PerkinElmer CLARUS 680 GC User manual

CLARUS 600/680 GC
User’s Guide
GAS CHROMATOGRAPHY

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Clarus 600/680 GC
User’s Guide

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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
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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.

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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

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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

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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

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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

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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.