of oven
temperature increase from one plateau to the next, and the
time the oven temperature is held constant at a plateau.

Timed Events Events that take place before or during a GC run as specified

in a timed events table.

Zone A heated area in the GC oven, injector, or detector.

Introduction

1-10

Glossary of Chromatographic Terms*

Adsorption – A process that occurs at the surface of a liquid or solid as a result of
the attractive forces between the adsorbent and the solute. These forces may be
physical or weakly chemical.

Analysis – The complete investigation of a sample by gas chromatographic
separation including identification of the sample components and quantitative
measurements.

Anode – The positively charged electrode in any electrical circuit to which
charged particles and ions are attracted.

Band Broadening – A process that occurs in the GC whereby the peak width for
a component increases the longer the component travels through the column.

Baseline – The detector signal to a recorder or integrator when only the carrier
gas is passing through the detector.

Baseline drift – Any regular change occurring in the baseline signal from the
detector, usually resulting from column temperature and/or gas flow changes.

Blank run – A run without the sample being injected.

Bleed – The evaporation of the stationary phase from a column.

Capillary column (wall coated open tubular column) – A small-internal-diameter

column whose inside wall is coated with a liquid phase.

Carrier gas – The mobile phase of the separation system. An inert gas which
transports the sample from the injector through the column to the detector. This
gas is usually helium, hydrogen, or nitrogen.

Column conditioning – A process for producing a stable column by heating the
column with carrier gas flowing to remove volatile impurities from the stationary
phase.

Detectors – Hardware that responds to sample components producing an
electrical signal that can be measured to quantitate the amount of each
component present.

Flow programming – The stored PPC program is interpreted as real column
mass flow settings or capillary column flow settings from which the inlet

*

Reference: Denney, R.C. A Dictionary of Chromatography.

Clarus 600/680 GC User’s Guide

1-11

pressure is calculated. This is dependent on the capillary control mode and
installed pressure or split control option.

Flow rate – The mass flow of carrier gas or detector gas in milliliters per minute.

Ghost peaks – Peaks that are not due to sample components, for example, peaks

produced by carrier gas impurities, septum, or components from previous
analyses.

Injection port – The hardware through which the sample is introduced to the
column by injection.

Linearity – Quantitatively all detectors will produce a linear response with
respect to solute concentration over a defined range, for example, the Linear
Range.

Liquid phase – The material in the column that causes the components to
separate because of partitioning of the components between the mobile phase
(carrier gas) and the stationary phase (liquid phase).

Lowest limit of detection – The smallest amount of sample that can be detected
by the detector being used. Usually defined as any signal that is as great as two
times the noise level. Also referred to as Minimal Detectable Quantity (MDQ).

Mobile phase – The gas which carries the solute (sample) along and over the
column material. This carrier gas is inert and usually helium, nitrogen, or
hydrogen.

Noise – Background signal fluctuations arising from a detector response. This
response is the result of the column installed, carrier gas purity, electronic
components, etc. The response of any detector is defined by the signal-to-noise
ratio.

Partition Coefficient – The differential solubility of a substance in two different
phases. In the case of gas–liquid chromatography, the sample components reach
an equilibrium between the gas phase (mobile) and the liquid phase (stationary).
Each component has a different partition coefficient thus causing separation in
the column.

Pressure programming – Pressure control through an independent four-step,
three-ramp program for each carrier gas channel.

Resolution – The degree of separation between two peaks.

Retention time – The time interval from the point of injection to the appearance

of the peak maximum, of a component’s signal.

Introduction

1-12

Septum – Silicone rubber material placed in the injection port through which the
injection is made. When the needle is withdrawn, the silicone rubber reseals,
thus not allowing any sample or carrier gas to escape.

Stationary phase – The liquid or solid adsorbent portion of the column that
retains components passing through the GC column.

Subambient – Below ambient temperature. The oven cools down below
ambient temperature with the use of either liquid nitrogen or liquid carbon
dioxide.

Syringes – Precision dispensing devices used to deliver sample to the GC.
Liquid and gas syringes are available.

Tailing – When a peak is not symmetrical or Gaussian shaped but the back end is
broadened, it is said to be tailing.

Temperature programming – A technique commonly used to increase the rate of
elution of the components. After the sample is injected into the oven at a specific
temperature, the temperature program increases the oven temperature to the
prescribed temperature at a defined rate (in

°C/min).

Unretained peak – A component that is not retained by the column. The time
taken for an unretained sample to pass through the column is the same time as the
time taken for the carrier gas to pass through.

Velocity programming – Programmed linear velocity where the PPC controller
interprets stored PPC programs as the average capillary column linear velocity
settings.

Touch Screen

Navigation

2

Touch Screen Navigation

2-2

Clarus 600/680 GC User’s Guide

2-3

Chapter Overview

You operate the Clarus GC using the touch screen on the front of the GC. The
touch screen is the interface between you and the instrument, enabling you to
control the Clarus GC in order for you to perform your analyses easily and
conveniently. The touch screen contains active areas that you touch to perform
the required action.

You may find it more convenient to use a stylus or you may like to touch the
active areas of the touch screen. Do not use sharp, pointed objects.

A light touch is all that is needed. You do not need to press forcefully on an
active area.

Please note that when you touch an active area, various processes are started in
the instrument. Some of these processes may take several seconds. Be patient and
wait for the process to complete before touching another active area on the touch
screen.

This chapter gives a brief overview on touch screen definitions and navigation.
For details on using the active method, method editor and tools menu see
chapters 3, 4 and 5.

Touch Screen Navigation

2-4

Touch Screen

The main display area on the touch screen is referred to as screens. You use
various screens to set up your Clarus GC to perform the analyses. These screens
contain:

• Entry fields which allow you to make entries,

• Buttons that you touch to start or stop actions or to display a dialog,

• Option Buttons that you select drop down menu options from a list,

• Boxes that you use to switch functions on or off and

• Radio Buttons that allow you to choose one of two or more options.

The Clarus GC is controlled by a collection of operating parameters called the
Active Method. You can prepare and save up to five methods and make any one
of them the Active Method. However, the fifth method is reserved for
TotalChrom and may be overwritten.

Clarus 600/680 GC User’s Guide

2-5

The following Status Screen shows the different sections of the user interface.

The Status Screen displays icons that provide quick access to major areas of the
system. The injector and detector buttons show graphic representations of the
devices for each channel. If a heated auxiliary zone is configured, the Aux button
with a thermometer appears active on the bottom of the screen. The Aux zone
button with the carrier gas icon indicates that the PPC carrier gas zone is active.
The icon buttons that represent the heated zones (injectors, detectors, oven, and
Aux if configured) include a light to indicate the ready/not ready status. A red
blinking light indicates not ready and a steady green light indicates ready status.

Click here to view the Signal. If

a method is not running the

The Title bar displays the
name of the active method.

The Run button provides

access to the Autosampler
and Manual Inject settings.

Channel B appears above

Channel A to emulate the
order on top of the GC.

The Icon buttons provide quick

access to all configured areas of
the instrument. An indicator
light shows the ready/not ready
status of each heated zone.

The status bar displays the
overall ready/not ready status
as well as text messages and
the real time clock/date

The bottom bar displays the

Tools pop up menu. When the
system is running the Stop
button also appears.

The Start button appears so
you can start or stop a run.

Touch Screen Navigation

2-6

Tabs

Some of the active method screens include tabs to allow you to switch views
associated with a specific channel.

Non-Configured Devices

If a device is installed but not configured, or configured as None, both the
graphic and light are grayed out.

Touching the button prompts the following dialog box.

Clarus 600/680 GC User’s Guide

2-7

The following screen capture shows the drop down list on the injector
Configuration screen used to set a device to None.

Non-installed Devices

If a device is not installed, a grayed out deactivated button with no indicator light
appears in the designated position.

Touching the button prompts the following dialog box:

Touch Screen Navigation

2-8

Run Button

The Run button displays the Manual injection and Autosampler settings if the
device is enabled. The bottom bar on these screens includes the Start button.
When the system is running, the Start button changes to the Stop button. Since
the Start button is only available on the Autosampler and Manual inject screens,
you must initiate a run from these screens. However, when the system is running,
the Stop button appears on all screens allowing you to Stop the run from
anywhere in the application. If the system is Paused, the Resume button appears
on all screens.

Autosampler Enabled

When an Autosampler is enabled, the Run button defaults to that screen. The
following screens show the enable check box on the configuration screen and the
associated Autosampler screen in the Active Method.

Clarus 600/680 GC User’s Guide

2-9

When the GC is ready, touch the Start button to begin the run. If you touch Start
before the system is ready, the run will start when the system reaches the ready
status.

When the Autosampler is disabled, touching the Run button displays the Manual
inject screen. When the instrument is ready, touch the Start button to begin the
analysis. The countdown enable check box is selected by default. You can stop
the countdown by pressing the Cancel button.

Manual Injection

If no Autosampler is installed or configured, the Run button displays the Manual
injection screen.

The enable check box is selected by default. Touching the start button initiates
the countdown starting from 5 seconds. When the countdown reaches 0, an
audible beep prompts you to inject the sample. The GC will then start to program
the oven and collect data. If the enable check box is deselected, the timer and
tone are disabled. The system starts as soon as the Start Button is pressed and you
make an injection simultaneously.

Touch Screen Navigation

2-10

Enabled Disabled

When the Stop button is pressed, an abbreviated Stop Menu appears.

Clarus 600/680 GC User’s Guide

2-11

Stop Menu

Stop Immediately – Touching this button immediately stops the Active Method
and closes the Stop Menu dialog..

Go to a temp, program step – Displays the Go to Temp dialog for you to select
the step you wish to go to at this time. Then press OK to activate the selected step.

Cancel – Cancels this Stop Menu dialog and returns you to the Active Method.

Signal Button

The Signal icon displays the graphic signal for the active method. If the system is
not running, a baseline appears on the graph.

The Signal screen displays the selected detector signal over a fixed time period
(2 minutes) with you selecting the scaling factor using the up and down arrow
buttons. The raw signal is unprocessed and can appear slightly larger than the
processed signal. The processed signal has gone through attenuation and offset
filters.

Raw signal

Processed signal

Touch Screen Navigation

2-12

The name of the channel appears on the top left of the screen. Detector controls
include Ignite and Autozero.

Display controls include scaling and zeroing.

Ignite Button

Pressing the Ignite button starts the ignition sequence for a PPC-enabled FID.
During ignition the plot and signal level are active.

For information on setting up manual pneumatics for the different detectors see
the various detector sections in chapter 4 “Setting Up the Detectors” and sections
in Chapter 3 on “Using the Active Method” and Viewing or Adjusting Carrier
Gas Pressure Using Manual Pneumatics.

AutoZero Button

Autozeroes the selected detector.

Signal Plot

The plot graph displays the signal from the selected detector in “real time.” The
window is 2 minutes wide. The signal commences at the y-axis and is plotted out
to start + 1.75 minutes. The signal then scrolls back so the start is now +1 minute,
the last 0.75 minutes are displayed from there, and the signal then scrolls out
again.

The signal is plotted continually before, during and after a run.

Signal Display and Scaling

The signal display at the top of the screen displays the signal level of the detector
in mV.

The default signal scale is 0-1024mV. The up/down arrows will adjust the
display between 1 and 1024mV by halving or doubling the current factor

Clarus 600/680 GC User’s Guide

2-13

Zero Display Button

The Zero Display button offsets the current signal level to 5% f.s.d. on the
display.

Heated Zones

The Status screen displays graphic icons to represent the devices installed in the
system.

Each type of injector and detector is represented with a customized graphic as
well as a text label. Heated zone buttons display a status light indicator in the
lower right corner. The indicator lights for individual zones follow the same
convention as the system status light that appears in the Status bar. Steady green
indicates that the zone is ready. A red blinking light indicates that the zone is not
ready.

Injector and Detector Buttons

The screen is organized with Channel B devices above Channel A to reflect the
position of the channels on top of the GC. Injector and detector buttons display

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the active method settings for each device. Touching a device icon displays the
selected screen as well as a row of tabs to allow easy access to the injector, oven,
detector, and events for that channel. Touching the alternate channel icon on the
top navigation bar displays the active screen and associated tabs for the other
channel if it is installed and configured. The active method screens include
navigation icons on the title bar that allow you to access the same elements
available from the Status screen.

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Oven Button

Clicking the oven button provides access to the oven program settings and graph.
You can set 1 to 10 program steps and up to 9 ramp rates. Use the up and down
scroll buttons to the right of the oven entries to view program steps 5 – 10.

If both channels are running and the Oven is accessed from the Status screen, it
defaults to Channel A. The oven program screen displays the same tabs and
navigation icons as the injector and detector active method screens.

Aux Zone Buttons

If a heated Aux Zone is configured, pressing the Aux button displays a screen
that follows the same format as the injector screens and shows the current
temperature.

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Navigation Bar

The navigation bar provides icons to allow users to seamlessly toggle between
channels as well as access the same main areas of the system available from the
status screen.

The following diagram shows the navigation bar of an Active Method with the
corresponding icons on the status screen.

Status Screen Active Method Navigation Bar

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Injectors

The injector elements that appear on a particular injector screen depend on
injector types as well as selected configuration options. Some injector types offer
a variety of options while others are more limited. The labels in the following
screen capture identify the main components of an Active Method injector
screen. This example shows a screen for a PSS injector with PPC.

Injector Tab for
Channel A-PSSI
selected

Active Method Name

Temp Ready/Not

Ready Light

Carrier Gas

Ready/NotReady
Light

Carrier gas

pressure, flow,
or velocity

Split Flow

Ready/Not Ready

Split Flow actual

value

System Status – Oven

Program Step

Time/Date Display

Split flow set

value

Carrier Gas

program button

Temp program

button

Temp Ready/Not

Ready Light

Channel B Parameters

Temp Set Point

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Program Buttons

The program button appears next to the temperature and Carrier Gas fields for a
programmable PSS or POC injector. If the program button associated with a
value is active, the entry field is grayed-out. You must go to the program screen
to modify the settings.

If the programmable injector is not configured to program the setting, the
program button is grayed out. In most cases, fields with a deactivated program
button are editable, allowing you to modify the setting directly.

Display Text

The text displayed next to the set point entry fields show the current values. If the
injector configuration allows you to display the value in other units, such as
velocity or flow, the display text shows the actual values for all of the available
options.

PSS

This section describes the main components of the PSS active method screen and
the relationship between program and configuration options.

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Configuration Options

The following screens show the configuration choices and how they correspond
to the entry fields in the active method.

Configuration Screen Active Method

Temperature Program

You can set injector (inlet) temperature programs by selecting, the program

button

on the active method screen is active.

Mode

Description

Inlet

In the inlet programmed mode, the injector is first heated to the
injector temperature that is entered in the method. The injector
then follows the injector temperature program that you defined.

Oven

The oven programmed mode is the default mode of operation. In
this mode, the injector setpoint equals the oven setpoint plus 5 °C.

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The temperature graph displays the set point value. The label below the graph
displays the current step. The text to the left of the graph displays the actual
temperature.

To modify the temperature program during a run, touch the program button. You
can modify the temperature, time, or rate. However, if the program is currently in
that step, the changes will be ignored.

Isothermal Program

If the program is isothermal, the program button is grayed out and the top-level
field is active. Changes entered in the field take effect immediately.

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Carrier Gas Program

The Carrier Gas options for PSS include flow, velocity, or pressure. If the option
for Capillary Control is selected, you can program the carrier gas according to
one of the three values. The following example shows that Pressure was
selected as shown in the following Configuration screen:

The corresponding actual values for the other units appear as read-only text on
the screen as shown in the following Active Method screen.

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.

Touching the Program button next to the field displays the associated Carrier
Pressure Program screen for the entry field value.

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Capillary Control Off

The following screens are examples when Capillary Control is off

Split Flow

The PPC system adds the split flow offset to the method's split flow rate setpoint
to obtain the Total split flow rate delivered to the inlet system. The total value is
equal to the setpoint flow rate (the flow at the column entrance) plus the offset
flow rate. The inlet system flow controller delivers the Total flow rate, not the
setpoint flow rate.

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Packed (Pkd)

The packed column injector has a fixed (non-programmable) temperature field.
The carrier gas can be programmed by Pressure or flow. The following
procedure shows how to navigate through the screens to configure PPC for a
packed column injector.

1. Select Configuration from the

Tools menu

2. Touch the Pneumatics button.

.

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3. Touch the PPC Connect button.

4. Touch the OK button.

5. Touch Carrier B to Configure

your Packed column injector for
PPC.

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2-26

6. Select Pres Read from the drop-

down menu. Then touch the OK
button.

7. Touch Close to close the Connect

PPC Device screen.

8. Touch OK on the Configuration

PPC screen.

9. Touch the B Injector button on the

Configuration screen.

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10. The Configure Injector B screen

appears.

11. Select Pressure or Flow from the

drop-down menu.

12. To exit out of Configuration,

touch the OK button then touch
the Close button.

13. Display the active method and

view the B-Pkd injector
parameters as shown on the right.

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POC

The packed on co lumn injector can be programmed by Inlet (POCI) or Oven
(POCO). The POC injector is configured and controlled according to the same
parameters as the PSS injector.

Packed On Column Inlet

Packed On Column Oven

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Capillary (Cap) Injector

1. From the Configuration menu,

select Cap from the drop-down
list.

2. Exit from Configuration and

display the active method screen.

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Oven

The Oven Temperature Program provides fields and a graph that reflect the
current temperature program as shown in the screen on the left below. Pressing
the Go to button invokes a dialog box that allows users to raise the temperature
to a value associated with another step. The last step of the current program is
selected by default. Radio buttons for steps that exceed the number of steps in the
current program are deactivated.

In the example below, step 2 is selected. As soon as the user touches the OK
button the change is implemented. The graph in the capture on the right shows
the immediate temperature rise and the departure from the program.

Graph and status bar show the
oven is ready to run a program.

Touching the Go to button displays
the Go to Temp dialog box to
select a step to go to. In this
example step 2 is selected. Press
the OK button to immediately raise
the oven temperature to the value
specified in step 4.

The blue line in the graph reflects
the departure from the program.

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Aux Zone

If the GC is configured with an auxiliary zone, the button appears on the status
screen. Touching the Aux button displays a dialog box with the setpoint and
actual temperature.

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Detectors

Detector screens provide you with a way to set and control a number of
parameters during a run, such as temperature, range, and attenuation. Other
active elements include a Heater Off button to turn off the detector and an
AutoZero check box. Selecting the AutoZero check box prompts the system to
zero the signal before the run and also activates the Signal button on the Signal
screen. The mV value next to the small signal icon that displays the current
signal. The read-only text displays details about configuration settings. The
following screen shows the major components that apply to all detector screens.
The subsections that describe each detector type includes details about settings
that are unique to that particular detector.

FID

The FID (Flame Ionization Detector) uses a hydrogen and air flame to generate
ions from the combustion of an organic compound. The detector collects and
measures the concentration of these ions to determine the amount of compound

Dynamic text

displays the
current signal

Selecting the
AutoZero checkbox
zeros the signal
before the run

Touch the

Ignite button
to light the FID

flame

Temperature

setpoint.

Actual

temperature

Indicator lights

show the gas
flow status

Selecting this

checkbox turns the

detector heater

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in the sample. The FID active method screen varies depending on whether the
detector is configured with manual or programmable pneumatics. This section
describes the screen components for each type of configuration.

Touching the Ignite button allows you to light the FID flame.

Auto-Ignition

The PPC controlled FID has flameout detection and an auto-ignite feature.
Flameout detection occurs 0.5 minutes into the PRE-RUN time and it measures
the user-entered baseline threshold level in mV. If the threshold level is exceeded,
the flame is considered lit, otherwise the Clarus GC detects that the flame is out
and auto-ignite automatically lights the flame before the start of a run.

With the FID temperature set, the air and hydrogen flows set, and auto-ignition
activated by setting a positive mV value for the flame offset, the FID attempts
auto-ignition at -0.5 min. before the system becomes ready. At this
Pre-run time the status bar flashes “

Flame Ignition” as the air flow is shut off,

hydrogen purges the FID for about 10 seconds, and the ignitor energizes for
ignition followed by a return of the air flow to the detector to sustain the flame.

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After the flame ignites, the FID output level is monitored to confirm ignition
before producing a READY signal. If ignition is not confirmed, the ignition
process repeats up to two more times if needed. If ignition is not achieved after
three attempts, the flame gases are set to off and a dialog box appears displays
the following message:

“Flame 1 or 2 failed to ignite.”

Touch the OK button. The status is made NOT READY and “FID 1 or 2
flameout” appears. If auto-ignition is attempted with the FID gases set to zero
flow, the message “No ignition. Flame gases are off” appears on the screen. To
proceed, go the PPC screen and touch Reset to the Configuration screen and reset
the air and hydrogen to their 450 and 45 mL/min flow rates.

Auto-Ignite

The auto-ignition process only occurs before the start of each run just prior to the
instrument becoming READY. However, the manual flame ignition process,
performed by touching the Ignite button, can be initiated at any time.

Auto-ignite proceeds in the following sequence:

1. When auto-ignite begins the Clarus GC equilibrates.

2. Once the two minutes of equilibration expire, PRE-RUN begins and the

AutoSystem detects that the flame is not lit and indicates this by alternately
flashing Flame? and Method 5 in the status bar.

3. After determining that the flame is not lit, the AutoSystem switches to a not

ready state and attempts to automatically ignite the flame. Flame Ignition 1
appears in the status bar.

4. The air flow is shut-off and hydrogen is purged through the FID for

10 seconds.

5. The ignitor energizes, the flame ignites (indicated by a pop sound), and air flow

is returned to sustain the flame. The FID output level is monitored to confirm
that the flame is lit. If a lighted flame is not confirmed, the AutoSystem
repeats the ignition process up to two more times.

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Configuration Settings

The following screens show the Active Method screen and the corresponding
settings in the Configuration screen.

Active Method Configuration Screen

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TCD

The Thermal Conductivity Detector (TCD) is a dual-channel detector which
measures the difference in thermal conductivity between carrier gas flowing
through a reference channel and carrier gas plus sample flowing through an
analytical channel.

Four tungsten-rhenium filaments are connected in a bridge circuit, two in each
channel. The TCD is set up with the same amount of carrier gas flowing through
both channels. The presence of a sample component in the carrier gas flowing
through the analytical channel changes the resistance of the filaments in that
channel. This unbalances the bridge and produces a signal proportional to the
amount of sample.

The following screens show the Active Method screen and the corresponding
settings in the Configuration screen.

Active Method Configuration Screen

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ECD

The Electron Capture Detector (ECD) is the most sensitive detector available for
the analysis of electrophilic compounds such as chlorinated hydrocarbons found
in pesticide residues. It is concentration-sensitive and nondestructive.

The ECD cell contains a nickel foil in a cylinder through which the carrier gas
flows. The coating of the foil's inner surface contains the radioactive isotope
Nickel-63 and has a nominal sensitivity of 15 mCi. To optimize detector
response, make-up gas is combined with column effluent.

Beta particles emitted from the isotope ionize the carrier gas. The resultant ions
and electrons travel to the collector anode assembly under the influence of a
pulsed polarizing voltage applied between the source and the collector. The
pulse frequency is varied to maintain a constant average current. The presence of
an electron absorbing species in the detector decreases the current as the
absorbed electrons form ions, which travel more slowly than electrons. The
pulse frequency of the polarizing supply is automatically controlled to maintain a
constant current and is used to form the detector output signal.

The ECD works with nitrogen carrier or makeup gas or a carrier or makeup gas
mixture of 95% argon/5% methane. When using capillary columns at low flows
(5 mL/min or less), helium or hydrogen may be used as the carrier gas provided
nitrogen or argon/methane is used as the make-up gas. A cross section view of
an ECD is shown below.

The 63 Ni radioactive foil coating and requires careful handling to ensure that it
does not create a safety hazard. In order to prevent a Thermal Runaway risk, the
GC shuts down if any heated zone exceeds 470º C. If this occurs, the following
message appears:

Warning

Instrument Shutdown

Thermal Runaway xxxxxx zone

Call your PerkinElmer service representative

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Instrument shutdown also occurs if there is a PRT (Platinum Resistance
Thermometer) or MPU (Micro Processor Unit) failure. In this case, the following
message appears:

Instrument Shutdown

xxxx zone PRT error

Call your PerkinElmer service representative

The ECD works with nitrogen carrier or makeup gas or a carrier or makeup gas
mixture of 95% argon/5% methane. When using capillary columns at low flows
(5 mL/min or less), helium or hydrogen may be used as the carrier gas provided
nitrogen or argon/methane is used as the make-up gas.

The following screens show the Active Method screen and the corresponding
settings in the Configuration screen.

Active Method Configuration Screen

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PID

The Photoionization Detector (PID) is designed to allow the effluent from a
chromatographic column to be ionized by ultraviolet light (provided the
ionization potential of the effluent is less than that of the UV source). The
current produced by the ion flow is measured by the detector and is proportional
to the concentration of the ionized material.

The following screens show the Active Method screen and the corresponding
settings in the Configuration screen.

Active Method Configuration Screen

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NPD

The nitrogen phosphorus detector (NPD) is a highly specific thermionic detector
for organically bound nitrogen and phosphorus.

The detector operates by electrically heating a glass bead, that contains an alkali
metal, to the point where it emits electrons. A mixture of hydrogen gas and air
flows around the bead to produce a hydrogen plasma. Stable intermediates are
formed in the hydrogen plasma which then capture the electrons emitted from the
bead to produce ions. A polarizing field directs these ions to the collector
electrode, thereby creating a current which is amplified. Sensitivity is affected
primarily by the air flow, and selectivity is affected primarily by the hydrogen
flow.

The following screens show the Active Method screen and the corresponding
settings in the Configuration screen.

Active Method Configuration Screen

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FPD

In the Flame Photometric Detector (FPD), the column effluent is mixed with
hydrogen and then burned in air. Light emitted from the flame passes through a
lens, a filter, and to a photomultiplier tube, which generates an electrical signal.
The Flame Photometric Detector is used for detecting sulfur, phosphorus, or tin
compounds, which produce chemiluminescent reactions with emissions at
wavelengths characteristic of the S2, Sn, and HPO species.

The following screens show the Active Method screen and the corresponding
settings in the Configuration screen.

Active Method Configuration Screen

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Timed Events

Events Tab

The Events tab displays the timed events table and buttons, valves, and Aux gas
controls.

Element Enabling

Timed events table Always

Aux gas button PPC configuration

Relays Always (see below for details)

Insert button Always

Edit button Always

Delete button Always

Clear button Always

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Timed Events Table

The timed events table displays the time, name, and value of each event. Timed
events may be added and removed while the GC is running. The next event to be
executed is automatically selected. Up to 32 events can be specified. The
configured hardware determines which events are available. Events that are not
applicable should not be available. The following table lists the available events.

The time range is -99 to 999 minutes. Events occurring after the temperature
program is complete are ignored.

Add

The Add button displays settings that allow you to specify an event to add to the
table.

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Error Messages

Edit

Touching this button displays the active method page for editing timed events. If
the GC is running, then edited events at times before the run time at which the
edited list is accepted do not occur until the next run.

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Delete

Clear

Touching the Clear button deletes the contents of the entire event table. A dialog
box confirms the action.

Pressing Yes clears the table. Touching the No button closes the dialog box and
retains the contents of the Events table.

If the table is empty, the following Error message appears:

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Value

The value box function depends on the event. For some events, such as Carrier
X, a numeric value is required. For others, such as TCD polarity, a choice
between two options is required.

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The PreVent/ProTect/MS Vent valves are never operated during a run and are not
required in the Timed Events list.

• No timed event should have the same time as another timed event.

• Time resolution is 0.01 minutes.

• Timed Events may be entered and removed in any sequence.

• Pressing the Clear button prompts a dialog box:

”This action will clear the entire table. Do you want to continue? “Yes”
“No”

• Timed Events are re-ordered chronologically after each entry. The

capacity is 32 entries.

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Relays

They appear as set in the configuration screen.

User can turn on the initial and/or current settings by touching the check box.

If GC is Ready, changing the initial setting will change the current setting.

The initial settings are stored in the method and are only changed if the user
modifies them.

The current settings are changed via Timed Events.

Any settings may be changed during a run.

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Aux Zones

Heated Aux Zone

If the GC is configured with an auxiliary zone, the activated button appears on
the status screen.

Touching the Aux button displays a dialog box with the setpoint and actual
temperature.

To modify the temperature, press the minus or plus button. Touch OK to
implement the value and close the dialog box.

Pneumatic Auxiliary Zones

Up to four pneumatic zones can be set for PPC carrier gas control. When one or
more of the aux zones is configured, the following button appears on the status
screen.

The same button also appears on the Events screen.

Touching the button displays the following screen:

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Aux Zones that have been set in PPC configuration display the configured unit
type and include a status indicator light. The initial values can be modified via
timed events. The current value is shown next to the initial value field.

Using the

Active Method

3

Using the Active Method

3-2

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3-3

Overview

The Clarus GC is controlled by a collection of operating parameters called the Active
Method. You can prepare and save up to five methods and make any one of them the
Active Method. However, the fifth method is reserved for TotalChrom (external
computer controlled software) and may be overwritten.

The operating parameters include the an oven temperature program; injector temperature
or injector temperature program; detector temperature or detector temperature program;
carrier gas pressure set for pressure flow or velocity; valve settings (for example, the
operation of a gas sampling valve or split/splitless operation of capillary column); a timed
events table, and a variety of parameters for controlling data output.

Active Method parameters are always saved when you turn the Clarus GC off, and
automatically reloaded when you turn it back on.

Using the Active Method

3-4

Editing the Active Method

If you have read and used the chapters in this manual sequentially, as recommended, by
now you have probably installed and conditioned one or two columns, and set up one or
two detectors. Also, you were probably not aware at the time that you modified certain
Active Method parameters. Since the conditions used then were not necessarily those
required by the analyses you want to perform, you should now edit the Active Method to
set your operating parameters.

Examples of how to perform the tasks listed below are described in the sections which
follow. You should, of course, substitute your values for ours.

• Setting up oven temperature programs

• Setting injector temperatures/programs (PSS and POC)

• Setting detector temperatures

• Viewing/setting carrier-gas pressure/programs (PPC)

• Viewing/setting carrier-gas flow/programs (PPC)

• Setting up valves

• Setting FID, PID, NPD, or FPD range

• Setting TCD filament current

• Routing detector output

• Attenuating detector signals

• Autozeroing a detector

• Building a timed events table

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Getting Ready to Edit the Active Method

 Close the oven door.

NOTE: If a column has been installed, make sure you have carrier gas flow through the

column before closing the oven door and elevating the oven temperature.

The Status screen icon buttons provide access to the active method
parameters.

NOTE: When you change an Active Method parameter, the change goes into effect immediately.

For example, if the system is READY and you change an injector temperature setpoint,
the status screen displays NOT READY until the new setpoint is reached.

Using the Active Method

3-6

Setting Up Oven and Inlet Temperature Programs

You can set up ramp programs (they are Init (1), 2, 3, through 10) using the Clarus GC
software.

1. From the System Status screen touch the oven button

to display the oven

program screen.

2. Once the Oven program screen appears.

3. Select a field by touching it and use the up and down arrow or keypad

buttons to enter a temperature, equilibration time and rate. Enter a

value of 0 in the Rate field to make that the last step. You will then see the word
END appear in the Rate field all the fields that follow are deactivated. You must
touch END and then touch the up arrow button to activate the next row. The
following figure shows a typical temperature step program.

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Figure 3-1. Typical temperature program steps.

Before you actually set up an oven temperature program, you should decide on the
Equilibration Time you need and change the default value if necessary (see below).

Configuring the Equilibration Time (Init)

When you change the oven temperature setpoint, the system heats or cools the oven to the
new setpoint, then equilibrates the column(s) for the specified Equilibration Time before
the instrument becomes READY.

NOTE: A minimum Equilibration Time of < 1 minute is recommended for temperature programs.

Longer equilibration times are recommended for initial oven temperatures of < 50°C.
An equilibration time of 0.0 minutes can be used for isothermal methods.

Setting a Coolant Timeout Value

The purpose of the coolant timeout value is to conserve coolant. If you select a coolant
timeout value when you configure the Clarus GC, the coolant solenoid shuts off if a GC
run is not started within this time period after the oven reaches the initial set temperature.
Once the coolant shuts off, the GC remains not ready and the following message will
appear, Coolant Timed Out: Touch OK to Continue.

NOTE: The coolant timeout must be greater than the equilibration time.

When you press OK, the coolant solenoid will then operate again and the oven will cool
to the initial temperature.

Using the Active Method

3-8

NOTE: When using a POC or PSS injector with the subambient accessory, the injector

temperature must not be set below the oven temperature. You can minimize coolant
consumption if using the oven subambient with the PSS or POC installed but not being
used, by deconfiguring the PSS or POC.

Setting a Coolant Cut-In Temperature

The coolant cut-in temperature is the temperature at which the coolant starts to cool the
oven. The default cut-in temperature is 60 °C. The allowable cut-in temperature range is
30 °C - 110 °C. We recommend that YOU NOTE THE AMBIENT TEMPERARTURE
AND SET the cut-in temperature 20 °C above your current ambient temperature.

For example: A room temperature of 20 °C uses a default temperature of 40 °C, whereas
a room temperature of 25 °C uses a 45 °C cut-in temperature. Examples for setting up
isothermal, 1, and 2 ramp programs follow.

NOTE: Higher cut-in temperatures cause more coolant to be consumed.

Setting Up an Isothermal Program

Setting up an isothermal program requires entering the following information in the
sequence shown:

• Initial oven temperature (Temp 1)

• The total run time for the initial temperature (Time 1)

• A temperature rate increase of 0 (Rate 1).

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To set up an isothermal program:

1. From the Oven tab set the initial temperature 1 to 75 ºC using the up and down

arrow or keypad

buttons.

2. Enter a temperature setpoint appropriate for your analysis, for example, 100 °C.

NOTE: The oven status changes to Not Ready. The changing oven temperature is displayed

under the oven icon as the oven heats up to the new setpoint. When the oven reaches the
new setpoint, the system equilibrates for the Equilibration time (Init) specified in Oven
Configuration screen and then becomes Ready.

For an isothermal run, Init. (TIME 1) is equivalent to the total run time. At the end of the
time (TIME 1), the system changes to Not Ready, it equilibrates, and then goes Ready.

To change the hold time:

 Go to the Oven tab and enter a Time appropriate for your analysis, for example,

25 min.

NOTE: Since a constant oven temperature is maintained for isothermal operation, the rate of

temperature increase must be set to. If the Active Method you are editing is already
isothermal, the RATE parameter will have been properly set at 0 and is indicated on the
screen by the word "End”.

Using the Active Method

3-10

NOTE: You can set the rate to 0 but whenever a RATE is set to “0,” any subsequent program

steps, if present, are deleted from the Active Method.

Setting Up a One-Ramp Temperature Program

Setting up a one-ramp program requires entering the following information in the
sequence shown:

• Initial oven temperature (Init 1)

• Hold Time for the initial temperature (Init 1)

• Rate of temperature increase from the initial to the final oven temperature (Init Rate 1)

• Final oven temperature (Init 2)

• Isothermal time for the final temperature (Init 2)

• Temperature increase of 0 °C/min which signifies the end of the RATE 2 step.

The following example shows how to convert an isothermal program into a one-ramp
program using the previous isothermal method oven temperature parameter as a starting
point.

Parameter

Value

Init Temp 50 °C

Init Time

5 min

Init Rate

2 °C/min

Temp 2

70 °C

Time 2 10 min

Rate 2 End (0 °C/min)

To set up a one-ramp program:

1. From the Oven tab, for the initial temp enter 50.

2. Enter 5 for initial time.

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3. Enter a ramp initial rate 1 of 2 °C/min.

4. For Temp 2, enter a temperature of 70 °C.

5. Enter a time of 10 min.

Setting Up a Multiramp Temperature Program

The following example shows how to expand the above one-ramp program to a two-ramp
program. The parameter values used in the example are shown below:

Parameter

Value

Rate 2

4 °C/min

Temp 3

100 °C

Time 3 5 min

Rate 3 0 °C/min

1. From the oven tab enter a rate of 4.

2. Enter a temperature of 100.

3. Enter a time of 5.

NOTE: You can enter RATE 3, TEMP 4, and TIME 4 to set up a third ramp.

Holding an Oven Temperature

While running a temperature program, you can hold the oven temperature by setting it to
the temperature of the unexecuted steps.

To hold an oven temperature during a temperature program:

1. In the System Status screen touch the oven button

.

Using the Active Method

3-12

2. After you touch oven button the Oven tab screen appears. Next, touch the go to

temp button

to display the Go To Temp (temperature) screen.

2. From this window touch the button for the temperature level that you want to hold.

Touch OK. Modify the temperature on the Oven tab screen using the up and down
arrow or keypad

buttons. When completed return to the system status

screen.

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The oven heats ballistically to the temperature value for oven Temp 2 and holds, instead
of executing the time associated with oven Temp 2.

Figure 3-2. Oven Temperature Program for Rate 1.

To hold the oven program at a specific time during or before a run, use an oven HOLD
timed event. See the section on Timed Events.

Using the Active Method

3-14

Setting Injector Temperatures

Packed, Capillary (Split/Splitless), Programmed On-Column, and
Programmed Split/Splitless

The examples in this section were derived by editing the Active Method with a capillary
injector installed and configured in position A (front), and a packed injector installed and
configured in position B (rear).

This section contains examples of how to:

 Display injector temperature screens

 Change injector temperatures

 Turn injector heaters off

 Turn injector heaters on

 Set oven programming mode

 Set inlet programming mode

Displaying Injector Temperature Screens

 From the System Status screen touch the injector button this will

display the injector tab page.

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3-15

The injector information displays:

Using the Active Method

3-16

Turning Injector Heaters On or Off

 To turn the Heater Off touch the check box.

As the injector cools off, the injector temperature is displayed on the above screen.

Changing Injector Temperatures

1. To turn the heaters on and modify temperatures, make sure the Heater Off check

box does not display a check mark.

2. Touch the Temp field and using the up and down arrow or keypad

buttons increase the value to 255 ºC

.

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Oven Temperature Programming Mode

In this mode the POC or PSS injector is configured as Oven. The injector temperature is
set to the oven temperature plus 5 °C. This is the default mode and the easiest mode to

operate in. For example, if the oven program is as follows:

Parameter

Value

Temp 1

50 °C

Time 1 2 min

Rate 1 5 °C/min

Temp 2

240 °C

Time 2

10 min

The initial injector temperature will be 55 °C. When the GC run begins, the injector will
hold this temperature for 2 minutes, then it will ramp up to 245

°C at 5 °C/min and hold

for 10 min.

Figure 3-3. PSS oven mode temperature program.

NOTE: Opening the oven door turns off the oven and the injector heater. Also, if you reset the

oven temperature during the run to the next level, the injector temperature will follow.

Using the Active Method

3-18

Inlet Temperature Programming Mode

The inlet temperature programming mode is used when the POC or PSS injector is
configured as Inlet. In this mode, the injector follows the injector temperature program
that you entered in the method.

The initial default values are: Initial (Temp 1) is 50 °C,
Injection Time is 999 min, and Inj Rate is 0. With non­programmed injectors, an entry of 0 turns the heated zone
off. With programmed injectors, a temperature of 0 is
possible. Therefore, when 0 is entered for the initial
injector setpoint, the following screen appears:

1. From the selected injector tab screen make sure that the injector heater is off.

2. Set the initial temperature to 50

°C.

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Setting Up a One-Ramp Injector Program

To set up a one-ramp injector program, enter the following parameters:

• Initial injector temperature (Init Temp)

• Isothermal time for the initial temperature (Init Time)

• Rate of temperature increase from the initial to the final injector temperature (Init

Rate)

• Final injector temperature (Temp 2)

• Isothermal time for the final temperature (Time 2)

• Temperature increase of 0

°C/min, which signifies the end of the Rate 2 step.

The following example shows how to build a one-ramp temperature program for your
POC or PSS injector. The parameter values used in the example are shown below:

Parameter

Value

Init Temp 60 °C

Init Time 0 min

Init Rate

100 °C/min

Inj Temp 2

250 °C

Inj Time 2 15 min

Inj Rate 2

End (0°C/min)

To set up a one-ramp injector program:

1. From injector tab screen touch the temp program button

.

Using the Active Method

3-20

3. The temp program screen appears for the selected injector. Use the up and down

arrow buttons or numeric keypad button to program the temperature, time and
rate. Refer to the table on the previous page for some examples for values to set
up a one ramp injector program.

4. When you have completed setting up the program touch Close button then the

system icon

on the navigation bar to return to the System Status screen.

NOTE: You can enter Rate 2, Temp 3, and Time 3 to set up a second ramp. An entry of 999 for

Rate 1 or 2 will cause the injector to ballistically heat up.

NOTE: If the Injector Time is set with the default value of 999, the injector temperature will hold

at the current temperature until the end of the oven program. Otherwise, the injector
temperature will hold for the time you have entered, or until the run ends.

NOTE: If you have the subambient option, the POC and PSS injectors are linked to the oven

subambient option; therefore, you cannot operate the injectors below the oven
subambient temperature.

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Viewing/Setting Carrier Gas Pressure/Flow/Velocity

NOTE: For a description of programmable pneumatics control (PPC), refer to “PPC

Fundamentals” In the Hardware Guide.

PPC enables you to select and set the carrier gas Pressure, Flow, or Velocity. In all three
modes, you can operate at a constant pressure, flow, or velocity or at a programmed
pressure, flow, or velocity. You can also make a pressure pulse, flow pulse, or velocity
pulse injection. In this case the initial pressure, flow, or velocity is quite high at the time
of injection. This minimizes the expansion in the injector liner as the liquid sample is
vaporized and increases the transfer time onto the column. This is recommended for
splitless operation of wide boiling point samples. In this case, you would actually
program the pressure, flow, or velocity down to the normal column pressure, flow, or
velocity for the remainder of the chromatographic run.

The following terms are used in PPC analysis:

Zero─ removes the flow controller from the GC method and sets the flow to 0.

Flow ─ enables the flow controller in the GC method and sets its initial flow to

30% of the nominal maximum flow rate (according to the installed flow-range
element and carrier gas type). The operator has the option to enter a different
flow rate and enter a flow program. When in the flow mode, the PPC system also
monitors the column inlet pressure. If the inlet pressure falls outside a selectable
range, a leak-check fault occurs.

Pressure ─ controls the column inlet pressure and reads the flow rate from the
flow sensor in the flow controller. The initial pressure in the method defaults to
5 psig. The operator has the option to enter a different initial pressure and
optionally enter a pressure program.

Carrier Gas Mass-Flow Controller Operation

Once the carrier gas operation mode has been selected (see the next section “Setting
Carrier Gas Pressure”), you can also modify the default setpoints in the active GC
method, edit the carrier-gas setpoints in stored methods, or generate a new method and
enter carrier-gas setpoints. The following parameters control the carrier gas.

Using the Active Method

3-22

Initial Carrier-Gas Setpoint

The carrier gas mass-flow controller receives set points of flow or pressure depending on
the configured carrier gas mode. The program calculates the initial set point from the
active GC method. The initial set point is established upon setting up a method, ending a
run, or resetting the GC. The flow rate is held constant at the initial value if no additional
carrier-flow entries are made in the GC method. The controller receives pressure set
points when operating in the pressure control mode.

Carrier-Gas Program

The GC method accommodates up to three additional carrier-gas program steps each
consisting of a hold time, ramp rate, and plateau set point. Sequential set points may be
greater than or less than the preceding set point. The PPC system programs the carrier­gas controller with a positive or negative ramp as required.

At the end of the GC oven program, the carrier gas resets to the initial set point value in
the method even if a carrier-gas program is in progress. The carrier gas also resets if the
end of the carrier-gas program occurs before the end of the oven program.

Carrier-Gas Timed Events

You can also use timed events to produce step changes in the set point. Carrier-gas events
can occur before or after a run starts. A carrier-gas event supersedes the method set point
value at the time the event occurs. However, if the carrier-gas program in the method
advances to a new step after a carrier-gas event, the new program step or ramp takes
control.

Leak Checking

The Clarus GC monitors the inlet pressure with a carrier gas mass-flow controller in use.
After selecting the carrier-gas Flow mode in configuration, you can enter the maximum
inlet pressure value. If the inlet pressure drops below or rises above the set limit for more
than one minute, a warning message appears.

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Setting Carrier Gas Pressure

To view or set the carrier pressure:

1. From the System Status screen touch the corresponding Injector button (A or B)

for which you want to set the carrier pressure. The injector screen appears.

In this example, the Clarus GC is configured with the PSS capillary mode on for
pressure (psi). If the option for capillary control has been selected during
configuration, you can program the carrier gas according to one of three values:
pressure, velocity, or flow. The carrier gas field on the injector tab screen
displays the set point value. The label below the field displays the current step.
The actual values for all the available configuration options are displayed to the
left as read only text on the screen.

2. Touch the program button

for Carrier Gas.

The Carrier Pressure Program window appears:

Using the Active Method

3-24

3. Touch the field, ranging from the Initial field to the step 4 field, and use up and

down arrow or keypad

buttons to enter a pressure, hold time and

rate.

NOTE: The rate for the range is 0 (end) to 99. A rate of 999 is a ballistic setting

(maximum).

CAUTION

The ballistic mode of programming is not recommended. Setting a
program rate will be more reproducible.

4. Touch Close to return to the injector screen.

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Setting Carrier Gas Flow using PPC

To view or set the carrier flow:

1. From the System Status screen touch the Injector button (for example, Pkd or

Cap) corresponding to the injector you wish to set the carrier gas flow. The tab
for the selected injector appears:

In this example, the Clarus GC is configured with the PSS capillary mode on for
flow. If the option for capillary control has been selected during configuration,
you can program the carrier gas according to one of three values: pressure,
velocity, or flow. The carrier gas field on the injector tab screen displays the set
point value. The label below the field displays the current step. The actual values
for all the available configuration options are displayed to the left as read only text
on the screen.

2. Touch the program button

for Carrier Gas.

Using the Active Method

3-26

The Carrier Pressure Program window appears:

3. Touch to highlight each individual field, ranging from the Initial field to the

step 4 field, and use up and down arrow or keypad

buttons to enter

a pressure, HOLD time and HOLD rate.

NOTE: The rate for the range is 0 (end) to 99. A rate of 999 is a go to setting.

CAUTION

The go to mode of programming is not recommended. Setting a
program rate will be more reproducible.

4. Touch Close.

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Viewing/Setting Carrier Gas Velocity

You can view/set carrier gas velocity using PPC.

To view or set the carrier gas velocity:

1. From the System Status screen touch corresponding Injector button for which

you wish to set the carrier gas velocity. The page for the selected injector
appears:

In this example, the Clarus GC is configured with the capillary mode on for
velocity (as shown by vel.-init displayed under the carrier gas field). If the option
for capillary control has been selected during configuration, you can program the
carrier gas according to one of three values: pressure, velocity, or flow. The
Carrier Gas field on the injector tab screen displays the set point value. The
label below the field displays the current step. The actual values for all the
available configuration options is displayed to the left as read only text on the
screen.

2. Touch the program button

for Carrier Gas.

Using the Active Method

3-28

The Carrier Velocity Program window appears:

3. Touch each individual field, ranging from the Initial field to the step 4 field, and

use up and down arrow or keypad

buttons to enter a velocity,

equilibration time and rate.

NOTE: The rate for the range is 0 (end) to 99. A rate of 999 is a go to setting

CAUTION

The go to mode of programming is not recommended. Setting a
program rate will be more reproducible.

4. Touch Close.