PerkinElmer TORION T-9 User manual

TORION®T-9
Gas Chromatograph/Mass Spectrometer (GC/MS)
User’s Guide
GC/MS

ii . Torion T-9 User’s Guide
Release History
Part Number Release Publication Date
09931327 D November 2017
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.
EU Importer:
PerkinElmer Ltd
Chalfont Road
Seer Green
Beaconsfield
Bucks
HP9 2FX
United Kingdom
On the internet: http://www.perkinelmer.com/contactus/
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 © 2017 PerkinElmer, Inc.
Produced in the U.S.A.
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.

Table of Contents . iii
CE Declaration of Conformity
Manufacturer: PerkinElmer, Inc.
710 Bridgeport Avenue
Shelton, CT 06484
Manufacturer: Torion®Technologies Inc.
732 East Utah Valley Drive, Suite 120
American Fork, Utah 84003
Telephone No. [phone]
Product: Torion T-9 GC/MS
Model Number: NTSST090500
The undersigned hereby declares, on behalf of PerkinElmer Incorporated of American Fork, Utah,
that the above-referenced product, to which this CE declaration relates, is in conformity with the
provisions of:
•Council Directive 2006/42/EC (May 17, 2006) on the Approximation of the Laws of the
Member States Relating to Machinery;
•Council Directive 2004/108/EC (December 15, 2004) on Electromagnetic Compatibility;
•Standards used: EN 61326-1:2006, EN 61326-2-6:2006
•Council Directive 2006/95/EC (December 12, 2006) on Low Voltage Equipment Safety;
•Standard used: IEC 61010-1:2001 / EN 6061-1 (Second Edition)
•Council Directive 2000/14/EEC amended by Directive 2005/88/EC (June 17, 2006) about
noise limits and labeling requirements machines intended for use outdoors.
The Technical Construction File required by this Directive is maintained at the PerkinElmer, 732 East
Utah Valley Drive, Suite 120, American Fork, Utah 84003.
Edgar Lee
CTO/VP

iv . Torion T-9 User’s Guide

Table of Contents
CE Declaration of Conformity ..........................................................................iii
Table of Contents................................................................................................1
1Introduction..................................................................................................... 7
Overview ............................................................................................................8
Conventions Used in this Manual .....................................................................8
About Notes, Cautions, and Warnings .........................................................8
2Safety Practices ............................................................................................... 11
Overview ............................................................................................................12
Precautions for the Instrument.............................................................................13
Precautions for Customers ...................................................................................15
Safe Handling of Gas Cylinders.............................................................................15
General Operating Conditions...............................................................................16
Environmental Conditions ....................................................................................17
Electrical Safety ..................................................................................................18
Electrical Requirements...................................................................................19
The AC Line Cord ...........................................................................................19
ElectroMagnetic Compatibility (EMC) ....................................................................21
Europe...........................................................................................................21
South Korea...................................................................................................21
United States (FCC)........................................................................................21
Pollution Degree.............................................................................................21
Installation Category ......................................................................................21
Warning Labels ...................................................................................................22
Warning Signs on the Instrument.........................................................................24
WEEE Instructions for PerkinElmer Products .........................................................25
Decontamination.................................................................................................26
Cleaning the Instrument .................................................................................26
3System Overview ............................................................................................. 27
What is solid phase microextraction (SPME)? ........................................................28
What is the Torion T-9 GC/MS?............................................................................29
About the Power Supply and Battery ...............................................................30
What is the Custodion SPME syringe? ...................................................................31
What is low thermal mass (LTM) gas chromatography? .........................................32
What is toroidal ion trap mass spectrometry (TMS)?..............................................34
4Basic Custodion Operations............................................................................. 37
Prepare the Custodion SPME Syringe for Sampling ................................................38
Using the Custodion ............................................................................................39
Sample Headspace Vapors from Liquid or Solid Samples...................................39
Sample Gases ................................................................................................40
Sample Liquids...............................................................................................40
Sample Solids.................................................................................................41
Sample Unknown Liquids and Solids ................................................................41
Performing an Injection with the Custodion Syringe ..............................................44
5Basic Operation................................................................................................ 45
Overview ............................................................................................................46
Startup...............................................................................................................47
Running with External Power and Carrier Gas...................................................47
Home Screen .................................................................................................50
Using the Custodion Syringe ...........................................................................51
Performing a System Blank Run ...........................................................................56

2 . Torion T-9 User’s Guide
System Blank .................................................................................................56
SPME Blank....................................................................................................60
Performance Validation........................................................................................63
Sample Concentration.....................................................................................69
Sample Analysis ..................................................................................................71
Using Alerts for Hazardous Compounds.......................................................76
Viewing Spectra of a Specific Scan..............................................................76
Review the Results of an Analysis.........................................................................82
Viewing the Results on the Torion T-9 GC/MS System.......................................82
Previous Results ........................................................................................82
Quantitative Analysis ......................................................................................85
Exporting Files ...............................................................................................87
Advanced Menu ..................................................................................................90
Procedure ......................................................................................................90
Activating a Procedure ...............................................................................90
Ending a Procedure ...................................................................................91
Selecting a Different Procedure ..................................................................92
Status/Diagnostics..........................................................................................93
Gas Chromatography Tab...........................................................................93
Mass Spectrometry Tab..............................................................................93
Versions Tab .............................................................................................94
Status Tab ................................................................................................94
Edit Tab....................................................................................................95
Current Problems Tab ................................................................................98
Performance Validation...................................................................................98
Manage Files..................................................................................................99
Methods ........................................................................................................100
System Settings .............................................................................................103
Setting the Date and Time .........................................................................103
Password ..................................................................................................104
Network Connection ..................................................................................104
Network Settings on the Instrument ...........................................................105
Power Management...................................................................................106
Shutdown ...........................................................................................................108
Turning off the System ...................................................................................108
Exiting the Software .......................................................................................109
6Software .......................................................................................................... 113
Software Programs..............................................................................................114
Chromion®....................................................................................................114
TightVNC Viewer ............................................................................................114
NIST..............................................................................................................114
Chromion Installation and Operation ....................................................................115
Chromion Main Screen.........................................................................................116
Connecting Chromion to a Networked Instrument ............................................118
Chromion Menu Bar.............................................................................................124
File Menu.......................................................................................................124
Edit Menu ......................................................................................................125
Preferences...............................................................................................125
Decimal Display.........................................................................................125
Data Review Tab .......................................................................................125
Real Time Plots Tab...................................................................................129
File Manager Tab.......................................................................................129
NIST Tab ..................................................................................................133

Table of Contents . 3
Target Library ...........................................................................................134
Hazard Levels............................................................................................134
Method Menu......................................................................................................137
Creating a New Method ..................................................................................138
Load and Delete Methods ...............................................................................140
Importing a Method........................................................................................141
Saving a Method ............................................................................................142
Save Method As .............................................................................................142
Rename Method.............................................................................................142
Export Method ...............................................................................................143
Send Method to Instrument ............................................................................143
Help Menu ..........................................................................................................145
Gas Chromatograph ............................................................................................146
Gas Chromatograph Mini Toolbar................................................................147
GC Settings Tab .............................................................................................148
Heaters.....................................................................................................148
Column .....................................................................................................148
Split Injection............................................................................................149
Sample Introduction ..................................................................................150
Readbacks ................................................................................................150
Solvent Delay ............................................................................................150
Retention Time Calibrations Tab......................................................................151
Target Library Editor ...........................................................................................153
Target Library Editor Mini Toolbar...............................................................153
Target List Setup Tab .....................................................................................157
Mass List...................................................................................................157
Deconvolution Parameters Tab (Target Library Editor)......................................162
Deconvolution Parameters Mini Toolbar ......................................................162
Target List Search .....................................................................................163
Unknown Identification ..............................................................................164
Unknown Libraries .....................................................................................165
Quant Overrides Tab ......................................................................................166
Quant Concentrations Tab ..............................................................................167
Quant Files Tab..............................................................................................169
Quant Review Tab..........................................................................................170
Groups Tab ....................................................................................................171
Performance Validation........................................................................................175
Performance Validation Mini Toolbar ...........................................................175
Performance Validation and Calibration Tab .....................................................177
Mass Item Table........................................................................................177
Tests Section.............................................................................................179
Deconvolution Parameters Tab (Performance Validation) ..................................180
Performance Validation Settings Tab................................................................180
Mass Range Tab.............................................................................................180
Tools..................................................................................................................181
Data Review...................................................................................................181
Data Review Mini Toolbar...........................................................................181
Setting the Cursor Mode ............................................................................189
Additional Functionality Icons .....................................................................191
Data Review Menu Items ...........................................................................197
Deconvolution Window ...................................................................................201
Spectra Graphs/Charts....................................................................................205
Add Peak to Library ........................................................................................205

4 . Torion T-9 User’s Guide
Peak Details ..............................................................................................206
Library Search................................................................................................208
NIST..............................................................................................................209
Mass Spectrometer..............................................................................................212
Mass Spectrometer Mini Toolbar.................................................................212
MS Parameters Tab ........................................................................................214
MS Calibrations Tab........................................................................................216
File Manager.......................................................................................................217
File Manager Mini Toolbar ..........................................................................217
Computer Section – Right click functionality ................................................218
SD Card Section – Right click functionality...................................................220
Supported File Types .................................................................................222
Library Editor ......................................................................................................223
Library Editor Mini Toolbar .........................................................................224
Real Time Plots ...................................................................................................231
Real Time Plots Mini Toolbar ......................................................................231
TIC Graph Tab ..........................................................................................232
Spectra Graph Tab.....................................................................................233
Data Logger Tab........................................................................................233
Logging.....................................................................................................234
Edit Data Logger Item List .........................................................................234
Clear Chart................................................................................................236
Desorption..........................................................................................................237
Desorption Mini Toolbar .............................................................................238
Log Data Tab ............................................................................................240
Batch Processing.................................................................................................242
Batch Processing Mini Toolbar ....................................................................242
Reports ..............................................................................................................244
Reports Mini Toolbar ......................................................................................244
Creating a Report...........................................................................................244
Header Information ...................................................................................246
Report Data ..............................................................................................246
TightVNC Viewer.................................................................................................251
NIST ..................................................................................................................252
7Advanced Operations....................................................................................... 253
Loading Operational Settings when Running an Analysis........................................254
Reset and Restart Buttons on the Instrument...................................................254
Deleting Sample Data from the SD Card ..........................................................255
8Maintenance .................................................................................................... 257
GC Injection Port Maintenance .............................................................................258
Accessing the GC Injection Port.......................................................................258
Septum Replacement......................................................................................258
Injection Liner and Seal Cleaning or Replacement ............................................259
How to “Bake Out” the GC Injection Port and Column ...........................................260
Changing the Battery...........................................................................................261
Changing the Carrier Gas Cartridge ......................................................................262
Removing/Replacing the SD Card.........................................................................263
9Troubleshooting............................................................................................... 265
Troubleshooting Guide.........................................................................................266
Torion T-9 GC/MS will not turn on ...................................................................266
Torion T-9 GC/MS will not turn off...................................................................266
Torion T-9 GC/MS cannot maintain vacuum .....................................................266
GC baseline is noisy, or drifts upward ..............................................................266

Table of Contents . 5
GC peaks are asymmetric ...............................................................................267
GC peaks are eluting late................................................................................268
Acquired mass spectra are noisy .....................................................................269
Results are not reproducible............................................................................270
There is no instrument signal ..........................................................................270
Acquired mass spectra are not correct .............................................................270
SPME fiber came off inside the GC inlet ...........................................................271
Torion T-9 GC/MS fails to identify a compound.................................................271
Torion T-9 GC/MS falsely identified a compound ..............................................271
Torion T-9 GC/MS fails to reach set temperatures.............................................271
Torion T-9 GC/MS is unable to run on battery power ........................................272
Torion T-9 GC/MS suddenly powers down........................................................272

6 . Torion T-9 User’s Guide

1
Introduction

8 . Torion T-9 User’s Guide
Overview
This chapter contains a brief introduction to the Torion T-9 GC/MS®and Custodion®products.
This user’s manual provides step-by-step instructions for operating and trouble-shooting the Torion
T-9 GC/MS and the Custodion line of solid phase microextraction (SPME) syringes. Both basic
operations (such as running a sample and changing the batteries) and advanced operations (such as
re-analyzing data and changing the instrument operating parameters) are included.
The Torion T-9 GC/MS is used to separate and identify volatile and semi-volatile organic compounds
present in gas, liquid and solid samples. The Custodion SPME syringe is used to extract various
classes of compounds (depending on the sorbent coating of the fiber) and to concentrate the sample
for improved sensitivity at low concentrations. The Custodion is used to introduce the sample into
the Torion T-9 GC/MS.
After injecting a sample into the Torion T-9 GC/MS it is separated into its chemical components.
Resolved components are characterized by retention time from the gas chromatograph (GC) and
mass spectral fingerprint from the toroidal ion trap mass spectrometer (TMS). The mass spectral
fingerprints of the chemicals are compared to a database of known mass spectral fragmentation
patterns, and are identified by the on-board library.
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.
UPPERCASE text, for example ENTER or ALT, refers to keys on the PC keyboard. '+' is used to show
that you have to press two keys at the same time, for example, ALT+F.
All eight digit numbers are PerkinElmer part numbers unless stated otherwise.
About 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.

Overview . 9
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.
D
Caution (Achtung)
Bedeutet, daß die genannte Anleitung genau befolgt werden
muß, um einen
Geräteschaden
zu vermeiden.
DK
Caution (Bemærk)
Dette betyder, at den nævnte vejledning skal overholdes nøje
for at undgå en
beskadigelse af apparatet
.
E
Caution (Advertencia)
Utilizamos el término
CAUTION
(ADVERTENCIA) para advertir
sobre situaciones que pueden provocar
averías graves en este
equipo
o en otros. En recuadros éste se proporciona información
sobre este tipo de circunstancias.
F
Caution (Attention)
Nous utilisons le terme
CAUTION
(ATTENTION) pour signaler les
situations susceptibles de provoquer de
graves détériorations de
l'instrument
ou d'autre matériel. Les détails sur ces circonstances
figurent dans un encadré semblable à celui-ci.
I
Caution (Attenzione)
Con il termine
CAUTION
(ATTENZIONE) vengono segnalate
situazioni che potrebbero arrecare
gravi danni allo strumento
o ad
altra apparecchiatura. Troverete informazioni su tali circostanze
in un riquadro come questo.
NL
Caution (Opgelet)
Betekent dat de genoemde handleiding nauwkeurig moet
worden opgevolgd, om
beschadiging van het instrument
te
voorkomen.
P
Caution (Atenção)
Significa que a instrução referida tem de ser respeitada para
evitar a
danificação do aparelho
.

10 . Torion T-9 User’s Guide
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.
D
Warning (Warnung)
Bedeutet, daß es bei Nichtbeachten der genannten Anweisung
zu einer
Verletzung
des Benutzers kommen kann.
DK
Warning (Advarsel)
Betyder, at brugeren kan blive
kvæstet
, hvis anvisningen ikke
overholdes.
E
Warning (Peligro)
Utilizamos el término
WARNING
(PELIGRO) para informarle
sobre situaciones que pueden provocar
daños personales
a
usted o a otras personas. En los recuadros como éste se
proporciona información sobre este tipo de circunstancias.
F
Warning (Danger)
Nous utilisons la formule
WARNING
(DANGER) pour avertir des
situations pouvant occasionner des
dommages corporels
à
l'utilisateur ou à d'autres personnes. Les détails sur ces
circonstances sont données dans un encadré semblable à
celui-ci.
I
Warning (Pericolo)
Con il termine
WARNING
(PERICOLO) vengono segnalate
situazioni che potrebbero provocare
incidenti alle persone
.
Troverete informazioni su tali circostanze in un riquadro come
questo.
NL
Warning (Waarschuwing)
Betekent dat, wanneer de genoemde aanwijzing niet in acht
wordt genomen, dit kan leiden tot
verwondingen
van de
gebruiker.
P
Warning (Aviso)
Significa que a não observância da instrução referida poderá
causar um
ferimento ao usuário.

2
Safety Practices

12 . Torion T-9 User’s Guide
Overview
This chapter describes the general safety practices and precautions that must be observed when
operating the Torion T-9.
This advice is intended to supplement, not supersede, the normal safety codes in the user's country.
It is also a supplement to the PerkinElmer standard Safety and Health Policy. The information
provided does not cover every safety procedure that should be practiced. Ultimately, maintenance of
a safe laboratory environment is the responsibility of the analyst and the analyst's organization.
Please consult all manuals supplied with the T-9 and accessories before you start working with the
instrument. Carefully read the safety information in this chapter and in the other manuals supplied.
When setting up the instrument or performing analyses or maintenance procedures, strictly follow
the instructions provided.
This equipment requires no specified inspection or preventive maintenance to ensure the continuous
functioning of its safety features.

Precautions for the Instrument . 13
Precautions for the Instrument
WARNING
AVERTISSEMENT
Be sure that all instrument operators read and understand
the precautions listed below. It is advisable to post a copy of
the precautions near or on the instrument shelf.
Assurez-vous que tous les opérateurs d'instruments lisent et
comprennent les précautions indiquées ci-dessous. Il est
conseillé de poster une copie des précautions à proximité ou
à l'étagère de l'instrument.
WARNING
AVERTISSEMENT
Do not operate the instrument with any covers or parts
removed. Disconnect the power supply whenever cover is
removed.
Ne faites pas fonctionner l'instrument avec des couvercles
ou des pièces enlevés. Débranchez l'alimentation électrique
chaque fois que le couvercle est enlevé.
WARNING
AVERTISSEMENT
Do not attempt to make adjustments, replacements or
repairs to this instrument except as described in the
accompanying user documentation.
N'essayez pas de faire des ajustements, des remplacements
ou des réparations à cet instrument, sauf comme décrit dans
la documentation de l'utilisateur qui l'accompagne.
WARNING
AVERTISSEMENT
Dispose of waste in accordance with the regulations
applicable to your locality, state and/or country.
Éliminer les déchets conformément à la réglementation
applicable à votre localité, votre état et / ou votre pays.
WARNING
AVERTISSEMENT
The protection provided by this equipment may be impaired
if the equipment is used in a manner not specified by
PerkinElmer.
La protection fournie par cet équipement peut être altérée si
l'équipement est utilisé de manière non spécifiée par
PerkinElmer.
The following precautions must be observed when using the instrument:
•The instrument is field portable and can be placed on the ground therefore before starting the
instrument ensure that it is placed on a level stable surface.

14 . Torion T-9 User’s Guide
•Do not block the side vents (if they are open) or rear vents and ports on the instrument to
prevent potential damage to the electronics or mechanical pumping systems.
•If there is blowing dust or rain, make sure that the side and top covers are closed.
•If the instrument is being used in an area where there is the potential for exposure to chemical
vapors make sure all of the covers are in place.
•If the instrument has been exposed to hazardous chemicals thoroughly decontaminate the
system by wiping with a 5% bleach solution before returning to the lab.
•This instrument is not intrinsically safe and should not be operated in explosive environments.

Precautions for Customers . 15
Precautions for Customers
WARNING
AVERTISSEMENT
The laboratory manager is responsible for warning operators
of this instrument about biohazardous materials that are
processed in this instrument and about wastes that result from
the operation of this instrument.
Le responsable du laboratoire est responsable de l'alerte des
opérateurs de cet instrument à propos des matériaux à risque
biologique qui sont traités dans cet instrument et à propos des
déchets résultant du fonctionnement de cet instrument.
WARNING
AVERTISSEMENT
The laboratory manager is responsible for disposing of any
biohazardous materials and minimizing any biohazards before
the equipment is removed from use, transported or processed
for disposal.
Le responsable du laboratoire est responsable de l'élimination
des matières dangereuses et minimise les risques biologiques
avant que l'équipement ne soit utilisé, transporté ou
transformé pour être éliminé.
•Appropriate venting, sample and waste collection needs to be provided.
Safe Handling of Gas Cylinders
Helium is the only gas required for use with the System. The major hazard associated with this gas
is suffocation. This can occur if the gas is allowed to escape in an enclosed area and displaces the
oxygen in the air. Helium is neither explosive nor combustible.
The Helium Gas comes in a 98 mL steel cylinder at 2500 psi that can be used for up to 150 analyses.

16 . Torion T-9 User’s Guide
General Operating Conditions
The Torion T-9 is field portable has been designed and tested in accordance with PerkinElmer
specifications and in accordance with industry safety requirements.
This equipment requires no specified inspection or preventive maintenance to ensure the continuous
functioning of its safety features.
The instrument can be used under the following conditions:
•Temperature: +5°C to +45°C (+41°F to +113°F)
•Relative humidity: 20% to 80%, without condensation
If possible, avoid any adjustment, maintenance and repair of the opened, operating instrument. If
any adjustment, maintenance and repair of the opened instrument is necessary, this must be done
by a skilled person who is aware of the hazard involved. Whenever it is likely that the instrument is
unsafe, make it inoperative. The instrument may be unsafe if it:
•shows visible damage
•fails to perform the intended measurement
•has been subjected to prolonged storage in unfavorable conditions
•has been subjected to severe transport stresses.