1 - Institute of Chemical Process Fundamentals of the CAS, vvi

1 - Institute of Chemical Process Fundamentals of the CAS, vvi
TRACE DSQ™
and
FOCUS DSQ
User’s Guide
PN 120156-0003
Revision B
Analyze
•
Detect
•
Measure
•
Control™
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Publication Info
TRACE DSQ or FOCUS DSQ User’s Guide, PN 120156-0003, Revision B. Printed October 2003.
Software: Xcalibur Data System, Ver. 1.4
Technical Content: B. Guckenberger, S. Quarmby
Technical Publications: K. Johns
Xcalibur™, TRACE DSQ, and PolarisQ, FOCUS DSQ, FOCUS GC, TRACE GC are trademarks and/or
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This publication is not part of the Agreement of Sale between Thermo Electron Corporation and the
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Published by Thermo Electron Corporation Technical Publications, Austin, Texas. Contact Editor at
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NOTE: TRACE DSQ or
FOCUS DSQ systems
operate reliably under
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If you maintain a system
outside the specifications
listed in this guide, failures
of many types may occur.
The repair of such failures
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Warranty and service
contract coverage.
This equipment has been tested and found to comply with the limits for a
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designed to provide reasonable protection against harmful interference when
the equipment is operated in a commercial environment. This equipment
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and used in accordance with the instruction manual, it may cause harmful
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be required to correct the interference at their own expense.
Regulatory Compliance
Thermo Electron thoroughly tests and evaluates its products to ensure full
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Your system (instruments and software) is CE compliant and meets
Electromagnetic Compatibility (EMC) and safety standards.
„
EN 55011 (1991) Group 1 Class A
„
EN 50082-1 (1992) IEC 801.2 (1991) Level 3
„
EN 50082-1 (1992) IEC 801-3 (1984) Level 2
„
EN 50082-1 (1992) IEC 801-4 (1988) Level 2
„
EN 50082-1 (1992) IEC 801-5 (1993) Class 3
User’s Guide, Revision B
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Important Information _____________________________________________________________________ TRACE DSQ or FOCUS DSQ
CAUTION
Instrument Damage
Please be aware that any changes you make to your system
may void compliance with one of more of these EMC or safety
standards, or warranty.
To ensure compliance with EMC and safety standards, order replacement
parts from only Thermo Electron factory-trained representatives. If you make
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these EMC or safety standards, or warranty. Changes to your system include
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Safety Compliance
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EN 61010-1 1993 plus Amendment 2, 1995
Standard Warranty
This standard warranty covers all products manufactured by Thermo Electron
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WARRANTY AND LIMITATIONS. Seller warrants that the products to be
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limited to repairing or replacing or issuing a credit for any product
delivered hereunder not conforming to this warranty.
2. The alternative remedies provided for herein are Buyer’s sole and
exclusive remedies.
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date of acceptance of any such product or 120 days after shipment,
whichever occurs first.
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the products covered hereby are excluded from this warranty.
5. Warranty on repaired or replaced parts is extended only to the expiration
date of an issued standard warranty, and only after receipt of written
authorization from Seller.
6. Seller makes no warranty as to expendable items including but not
limited to electron multipliers, filaments, O-rings, vacuum gauge tubes,
fuses, septa, lamps, sources, reaction tubes, and solvents.
4
| User’s Guide, Revision B
TRACE DSQ or FOCUS DSQ______________________________________________________________________Important Information
7. Moreover, after initial installation, any readjustment, recleaning or
recalibration is expressly excluded from this warranty.
8. The warranty will be null and void and Seller will not be liable under this
warranty upon the occurrence of the following events unless Seller’s prior
written consent to the continuation of this warranty is granted:
a. In the event Buyer installs products or physically moves products
from their position of installation at time of acceptance by Buyer, or
b. In the event Buyer transfers ownership of products to third parties
other than Buyer.
9. Seller will not be liable under this warranty unless:
(i) Seller is promptly notified in writing by Buyer upon discovery of the
failure of any products to conform to this warranty,
(ii) when possible, such, product is returned to Seller with Seller’s written
approval, transportation charges prepaid by Buyer,
(iii) such product is received by Seller not more than ten (10) days after
the last day of the applicable warranty period,
(iv) Seller’s examination of such product shall disclose to Seller’s
reasonable satisfaction that such defects or failures have not been
caused by misuse, neglect, improper installation by Buyer, repair,
alteration or accident, including but not limited to failure of electric power,
excessive or erratic power, failure of environmental control equipment as
defined in Seller’s published specifications, failure of Buyer’s selfmaintenance program, or failure of Buyer to maintain product in
accordance with Seller’s manual or instructions.
10. All claims under warranty must be made promptly after occurrence of
circumstances giving rise thereto and must be received within the
applicable warranty period by Seller or its factory-trained representative.
Such claims should include the product type and serial numbers and a full
description of the circumstances giving rise to the claim. At it discretion,
Seller may authorize the prepaid return to Seller’s plant or designated
repair center of products or parts that prove to be defective, or Seller may
repair or replace at Buyer’s premises. Before any products are returned
for repair and / or adjustment, written authorization from Seller for the
return and instructions as to how and where the product should be
shipped must be obtained.
11. When any product is returned for examination and inspection or for any
other reason, Buyer shall be responsible for all damage resulting from
improper packing or handling and for loss in transit, notwithstanding any
defect or nonconformity in the product.
User’s Guide, Revision B
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Important Information _____________________________________________________________________ TRACE DSQ or FOCUS DSQ
If it is found that the defective product returned to Seller has been
caused by the fault of the Buyer, or has been returned without cause and
is still serviceable, Seller shall notify Buyer and shall return such product
to Buyer at Buyer’s expense; in addition, a charge for testing and
examination, may at Seller’s discretion, be made on products so
returned.
12. Seller will not authorize return or repair or replacement at Buyer’s lab of
defective products that have been used for the analysis of toxic,
carcinogenic, mutagenic or corrosive / irritant chemicals until said
products are certified to have been decontaminated by Buyer.
Seller shall not warranty products that have not been decontaminated,
and Seller shall have no obligation to repair or replace such products. Any
products returned to Seller for examination shall be sent prepaid via the
means of transportation indicated as acceptable to Seller.
13. Seller reserves the right to reject any warranty claim not made in
accordance with the foregoing procedures or any warranty claim on any
item that has been altered or has been shipped by non-acceptable means
of transportation.
14. Except as above expressly provided, no warranty is made as to the
merchant ability of the goods to be delivered, nor is except as expressly
provided above, no warranty is made as to the fitness of such goods for
any particular purpose.
15. Statements, expressed or implied, by any person, including employees or
factory-trained representatives of Seller, that are inconsistent or in
conflict with this warranty shall not be binding upon Seller unless said
statement is in writing and signed by an officer of Seller.
a. Liability: In no event shall Seller be liable to buyer or any other party
for incidental, consequential, or special damages.
b. Damages: Seller’s liability (whether by reason of breach of warranty,
breach of contract, tort, or otherwise and irrespective of Seller’s
negligence) for damages shall in no event exceed the payment, if
any, received by seller for the unit or productor service furnished or
to be furnished, as the case may be, which is the subject of claim or
dispute.
August 1998
This warranty shall be governed by the laws of the State of California
P / N QSF-PR-0012 Rev A
6
| User’s Guide, Revision B
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Contents
Important Information ________________________________ 3
Contact Us... ............................................................................................... 7
Reader Survey... ......................................................................................... 7
Customer Registration... ............................................................................. 7
Read Me ____________________________________________ 11
Where to Find More Information .............................................................. 12
About Your TRACE DSQ or FOCUS DSQ System .................................... 13
Safety Information .................................................................................... 16
Typographical Conventions ....................................................................... 18
Changes to the Manual ............................................................................. 18
Chapter 1
Getting Connected __________________________________ 19
1.1 Getting the Right Tools ...................................................................... 21
1.2 Verifying Site Preparation .................................................................. 23
1.3 Unpacking the Instruments ............................................................... 24
1.4 Connecting the Gas Lines .................................................................. 26
1.5 Installing the Data System ................................................................. 31
1.6 Installing the Gas Chromatograph ..................................................... 33
1.7 Installing the Mass Spectrometer ...................................................... 38
1.8 Starting Up the System ..................................................................... 45
1.9 Confirming Readbacks ....................................................................... 47
1.10 Running Diagnostics ........................................................................ 49
1.11 Checking the RF Dip Calibration ...................................................... 51
1.12 Checking the RF Gain Calibration .................................................... 53
1.13 Checking the Air/Water Spectrum ................................................... 56
1.14 Leak Checking ................................................................................. 59
1.15 Checking the Initial Tune ................................................................. 60
1.16 Stabilizing the Instrument ................................................................ 64
1.17 Running EI Qualification Tests ......................................................... 66
1.18 Running CI Qualification Tests ......................................................... 70
1.19 Installing Upgrade Options .............................................................. 77
1.20 Providing Basic Training ................................................................... 78
User’s Guide, Revision B
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Contents _________________________________________________________________________________ TRACE DSQ or FOCUS DSQ
Chapter 2
Getting Started _____________________________________ 81
2.1 Using Desktop Icons .......................................................................... 83
2.2 Configuring Instruments for Use ....................................................... 84
Chapter 3
Running Your 1st Sample ____________________________ 93
3.1
3.2
3.3
3.4
3.5
3.6
3.7
3.8
Appendix A
Calibrating and Tuning the Instrument ............................................... 95
Setting Up Methods .......................................................................... 98
Running Methods ............................................................................ 102
Analyzing the Data: Compounds With a Known Retention Time .... 109
Analyzing the Data: Compounds With a Known Ion Pattern ........... 119
Analyzing the Data: Peak Height and Area ...................................... 122
Analyzing the Data: Signal-to-Noise Ratio ........................................ 124
Automating Processing .................................................................... 127
Preinstallation Checklists ___________________________ 129
A.1 Preinstallation Checklist ................................................................... 130
A.2 Installation Checklist ......................................................................... 131
Appendix B
Additional Helps ___________________________________ 133
B.1 Assembling Swagelok Fittings ......................................................... 134
B.2 Using a Swagelok Tee or Cross ....................................................... 137
B.3 Adjusting the RF Null ........................................................................ 138
B.4 Automatic Tune Flow Chart .............................................................. 141
B.5 Adjusting the RF Dip Calibration ....................................................... 142
B.6 Reinstalling the Data System ........................................................... 143
Index ______________________________________________ 145
10 | User’s Guide, Revision B
Read Me
In This Chapter
Where to Find More Information, pp. 12
Typographical Conventions, pp. 18
Changes to the Manual, pp. 18
Analyze
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Detect
•
Measure
•
Control™
User’s Guide, Revision B
| 11
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Read Me
Where to Find More Information_____________________________________________________________ TRACE DSQ or FOCUS DSQ
This chapter explains: how this book is organized and designed, specifications
about your system, and where to find more information about your system.
Be sure to tear out the Contact Us... card located at the front of this book and
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Electron Corporation gift and complimentary application and technical reports.
Before shipping your system, Thermo Electron Corporation installed the
Xcalibur Data System, Ver. 1.4 on your computer’s hard drive.
Where to Find More Information
Look at your Xcalibur Installation CD for a complete set of hardware and
software documentation.
Figure i-1. Xcalibur 1.4 TRACE DSQ Installation CD Screen
12 | User’s Guide, Revision B
Read Me
TRACE DSQ or FOCUS DSQ_______________________________________________ About Your TRACE DSQ or FOCUS DSQ System
Figure i-2. Xcalibur 1.4 Home Page
Xcalibur software provides you with:
Instrument Configuration—after installation, access to this module is
outside the Xcalibur home page and located as a Windows desktop icon. Use
this module to configure your instruments for use with Xcalibur.
Instrument Setup—use this module to set up instrument methods and as
quick access to the Tune program for calibrating your instrument for
sensitivity and mass assignments.
The remaining Xcalibur modules fulfill your data acquisition and data
processing needs. Data Acquisition—store mass spectra peaks as they
evolve and monitor the total ion chromatogram (TIC) or the intensity of a
selected ion. Data Processing—integrate chromatograms, view mass
spectral data, compare spectra to reference libraries, quantify and qualify
data, and customize and automate reports.
About Your TRACE DSQ or FOCUS DSQ
System
The TRACE DSQ or FOCUS DSQ is a powerful quadrupole mass
spectrometer (MS mass spectrometer), with features benefiting those in the
chemical science industry—analysts, technicians, and chemists.
The TRACE DSQ system includes the TRACE DSQ mass spectrometer, the
TRACE GC, and the Xcalibur Ver. 1.4 or higher software on a computer.
The FOCUS DSQ system includes the FOCUS DSQ mass spectrometer, the
Focus GC, the Xcalibur Ver. 1.4 or higher software on a computer.
User’s Guide, Revision B
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Read Me
About Your TRACE DSQ or FOCUS DSQ System ______________________________________________ TRACE DSQ or FOCUS DSQ
Table i.1 TRACE DSQ System Specifications
Specifications
Features
Options
Certification: Electromagnetic Compatibility
(EMC) and FCC Class A
Electron Ionization (EI) with
Exchangeable Ion Volumes
Autosamplers: Liquid or
Headspace
Dimensions: l 68 cm x w 33 cm x h 44 cm
70 L/s Turbomolecular Pump
Chemical Ionization (CI)
Space Requirements: 2 m (6 ft)
RF-Only Curved Quadrupole Prefilter Data System Software
Options: NIST, Wiley, or
Pfleger-Maurer-Weber
Library, EnviroLab Forms,
ToxLab 2.0
Weight: 45 kg (98 lbs)
Ion Source Temperature up to
300 °C and GC Interface
Temperature up to 350 °C
Direct Probes System (DIP or
DEP)
Power: 120 V ac or 230 V ac, 50/60 Hz
Mass Range 1 – 1050 u (Unit Mass
Resolution)
Inlet valve
Temperature: 15-31 °C (59-88 °F)
Scan Rate up to 10,000 U/s
PPINICI (Pulsed Positive Ion,
Negative Ion CI)
Humidity: 40-80%
Full Scan, SIM, and Simultaneous
Full Scan/SIM
Programmable Temperature
Vaporizer or Cold On-Column
Injector
Post-Acceleration ±10 kV
Conversion Dynode
Turbomolecular Pumps:
250 L/s or 200/200 L/s SplitFlow
Xcalibur Ver. 1.4 Running Under
Microsoft® Windows® XP
Professional with Office XP
Ion Gauge with internal
vacuum protection safety
14 | User’s Guide, Revision B
Read Me
TRACE DSQ or FOCUS DSQ_______________________________________________ About Your TRACE DSQ or FOCUS DSQ System
Table i.2 Focus DSQ System Specifications
Specifications
Features
Options
Certification: Electromagnetic Compatibility
(EMC) and FCC Class A
Electron Ionization (EI) with
exchangeable Ion Volumes
Autosamplers: Liquid or
Headspace
Dimensions: l 68 cm x w 33 cm x h 44 cm
70 L/s Turbomolecular Pump
Data System Software
Options: NIST, Wiley, or
Pfleger-Maurer-Weber
Library, EnviroLab Forms,
ToxLab 2.0
Space Requirements: 2 m (6 ft)
RF-Only Curved Quadrupole Prefilter Direct Probes System (DEP
or DIP)
Weight: 45 kg (98 lbs)
Ion Source Temperature up to
300 °C and GC Interface
Temperature up to 350 °C
Inlet Valve
Power: 120 V ac or 230 V ac, 50/60 Hz
Mass Range 1– 1050 u (Unit Mass
Resolution)
Ion Gauge with internal
vacuum protection safety
Temperature: 15-31 °C (59-88 °F)
Scan Rate up to 10,000 u/s
Humidity: 40-80%
Full Scan, SIM, and Simultaneous
Full Scan/SIM
Post-Acceleration ±10 kV
Conversion Dynode
Xcalibur Ver. 1.4 Running Under
Microsoft® Windows® XP
Professional with Office XP
User’s Guide, Revision B
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Read Me
Safety Information _________________________________________________________________________ TRACE DSQ or FOCUS DSQ
Safety Information
Y
Read each instruction carefully before using the procedure.
Y
Follow all instructions marked on the product and in the manuals.
Y
Contact Tech Support to enroll in Instrument Training to prevent
accidents and to get maximum use of the instrument.
Y
Look for safety alerts (see the following) placed in this manual and on
the instrument to protect you from injury and the instrument from
damage.
CAUTION
Instrument Damage
This safety alert contains information to prevent instrument
damage or alert against practices that could possibly void the
manufacturer’s warranty.
CAUTION
Personal Injury
A CAUTION safety alert indicates a potential hazard exists
that MAY result in minor or moderate personal injury. These
safety alerts also warn against unsafe practices.
WARNING
Personal Injury
A WARNING safety alert indicates a potential hazard exists
that COULD result in death or serious personal injury.
DANGER
Personal Injury
A DANGER safety alert indicates a potential hazard exists that
WILL result in death or serious personal injury.
16 | User’s Guide, Revision B
Read Me
TRACE DSQ or FOCUS DSQ__________________________________________________________________________ Safety Information
Safety Alerts Found on Instruments
Read Manual
Please READ the manual before using to PREVENT an
imminent or potential hazard.
Personal Injury
Indicates imminent or a potential personal injury hazard exists.
Please use caution and consult the manual for details.
Burn Hazard
Indicates a hot surface. Make sure the part is room
temperature before touching.
Explosion Hazard
Indicates risk of explosion from flammable gas or liquid. Use
proper ventilation.
Shock Hazard
Indicates risk of electrical shock. Make sure the instrument is
unplugged.
Material Hazard
Wear impermeable laboratory gloves.
Eye Hazard
Wear safety glasses.
Lifting Hazard
Use proper lifting technique.
User’s Guide, Revision B
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Read Me
Typographical Conventions__________________________________________________________________ TRACE DSQ or FOCUS DSQ
Typographical Conventions
Typographical conventions describe how information is presented to our
readers.
For example, some text is specially formatted to help you quickly find
information contained in the document. For example,
Y
Bold is used for information required by or for the reader.
Y
References are emphasized in italics.
Y
Special terms are emphasized in bold and italic.
Notes provide important or helpful information about the current topic. In
addition, notes can contain troubleshooting information.
Changes to the Manual
Your comments and suggestions help us to correct errors and improve the
documentation. Please send your suggestions and comments to:
Editor, Technical Publications
Thermo Electron Corporation
2215 Grand Avenue Parkway
Austin, TX 78728
FAX: (512)-251-1547
E-mail: [email protected]
View and Download Manuals: http://www.tmqaustin.com/fr_manuals.htm
18 | User’s Guide, Revision B
NOTE: Notes are
contained in margin boxes
like this. They provide
important or helpful
information about the
current topic.
Getting
Connected
In This Chapter
1.1 Getting the Right Tools, pp. 21
1.2 Verifying Site Preparation, pp. 23
1.3 Unpacking the Instruments, pp. 24
1.4 Connecting the Gas Lines, pp. 26
1.5 Installing the Data System, pp. 31
1.6 Installing the Gas Chromatograph, pp. 33
1.7 Installing the Mass Spectrometer, pp. 38
1.8 Starting Up the System, pp. 45
1.9 Confirming Readbacks, pp. 47
1.10 Running Diagnostics, pp. 49
1.11 Checking the RF Dip Calibration, pp. 51
1.12 Checking the RF Gain Calibration, pp. 53
1.13 Checking the Air/Water Spectrum, pp. 56
1.14 Leak Checking, pp. 59
1.15 Checking the Initial Tune, pp. 60
1.16 Stabilizing the Instrument, pp. 64
1.17 Running EI Qualification Tests, pp. 66
1.18 Running CI Qualification Tests, pp. 70
1.19 Installing Upgrade Options, pp. 77
1.20 Providing Basic Training, pp. 78
Analyze
•
Detect
•
Measure
•
Control™
User’s Guide, Revision B
| 19
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Chapter 1, Getting Connected ______________________________________________________________ TRACE DSQ or FOCUS DSQ
This chapter contains step-by step instructions for factory trained Field Engineers
installing the TRACE DSQ or FOCUS DSQ system and for experienced users
finding it necessary to re-setup the instrument.
20 | User’s Guide, Revision B
NOTE: This chapter
is primarily written for
factory trained Field
Engineers.
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ___________________________________________________________________ 1.1 Getting the Right Tools
1.1 Getting the Right Tools
Use this table to determine the tools and parts you will need to take with you
to the installation. However, keep in mind some items are included with the
system.
Table 1-1
Required Tools
Tools Needed
• Brass back ferrules, Swagelok (PN A0101-02500)
• Brass front ferrules, Swagelok (PN A0101-08500)
• Brass nuts, Swagelok (PN A0101-15500)
• Cable, PC to mass spectrometer, 15 ft Ethernet crossover (PN
76396-0052)
• Cable, PC to GC (PN 230 980 00)
• Cable, GC to mass spectrometer remote start (PN 76396-0050)
• Capillary column, 5MS, 15 m, 0.25 mm i.d., 0.25 µm (PN 763173015)
• Column Measuring Tool (PN 119640-0550)
• Copper tubing, clean (PN 76381-0041 or Mueller Industries
refrigeration tubing, 1/8-in. o.d., 0.030-in. wall)
• CI ion volume (PN 119650-0230), if applicable
• Digital voltmeter (Fluke model 77 or equivalent)
• Dusting spray containing tetrafluoroethane (Falcon® Dust-Off®,
MicroCare® MicroBlast™, or equivalent)
• Flashlight, small hand-held
• Flow meter (ADM 1000 or equivalent)
• Forceps (PN 76360-0400)
• Gas filter, helium (PN A0950-01600)
• Gloves, clean, lint and powder free (medium PN 23827-0008, large
PN 23827-0009)
• Hex nut driver, 5.5 mm
User’s Guide, Revision B
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Chapter 1, Getting Connected
1.1 Getting the Right Tools __________________________________________________________________ TRACE DSQ or FOCUS DSQ
Table 1-1
Required Tools (Continued)
• Injector ferrule, for 0.25 mm column (PN 290 134 88)
• Ion volume tool (PN 119270-0001)
• I/R tool and guide bar, if applicable
• Leak detector (GL Sciences, Inc. Model LD-228 or equivalent)
• Magnifying glass
• Methanol or other suitable solvent
• Potentiometer adjustment tool
• Power cords with appropriate plugs
• Preinstallation Guide (PN 120156-0001)
• Scoring wafer (or sapphire scribe) to cut capillary column
• Screwdriver, flat blade
• Screwdriver, phillips #1
• Screwdriver, phillips #2
• Syringe, 10 µL, 70 mm needle (PN 365 001 03)
• Tape measure
• Teflon® thread tape
• Tissue, lint free
• Tubing cutter
• Test mix, octafluoronaphthalene and benzophenone
(PN 120150-TEST)
• Transfer line ferrule, 0.4 mm i.d. (PN A0101-18100)
• Wrench set, (Allen) 1.5, 2, 2.5, 3, 4, 5 mm (PN 3812-0100)
• Wrench set, (Open ended) 5–17 mm
• Wrench, (Adjustable) 12-in.
• Wrench, (Allen) 1/16-in.
• Wrench set, (Open ended) 1/4-in., 5/16-in., 7/16-in. (2), 9/16-in.,
1/2-in.
22 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ_________________________________________________________________ 1.2 Verifying Site Preparation
1.2 Verifying Site Preparation
Tools Needed
• Digital voltmeter (Fluke model 77 or equivalent)
• Preinstallation checklist from customer
• Preinstallation Guide (PN 120156-0001)
• Tape measure
Frequency
Day 1
Review the customer’s Preinstallation Checklist, keeping these items in mind:
Y
The customer is responsible for providing a completed Preinstallation
Checklist prior to the installation. If the checklist is lost or unreadable,
you can make a copy of A.2 Installation Checklist, pp. 131 and
determine if the installation can still be performed.
Y
All preinstallation requirements are listed in the TRACE DSQ
Preinstallation Guide (PN 120156-0001), so you only need to doublecheck that the proper workbench, power outlets, power cords,
temperature, and gases are available.
User’s Guide, Revision B
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Chapter 1, Getting Connected
1.3 Unpacking the Instruments_______________________________________________________________ TRACE DSQ or FOCUS DSQ
1.3 Unpacking the Instruments
Tools Needed
• Original purchase order
• Packing slip
• Installation report (supplied by service organization)
Frequency
Day 1
1
Unpack the instruments to confirm that each item the customer
ordered arrived without incident.
WARNING
Personal Injury
Lifting Hazard
Use proper lifting techniques, as several items are heavy.
2
3
Check for damage.
a.
Check carefully for obvious damage—tip indicators displaying a
tipped condition or evidence of rough handling.
b.
If external damage is apparent, note this fact on the installation
report, and describe briefly the extent of the damage. Have the
customer sign or initial next to your comments.
Confirm that the shipment is complete.
a.
Open and carefully remove all items from all shipping
containers. The packing list is located in the installation packet.
b.
Verify that each item listed on the customer's purchase order
and packing list is included with the shipment. If any items are
missing, make a note on the installation report and
immediately contact the factory Quality Representative at 512251-1400.
24 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ_______________________________________________________________ 1.3 Unpacking the Instruments
4
Set up the instruments.
Figure 1-1 TRACE DSQ System Layout (Front)
NOTE: Install optional
accessories, for example,
the autosamplers after the
installation and
qualification tests are
complete.
5
a.
Place the instruments from left to right, in this order: Mass
Spectrometer, GC, and the computer monitor, with the midtower CPU beside the monitor or under the bench.
b.
Place the rotary-vane pump on the floor. If placed on the
bench, excess vibration could affect instrument performance.
Inspect and store the shipping containers.
a.
Carefully inspect ALL boxes and packing materials for missed
items.
b.
Put packing materials back into shipping crates, and store the
empty boxes.
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Chapter 1, Getting Connected
1.4 Connecting the Gas Lines ________________________________________________________________ TRACE DSQ or FOCUS DSQ
1.4 Connecting the Gas Lines
Tools Needed
• Brass back ferrules, Swagelok (PN A0101-02500)
• Brass front ferrules, Swagelok (PN A0101-08500)
• Brass nuts, Swagelok (PN A0101-15500)
• Copper tubing, clean (PN 76381-0041 or Mueller
Industries refrigeration tubing, 1/8-in. o.d.,
0.030-in. wall)
• Gas filter, helium (PN A0950-01600)
• Leak detector (GL Sciences, Inc. Model LD-228 or
equivalent)
• Teflon® thread tape
• Tubing cutter
• Wrench, (Adjustable) 12-in.
• Wrench, (Open ended) 7/16-in. (2)
• Wrench, (Open ended) 1/2-in.
• Wrench, (Open ended) 9/16-in.
Frequency
Day 1
Assembly Tips:
Y
To insure safe, leak-tight connections, follow these instructions: B.1
Assembling Swagelok Fittings, pp. 134 before assembling the
swagelok fittings.
Y
Leave enough slack in the tubing so the GC and mass spectrometer
may be moved at least 40 cm (16-in.) away from each other. This
ensures that column connections and system maintenance are easily
performed.
Y
Forming Shock Loops with the tubing helps to dampen vibrations that
can loosen the fittings.
26 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ_________________________________________________________________1.4 Connecting the Gas Lines
1
Connect the GC Carrier Gas.
Figure 1-2 GC Carrier Gas Connections (Back)
2
Install the Carrier Gas Regulator and Gas Filter.
a.
Connect the Carrier Gas Regulator.
b.
Set the Gas Filter as close as possible to the GC. It should be
easy to access since it must be changed regularly. Do not put it
behind the GC where hot air from the exhaust vents will hit the
gas filter. Mount it to the side of the GC or MS or on top.
CAUTION
Instrument Damage
Do not loosen or remove caps from the Gas Filter until
PURGED lines are connected. Loosening or removing caps
early contaminates the filter.
3
4
Prepare the Supply Line.
a.
Run a Supply Line from the Carrier Gas Regulator to the Gas
Filter but do not remove the Caps on the Gas Filter.
b.
Run a Supply Line from the Gas Filter to the Carrier Gas
Input on the GC. Do not connect it to the Gas Filter or GC yet.
c.
Include a Shock Loop to isolate vibration and allow enough
tubing to move the GC at least 40 cm (16-in.)
Purge the Supply Line.
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Chapter 1, Getting Connected
1.4 Connecting the Gas Lines ________________________________________________________________ TRACE DSQ or FOCUS DSQ
a.
Turn on the Carrier Gas supply and set the Regulator to 5 psi
(35 kPa).
b.
Purge the line for 2-min to remove air and debris.
c.
Without turning off the Carrier Gas, quickly remove the Inlet
Cap from the Gas Filter and attach the Supply Line.
d.
Remove the Outlet Cap from the Gas Filter and attach the
Supply Line.
e.
Before attaching the Supply Line to the GC, purge it for
10-min.
f.
Attach the Supply Line to the Carrier Gas Input on the GC. If
the GC is equipped with an additional inlet, you can use a
Swagelok tee union to connect the Supply Line to the second
Carrier Gas Input.
5
Set the Carrier Gas Regulator to 80 psi (550 kPa).
6
(Upgrade Option) Connect the CI Reagent Gas, otherwise proceed
to Step 10 Leak check all the gas lines., pp. 30
If the system is equipped with the chemical ionization upgrade
option, you must connect CI Reagent Gas. Methane is the most
common CI Reagent Gas.
Figure 1-3 CI Reagent Gas Connections (Back)
7
Install the Reagent Gas Regulator to the Reagent Gas Cylinder.
28 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ_________________________________________________________________1.4 Connecting the Gas Lines
WARNING
Personal Injury
Explosive or Corrosive Gas Hazard
CI reagent gases are often flammable or corrosive. You must
vent the gas to a fume hood or other suitable exhaust. The CI
reagent gas supply line must be leak tight.
8
9
Prepare the Reagent Gas Supply Line.
a.
Run a Supply Line from the Reagent Gas Regulator to the CI
Reagent Gas Input located on the Mass Spectrometer.
b.
Do not connect it yet.
c.
Include a Shock Loop to isolate vibration and allow enough
tubing to move the Mass Spectrometer at least 40 cm (16-in.)
Purge the Supply Line.
a.
Route the Supply Line to a vent hood or other suitable
exhaust.
b.
Turn on the Reagent Gas supply and set the Regulator to
30 psi (200 kPa).
c.
Purge the line for about 15 seconds to remove air and debris.
d.
Set the Reagent Gas Regulator to 5-10 psi (35-70 kPa). Lower
supply pressures produce more stable CI reagent gas flows.
e.
Turn off the Reagent Gas supply.
f.
Attach the Supply Line to the CI Reagent Gas Input on the
Mass Spectrometer.
g.
Turn on the Reagent Gas supply.
CAUTION
Instrument Damage
Do not exceed 35 psi (240 kPa) or damage to the CI Reagent
Gas Flow Module results.
User’s Guide, Revision B
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Chapter 1, Getting Connected
1.4 Connecting the Gas Lines ________________________________________________________________ TRACE DSQ or FOCUS DSQ
10
Leak check all the gas lines.
a.
Use an electronic hand-held leak detector (sensitivity: helium
0.01 mL/min) to check all gas fittings for leaks.
CAUTION
Instrument Damage
Do not use liquid soap leak detectors (such as Snoop) to
check for leaks. Liquid soap leak detectors may contaminate
your system.
b.
Leak check the Carrier Gas Supply Line.
c.
Leak check the Reagent Gas Supply Line.
30 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ________________________________________________________________ 1.5 Installing the Data System
1.5 Installing the Data System
The data system is the computer and Xcalibur software.
Tools Needed
• Cable, PC to Mass Spectrometer, 15 ft Ethernet
crossover (PN 76396-0052)
• Cable, serial, PC to GC (PN 230 980 00)
Frequency
Day 1
1
Setup the Data System as demonstrated in Figure 1-4.
Figure 1-4 Data System Power Connections (Back View)
a.
Plug the power cords for the computer, monitor, and printer
(upgrade option) into Wall Outlet #3.
b.
Set up and connect the keyboard, mouse, monitor cable, and
printer cable if applicable.
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Chapter 1, Getting Connected
1.5 Installing the Data System _______________________________________________________________ TRACE DSQ or FOCUS DSQ
2
3
Connect the GC serial cable and the mass spectrometer’s Ethernet
cables.
a.
Connect the GC Serial Cable to the computer’s COM1 port.
b.
Connect the Ethernet Cable, which is supplied with the Mass
Spectrometer to the computer’s Ethernet port. The
computer has two Ethernet ports. The Ethernet port on a card
is for the instrument, whereas, the Ethernet port built into the
motherboard may be used for a local area network.
Turn on the computer, monitor, and printer.
a.
Set the time and date.
b.
Set up passwords, if desired.
c.
Test the printer and install drivers1 as necessary.
Computers purchased from the Thermo Electron Corporation factory
have been fully setup and tested with the Xcalibur 1.4 data system
software. However, if you experience the rare situation where you
need to reinstall software on a new computer or new hard drive,
follow these instructions: B.6 Reinstalling the Data System, pp. 143.
1.Tune reports will not display if a printer driver is not installed.
32 | User’s Guide, Revision B
NOTE: Be sure you use
the supplied shielded,
crossover cable to connect
to the instrument. If you
need a longer cable, you
can connect a standard
Category 5 Ethernet
cable between the
computer and the supplied
cable.
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ__________________________________________________________ 1.6 Installing the Gas Chromatograph
1.6 Installing the Gas Chromatograph
Tools Needed
• Capillary column, 5MS, 15 m, 0.25 mm i.d., 0.25 µm
(PN 76317-3015)
• Gloves, clean, lint and powder free
• Injector ferrule, for 0.25 mm column
(PN 290 134 88)
• Leak detector (GL Sciences, Inc., model LD-228, or
equivalent)
• Magnifying glass
• Methanol or other suitable solvent
• Scoring wafer (or sapphire scribe) to cut capillary
column
• Tissue, lint free
• Wrench, (Open ended) 6 mm
Frequency
Day 1
1
Check the GC configuration against the sales order.
2
Connect the Transfer Line Cable to the left of the GC.
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Chapter 1, Getting Connected
1.6 Installing the Gas Chromatograph _________________________________________________________ TRACE DSQ or FOCUS DSQ
Figure 1-5 Power Connections (Back View)
3
Plug the power cord into the back of the GC and then into Wall
Outlet #2.
4
Connect the Column to the Injector.
The test column is conditioned at the factory and requires no
additional conditioning.
Focus GC users must set up instrument parameters using the virtual
Keypad button located on the Xcalibur Home Page.
Figure 1-6 Focus GC Instrument Status View
34 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ__________________________________________________________ 1.6 Installing the Gas Chromatograph
Refer to the Focus GC User’s Manual for instructions on using the
keypad.
The arrow in Figure 1-7, points to an exploded view of the injector.
.
1
6
5
2
3
4
4
1
Injector
4
Column
2
Injector Ferrule
5
Column Outlet
3
Injector Nut
6
Transfer Line
Figure 1-7 GC Injector (Front View)
NOTE: Wear clean, lint
and powder free gloves
when you handle the
Column and Injector
Ferrule.
a.
Unwind the Column (4) about a half-turn.
b.
Wipe about 100 mm (4-in.) of the Column (4) with a tissue
soaked in methanol.
c.
Insert the Column (4) through the Injector Nut (3) and Ferrule
(2) open-end-up.
d.
Wipe the Column (4) again with a tissue soaked in methanol.
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Chapter 1, Getting Connected
1.6 Installing the Gas Chromatograph _________________________________________________________ TRACE DSQ or FOCUS DSQ
5
6
e.
Score and then break the Column (4) about 2.5 cm (1-in.) from
the end with a Scoring Wafer. With the magnifying glass,
check for an even, flat cut. Repeat if necessary.
f.
Insert the Column (4) into the Injector (1) so that the end of
the Column (4) is the proper distance from the back of the
Injector Nut (3). Proper distances are as follows: splitless =
64 mm, split = 40 mm, PTV = 30 mm.
g.
Finger-tighten the Injector Nut (3) and then give it an
additional 1/4-turn with the wrench.
h.
Score and then break the Column Outlet (5) about 2.5 cm
(1-in.) from the end with a Scoring Wafer.
i.
Turn on the GC.
Setup the GC.
a.
Set the Oven, Injector, and Transfer Line temperatures to
30 °C.
b.
Set the Injector flow to 1.0 mL/min.
c.
Turn the Vacuum Compensation Off (under the Right, or Left
Carrier menu).
d.
Dip the Column Outlet (5) in a small vial of methanol. Bubbles
indicate there is flow through the Column (4).
e.
Allow the Column (4) to purge for at least 10-min.
Perform a Column Characterization.
a.
Raise the Oven and Injector temperatures to 50 °C and allow
them to stabilize.
b.
Run Column Eval key to characterize the column. This takes
several minutes.
c.
Expect a K-factor of about 0.7 – 0.9 for a 15 m, 0.25 mm i.d.
column. If the column does not report a K-factor within this
range or within 0.1 units of the previous stored value, check for
a leak or broken column using the leak detector. The K-factor is
a measured resistance for the Column. A K-factor that is too
low may indicate a leak in the system, while a K-factor that is
too high may indicate a blockage.
36 | User’s Guide, Revision B
NOTE: Sliding a Septum
on the Column before the
Injector Nut will help you
measure the proper
distance between the Nut
and the end of the
Column. If you want to
remove it later, cut the
Septum from the center to
the edge.
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ__________________________________________________________ 1.6 Installing the Gas Chromatograph
CAUTION
Instrument Damage
Do not raise the oven temperature until you are sure the
system is leak free. At temperatures above 100 °C, the column
will be destroyed if exposed to oxygen.
d.
7
Raise the Oven temperature to 150 °C and allow it to stabilize.
Perform a column Leak Check.
a.
Run the automated Leak Check on the GC.
b.
If the report indicates a leak, look for and fix leaks at all the
fittings in the GC using the leak detector.
c.
Repeat the Column Evaluation and Leak Check until no leaks
are indicated.
d.
Raise the Injector temperature to 220 °C.
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Chapter 1, Getting Connected
1.7 Installing the Mass Spectrometer _________________________________________________________ TRACE DSQ or FOCUS DSQ
1.7 Installing the Mass Spectrometer
Tools Needed
• Cable, GC to Mass Spectrometer remote start (PN
76396-0050)
• Column Measuring Tool (PN 119640-0550)
• Gloves, clean, lint and powder free
• Leak detector, hand-held electronic (GL Sciences Inc.,
model LD-228, or equivalent)
• Magnifying glass
• Methanol or other suitable solvent
• Potentiometer adjustment tool
• Scoring wafer (or sapphire scribe) to cut capillary
column
• Tissue, lint free
• Transfer line ferrule, 0.4 mm i.d. (PN A0101-18100)
• Wrench, Open ended 5/16-in.
• Wrench, 2, Open ended 7/16-in.
Frequency
Day 1
1
Install the Rotary-Vane Pump.
a.
Set the Rotary-Vane Pump on the floor behind the system.
The pump should not be placed on the workbench as it
produces excessive vibration that may affect the performance
of the system.
38 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ__________________________________________________________ 1.7 Installing the Mass Spectrometer
1
14
2
13
3
12
4
11
5
6
7
8
10
9
1
Foreline Vacuum Hose
8
Drain Plug
2
Inlet Port
9
MIN (minimum level mark)
3
Gas-Ballast Control
10
Mode Selector
4
Oil Filler Plugs
11
On/Off Switch
5
Outlet Port
12
Handle
6
MAX (maximum level mark)
13
Voltage Indicator
7
Oil-Level Sight-glass
14
Electrical Inlet Connector
Figure 1-8 Rotary-Vane Pump
b.
Check the Voltage Indicator (13) to verify the Rotary-Vane
Pump is configured for the same voltage as the Mass
Spectrometer.
c.
Remove one of the Oil Filler Plugs (4).
d.
Add oil to the Oil Filler Plug (4) opening half way between the
MIN (9) and MAX (6) level marks.
e.
If the oil level goes above the MAX (6) level mark, remove the
Drain Plug (8) and drain the excess oil from the pump.
f.
Replace the Oil Filler Plug (4).
g.
Connect the Foreline Vacuum Hose (1).
h.
Connect the Outlet Port (5) to a suitable exhaust.
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Chapter 1, Getting Connected
1.7 Installing the Mass Spectrometer _________________________________________________________ TRACE DSQ or FOCUS DSQ
Figure 1-9 Rotary-Vane Pump Power Connection (Back View)
i.
2
3
Plug the power cord into the Mech Pump plug located on the
back of the Mass Spectrometer.
[Upgrade Option] Repeat this procedure for a second Rotary-Vane
Pump, which is included with the Sample Probe upgrade option.
a.
Plug the second pump into the Accessory plug on the back of
the Mass Spectrometer.
b.
Make sure the Inlet Valve Vacuum Hose exits the Mass
Spectrometer just above the Foreline Vacuum Hose.
Connect the transfer line, Ethernet, and remote start cables.
a.
Confirm the Transfer Line Cable is plugged into the left side of
the GC.
b.
Carefully push the GC next to the Mass Spectrometer, making
sure the Transfer Line extends into the GC.
c.
Connect the Ethernet cable leading from the computer to the
back of the Mass Spectrometer.
d.
Connect the Remote Start Cable to the GENERIC H/S port
located on the GC to the GC START port located on the Mass
Spectrometer.
40 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ__________________________________________________________ 1.7 Installing the Mass Spectrometer
4
5
Inspect the Mass Spectrometer.
a.
Remove the covers (front, top, and left side) from the Mass
Spectrometer. Detailed instructions for removing covers are in
the TRACE DSQ Hardware Manual (PN 120156-0002).
b.
Remove the shipping foam that secures the Vacuum Manifold
Cover. Store the foam with the Mass Spectrometer
accessories in case the instrument needs to be moved in the
future.
c.
Check the Mass Spectrometer configuration against the sales
order.
d.
Look for anything that might have come loose during shipping.
e.
Verify that the Ion Volume is fully inserted.
You can use the Ion Volume Tool to push on
the Ion Volume. The Ion Volume is held
loosely in the Ion Source at room temperature
so that it does not seize when the source
heats to 300 °C.
Ion Volume
Connect the GC Column to the MS Transfer Line.
a.
Lower the oven temperature to 30 °C and allow it to cool
before continuing.
CAUTION
Personal Injury
Burn Hazard
The oven and transfer line may be hot. Allow them to cool to
room temperature before touching them. Do not touch the hot
injector.
b.
Unwind about one-turn of the Column from the end of the
Column Outlet.
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Chapter 1, Getting Connected
1.7 Installing the Mass Spectrometer _________________________________________________________ TRACE DSQ or FOCUS DSQ
.
2
1
3
4
5
1
Column Measuring Tool
4
Column
2
Transfer Line Ferrule
5
Septum
3
Transfer Line Nut
Figure 1-10 Column Measuring Tool and Transfer Line
c.
Wipe about 300 mm (12-in.) of the Column (4) with a tissue
soaked in methanol.
d.
Insert the Column (4) through the Septum1 (5), Transfer Line
Nut (3), and Ferrule (2). Wipe the Column (4) again with a
tissue soaked in methanol.
e.
Screw the Transfer Line Nut (3) onto the Column Measuring
Tool (1).
f.
Push the Column (4) passed the end of the Column
Measuring Tool (1), then score and break the end of the
Column (4) with a Scoring Wafer. Using a magnifying glass,
check for an even, flat cut. Repeat if necessary.
g.
Pull the Column (4) back so that it is flush with the end of the
Column Measuring Tool (1).
h.
Tighten the Transfer Line Nut (3).
i.
Slide the Septum (5) up to the back of the Transfer Line Nut
(3).
j.
Remove the Column (4), Transfer Line Nut (3) and Ferrule (2)
from the Column Measuring Tool (1).
1.Sliding a Septum on the Column before the Transfer Line Nut will help you measure the
proper distance between the nut and the end of the column. If you want to remove it later,
cut the Septum from the center to the edge.
42 | User’s Guide, Revision B
NOTE: Wear clean, lint
and powder free gloves
when you handle the
Column and Transfer Line
Ferrule.
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ__________________________________________________________ 1.7 Installing the Mass Spectrometer
.
1
4
3
2
1
Septum
3
Transfer Line Union
2
Transfer Line Nut
4
Transfer Line
Figure 1-11 Transfer Line (Front)
6
k.
Insert the Column into the Transfer Line (4). Be careful not to
move the Septum (1). For proper operation, the Column must
extend approximately 1 mm passed the end of the Transfer
Line.
l.
Tighten the Transfer Line Nut (2) and the Transfer Line Union
(3).
Condition the Transfer Line Ferrule.
Graphite/Vespel ferrules like the Transfer Line Ferrule require
conditioning to insure a leak tight seal.
a.
Raise the oven temperature to 300 °C.
b.
Wait for 10-min.
c.
Lower the oven temperature to 30 °C and allow it to cool
before continuing.
CAUTION
Personal Injury
Burn Hazard
The oven may be hot. Allow it to cool to room temperature
before opening it. The injector will still be hot, so don’t touch it!
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Chapter 1, Getting Connected
1.7 Installing the Mass Spectrometer _________________________________________________________ TRACE DSQ or FOCUS DSQ
d.
7
Re-tighten the Transfer Line Nut (2) and the Transfer Line
Union (3).
Setup the GC.
a.
Make sure the Column does not have any sharp bends and
that it does not touch any metal objects or walls inside the
Oven.
b.
Raise the Oven temperature to 40 °C.
c.
Turn the Vacuum Compensation On (under the Right, or Left
Carrier menu).
8
Replace the covers to the MS, in this order: left, top, and front.
9
Plug the power cord for the Mass Spectrometer into Wall Outlet #1.
Figure 1-12 Mass Spectrometer Power Connection (Back)
10
Double-check all vacuum, gas, and electrical connections.
44 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ___________________________________________________________________ 1.8 Starting Up the System
1.8 Starting Up the System
Tools Needed
None
Frequency
Day 1
1
Turn the Mass Spectrometer on by setting the Main Circuit Breaker
to ON (I) to:
•
Turn on the Rotary-Vane Pump
•
Allow the Fore pressure to reach the proper operating pressure
•
Turn on the Turbomolecular Pump
CAUTION
Instrument Damage
Damage occurs if you turn on the mass spectrometer without
column flow. This forces air to be drawn through the column,
damaging it. This large air leak into the mass spectrometer will
also cause the ion source to require cleaning.
2
Set the Transfer Line to 250 °C.
3
Start Xcalibur to establish communication and initialize each
instrument configured for use.
a.
Wait about 60-seconds for the Mass Spectrometer to initialize.
b.
Then, look for Xcalibur to display a screen “There is not
sufficient vacuum.”
c.
Choose Ignore so you can continue to monitor the instrument
status.
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Chapter 1, Getting Connected
1.8 Starting Up the System __________________________________________________________________ TRACE DSQ or FOCUS DSQ
d.
4
If you see any other error messages, check that all instruments
are connected and turned on. Also, consult the
Troubleshooting section of the TRACE DSQ or FOCUS DSQ
Hardware Manual (PN 120156-0002).
Start Tune.
Click the Instrument Tune desktop icon
desktop.
46 | User’s Guide, Revision B
from the Windows
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ___________________________________________________________________ 1.9 Confirming Readbacks
1.9 Confirming Readbacks
Tools Needed
None
Frequency
Day 1
Once the instruments have been initialized, check the Mass Spectrometer
Instrument Status Tabs to confirm the vacuum and heater readbacks are
OK before running diagnostics. Otherwise, improper vacuum will cause
damage to the filament during the Ionization/Lens Test.
Information contained in the Instrument status tabs let you watch the Mass
Spectrometer heat up and pump down.
1
In the Tune window, select the Vacuum tab to validate the Fore
Pressure, Turbo Pump status, and Ion Gauge status.
a.
Verify that the Fore Pressure is less than 300 mTorr.
.
Figure 1-13 TRACE DSQ Vacuum Status
NOTE: If the fore
pressure is not less than
300 mTorr within 5-min,
there is a large leak
which must be fixed
immediately.
It should reach this level within 5-min after turning on the system. If it
doesn’t, there is a large leak which must be fixed immediately.
Consult the TRACE DSQ or FOCUS DSQ Hardware Manual
(PN 120156-0002) for troubleshooting a large leak.
b.
Make sure the turbomolecular Pump Switch is ON. Within
5-min after turning the turbomolecular pump, the readback for
the Turbo Pump should be OK indicating it has reached
operating speed.
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Chapter 1, Getting Connected
1.9 Confirming Readbacks___________________________________________________________________ TRACE DSQ or FOCUS DSQ
c.
2
Wait until the Ion Gauge Pressure is less than 1 x 10 -4 Torr. If
the system is not equipped with an ion gauge, wait at least
15-min.
Select the Heaters tab to confirm the Ion Source Temp to 200 oC.
Figure 1-14 Mass Spectrometer Heaters Readbacks
Use this tab to view the temperature. To set the temperature go to
Tune | Instrument | Set Temperatures to display the Temperature
Settings screen. Then Set the Ion to 200 and select OK to return to
the Tune window.
48 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ____________________________________________________________________ 1.10 Running Diagnostics
1.10 Running Diagnostics
Tools Needed
None
Frequency
Day 1
After confirming that the heaters and vacuum readbacks are OK, run Xcalibur
diagnostics to test other internal components for functionality.
CAUTION
Instrument Damage
Make sure the vacuum readbacks are OK before running
diagnostics. Otherwise, improper vacuum will cause damage
to the filament during the Ionization/Lens Test.
1
Open the Tune window Diagnostic screen.
Select Tune | Diagnostics | Run Tests to display the Diagnostics
screen.
Figure 1-15 Tune Window Diagnostics Screen
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Chapter 1, Getting Connected
1.10 Running Diagnostics ___________________________________________________________________ TRACE DSQ or FOCUS DSQ
2
Run each test listed in the Diagnostic Tests group box individually so
that you can closely monitor each test’s readbacks and note any
failures.
If a diagnostic fails, then view the help topic for that diagnostic.
However, don’t run the RF Dip and RF Gain Calibrations tests until
the next procedure.
50 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ__________________________________________________________ 1.11 Checking the RF Dip Calibration
1.11 Checking the RF Dip Calibration
Tools Needed
None
Frequency
Day 1
NOTE: Run this test
only after the heaters
and vacuum have
stabilized.
After you have finished running the Xcalibur diagnostics from the Diagnostics
Tests group box and they have all passed, then it’s time to check the RF Dip
Calibration. However, run this test only after the heaters and vacuum have
stabilized.
1
Open the Tune window Diagnostic screen.
Select Tune | Diagnostics | Run Tests to display the Diagnostics
screen.
Figure 1-16 Tune Diagnostic Screen
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Chapter 1, Getting Connected
1.11 Checking the RF Dip Calibration _________________________________________________________ TRACE DSQ or FOCUS DSQ
2
Select the RF Dip Calibration button to display the RF Dip Calibration
screen.
NOTE: The RF Dip
Calibration looks different
than the Polaris Q RF Dip
calibration. This is normal
as the TRACE DSQ use a
more comprehensive
algorithm. The RF
frequency is set correctly if
the Setpoint and Actual are
within 0.2 kHz.
Figure 1-17 RF Dip Calibration Screen
3
a.
Allow the display to stabilize for approximately 15 seconds.
b.
Verify that the Setpoint and Actual are within 0.2 kHz.
c.
If they are not, follow these instructions:B.5 Adjusting the RF
Dip Calibration, pp. 142.
Press Close to return to the Diagnostics screen.
52 | User’s Guide, Revision B
NOTE: If the Rod DC
Test Fails after the RF Dip
Calibration and RF Gain
Calibration pass, follow the
instructions in B.3
Adjusting the RF Null, pp.
138.
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ_________________________________________________________ 1.12 Checking the RF Gain Calibration
1.12 Checking the RF Gain Calibration
Tools Needed
• Potentiometer adjustment tool
• Wrench, (Allen) 3 mm
Frequency
Day 1
After you see a successful RF Dip Calibration, check the RF Gain Calibration.
1
Open the Tune window Diagnostic screen.
Select Tune | Diagnostics | Run Tests to display the Diagnostics
screen.
Figure 1-18 Tune Diagnostic Screen
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Chapter 1, Getting Connected
1.12 Checking the RF Gain Calibration ________________________________________________________ TRACE DSQ or FOCUS DSQ
2
Select the RF Gain Calibration button to display the RF Gain
Calibration screen and run the RF Gain Calibration test.
1
2
3
4
1
Target RF (blue line)
3
RF Modulation (white line)
2
Detected RF (yellow line)
4
m/z 1050 (red/purple vertical line)
Figure 1-19 RF Gain Calibration Screen
This screen plots these values versus m/z:
•
Target RF (1) ramp is linear and corresponds to the ramp used to
scan the quadrupole to produce a mass spectrum.
•
Detected RF (2) measures the actual RF applied to the
quadrupole. It must be a linear ramp all the way to the m/z 1050
line (4).
•
RF Modulation (3) measures the power output of the RF
generator. It is usually slightly curved.
a.
Allow the display to stabilize for approximately 15 seconds.
b.
Verify that the Detected RF is linear to the m/z 1050.
If the Detected RF is not linear to the m/z 1050, the mass calibration
may be incorrect. At this point, check the mass calibration by viewing
the calibration gas spectrum (detailed instructions are in Step 4 Check
the calibration gas spectrum., pp. 61.)
If the masses are not within 2 m/z of the theoretical m/z, wait until the
automatic tune calibration is finished to pass the RF Gain Calibration
Diagnostic.
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TRACE DSQ or FOCUS DSQ_________________________________________________________ 1.12 Checking the RF Gain Calibration
If the Detected RF shows noise or spikes, shut down the instrument
and check for dust or fibers on the quadrupole and prefilter, or check
for loose connections between the RF Coil, Low Pass Filter, and
Quadrupoles.
3
Select the Close button to return to the Diagnostics screen.
4
Press Close to return to the Tune window.
5
Proceed to step1.13 Checking the Air/Water Spectrum, pp. 56.
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Chapter 1, Getting Connected
1.13 Checking the Air/Water Spectrum________________________________________________________ TRACE DSQ or FOCUS DSQ
1.13 Checking the Air/Water Spectrum
Tools Needed
None
Frequency
Day 1
After successfully completing the RF Gain Calibration test, it’s a good time to
check the air/water spectrum to look for leaks.
1
In the Tune window, select the Vacuum tab from the Status display.
Figure 1-20 Tune Window, Vacuum Tab
a.
Verify that the Fore Pressure is less than 50 mTorr. For some
instruments that have been exposed to high humidity while
vented for an extended period of time, this may require several
hours. This is common for an instrument shipped with the 200/
200 L/s pumping option, because the large surface of the
turbomolecular pump requires time to outgas.
b.
If the system has an ion gauge, verify that the Ion Gauge
Pressure is less than 7 x 10-5 Torr
c.
If the pressure is too high, there is a leak that must be fixed
immediately. Refer to the TRACE DSQ or FOCUS DSQ
Hardware Manual (PN 120156-0002) for troubleshooting
instructions.
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TRACE DSQ or FOCUS DSQ________________________________________________________ 1.13 Checking the Air/Water Spectrum
2
3
Make sure the calibration gas has been off for at least 5-min.
Because, the calibration gas flow module introduces air into the
instrument.
Check the Air/Water Spectrum.
a.
Open the autotune.dsqtune tune file by selecting File | Open
| autotune.dsqtune.
b.
Select Experiment | Full Scan and scan from m/z 10 to 90.
c.
Select Instrument | Fil/Mult/Dyn On to turn the instrument
on.
d.
Compare the Air/Water Spectrum with those in Figure 1-21
through Figure 1-23to determine whether or not you have a
leak.
Usually, if m/z 28 is larger than m/z 18 there is a leak. refer to
procedure 1.14 Leak Checking, pp. 59.
NOTE: Figure 1-21
through Figure 1-23 were
acquired with a 250 L/s
turbomolecular pump
system. Relative
abundance of air/water
ions can vary depending
upon the pump option and
the amount of air in the
helium supply. Nitrogen is
typically the most
abundant contaminant in
any helium supply.
.
Figure 1-21 Air/Water Spectrum (No Leak)
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Chapter 1, Getting Connected
1.13 Checking the Air/Water Spectrum________________________________________________________ TRACE DSQ or FOCUS DSQ
.
Figure 1-22 Air/Water Spectrum (Small Leak)
.
Figure 1-23 Air/Water Spectrum (Large Leak)
58 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ_________________________________________________________________________ 1.14 Leak Checking
1.14 Leak Checking
Tools Needed
• Dusting spray containing tetrafluoroethane (Falcon®
Dust-Off®, MicroCare® MicroBlast™, or equivalent)
• Leak detector (GL Sciences, Inc. Model LD-228 or
equivalent)
Frequency
When the Air/Water spectrum indicates m/z 28 ion is larger
than m/z 18
1
2
Check for external leaks.
a.
Use the leak detector to check all gas fittings for leaks. These
include the carrier gas and CI reagent gas lines. Also check the
capillary column connection to the injector. Even a small leak in
a gas line can allow air to enter.
b.
Use the leak detector to check the septum for a leak. Replace if
necessary.
Check for vacuum leaks.
a.
Scan from m/z 50 to 100 by selecting Experiment | Full Scan.
b.
Spray dusting spray near the suspected leak while monitoring
for an increase in m/z 69 and 83. Common leaks occur at the
transfer line capillary column connection and the vacuum
manifold cover.
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Chapter 1, Getting Connected
1.15 Checking the Initial Tune________________________________________________________________ TRACE DSQ or FOCUS DSQ
1.15 Checking the Initial Tune
Tools Needed
None
Frequency
Day 1
After a successful Air/Water check, check the initial tune of the system.
1
Make sure the instrument is on, select Instrument | System On.
2
Make sure the filament is on, select Instrument | Fil/Mult/Dyn On.
3
Check the background spectrum.
a.
Select Experiment | Full Scan and scan from m/z 10 to 650.
b.
Verify that the background spectrum is similar to Figure 1-24.
The background may be higher the first day after being
pumped down.
60 | User’s Guide, Revision B
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ________________________________________________________________ 1.15 Checking the Initial Tune
Figure 1-24 Background Spectrum (m/z 10 - 650)
4
Check the calibration gas spectrum.
a.
Select Experiment | Full Scan and scan from m/z 50 to 650.
b.
Select Instrument | Calibration Gas | EI/NICI to turn the EI
Calibration Gas on.
c.
Verify that all peaks are present (m/z 69, 131, 264, 414, and
502) as in Figure 1-25.
Figure 1-25 Calibration Gas Spectrum (m/z 50 - 650)
5
Run a Full Automatic Tune if ions are within ±12.5% or ±20 m/z
units, whichever is smaller, then run a full automatic tune to calibrate
the instrument.
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1.15 Checking the Initial Tune________________________________________________________________ TRACE DSQ or FOCUS DSQ
www.thermo.com
a.
Run an Automatic Tune by selecting Tune | Automatic Tune
to display the Automatic Tune screen. Select these options:
Figure 1-26 Automatic Tune - Full
6
b.
Select the options indicated in Figure 1-26 Automatic Tune Full. Except, select the Resolution Calibration option for
Negative Ions only if the instrument will be used for negative
chemical ionization. This calibration may require that the mass
spectrometer gain be increased from 1 x 105 to 3 x 105 in order
to pass. Only increase the mass spectrometer gain if the
calibration fails on the first attempt. The tune report will display
m/z -452 when this calibration has been run. It is normal for
this ion to display poor resolution. The resolution for negative
ions can be tuned once the instrument is switched to Negative
Chemical Ionization mode.
c.
Press the Advanced button to access the Advanced
Calibration screen. Using the Advanced Calibration Screen
lets you compensate for a dirty instrument by adjusting the
lens values, while still allowing you to use full tuning options.
For example, if you adjust the lenses by resetting the Prefilter
Offset and Ion Offset values, you can save these values to the
Cal_tune.dsqtune file. And then after getting a successful
tune, return to the Advanced Calibration screen to press the
Restore button, which restores the factory default tuning
factors which are optimal for a clean instrument.
Run a Manual Calibration if ions are further away by selecting Tune
| Manual Calibration to display the Manual Calibration screen.
However, this option is only available if you selected Enable manual
calibration (located on the Service tab) during Instrument
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TRACE DSQ or FOCUS DSQ________________________________________________________________ 1.15 Checking the Initial Tune
Configuration. See the Tune Help Topic: Manual Calibration Screen
for detailed information.
7
Press OK to return to the Tune window.
8
Turn the filament off by selecting Instrument | Fil/Mult/Dyn Off.
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Chapter 1, Getting Connected
1.16 Stabilizing the Instrument _______________________________________________________________ TRACE DSQ or FOCUS DSQ
1.16 Stabilizing the Instrument
Tools Needed
None
Frequency
End of Day 1
Once the initial tune looks good, allow the system to bake-out the vacuum to
stabilize, and allow the gas lines to purge before performing the installation
qualification tests tomorrow.
1
Replace any covers that were removed.
2
Set the CI Reagent Gas Flow to 2.5 mL/min.
3
Perform a column leak check.
a.
Run the automated Leak check on the GC.
b.
If the report indicates a leak, then look for and fix leaks at all
the fittings in the GC using the leak detector.
c.
Repeat this step, until no leaks are indicated.
CAUTION
Instrument Damage
Do not raise the oven temperature until you are sure the
system is leak free. At temperatures above 100 °C, the column
will be destroyed if exposed to oxygen.
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Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ________________________________________________________________ 1.16 Stabilizing the Instrument
4
Set the GC Oven Temperature to 250 ºC.
5
Set the Ion Source Temperature to 250 ºC.
6
Allow the CI Reagent Gas Flow to purge.
7
Allow the Ion Source and Oven to bake-out overnight.
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Chapter 1, Getting Connected
1.17 Running EI Qualification Tests ___________________________________________________________ TRACE DSQ or FOCUS DSQ
1.17 Running EI Qualification Tests
Tools Needed
• Syringe, 10 µL, 70 mm needle (PN 365 001 03)
• Test mix, octafluoronaphthalene and benzophenone
(PN 120150-TEST)
Frequency
Beginning of Day 2
Instrument Methods are already loaded inside the computer for use in
running the qualification tests. These methods were used during the factory
qualification tests. They can be found in \Xcalibur\Examples\Methods and are
organized by GC configuration. Choose the *EI.meth for EI.
1
Set the Ion Source Temperature to 200 ºC.
2
Set the GC Oven Temperature to 40 ºC.
3
Turn off the CI Reagent Gas.
4
Wait at least 30-min for the system to stabilize.
5
Check Air/Water Spectrum.
a.
Scan from m/z 10 to 90 by selecting Experiment | Full Scan.
b.
Turn instrument on by selecting Instrument | Fil/Mult/Dyn
On.
c.
Compare the Air/Water Spectrum with those in Figure 1-21
through Figure 1-23 to determine whether or not you have a
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TRACE DSQ or FOCUS DSQ____________________________________________________________ 1.17 Running EI Qualification Tests
leak. Usually, if m/z 28 is larger than m/z 18 there is a leak, go
to procedure 1.14 Leak Checking, pp. 59.
NOTE: When archiving
data, include the Mass
Spectrometer serial
number and sales order
number.
d.
6
7
8
Archive the Air/Water Spectrum.
Check Background Spectrum.
a.
Scan from m/z 10 to 650 by selecting Experiment | Full Scan.
b.
Verify that the Background Spectrum is similar to Figure 1-24
Background Spectrum (m/z 10 - 650).
c.
Archive the Background Spectrum.
Check the Calibration Gas Spectrum.
a.
Scan from m/z 50 to 650 by selecting Experiment | Full Scan.
b.
Turn the EI Calibration Gas On.
c.
Verify that all peaks are present (m/z 69, 131, 264, 414, and
502) as in Figure 1-25 Calibration Gas Spectrum (m/z 50 - 650).
Run a Full Automatic Tune.
a.
Run a full automatic tune by selecting Tune | Automatic Tune
to display the Automatic Tune Screen.
Figure 1-27 Automatic Tune - Full
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1.17 Running EI Qualification Tests ___________________________________________________________ TRACE DSQ or FOCUS DSQ
b.
Check the tests indicated in Figure 1-27 Automatic Tune - Full
and select OK.
c.
When finished, archive the Tune Report.
d.
Turn the instrument off by selecting Instrument | Fil/Mult/
Dyn Off.
e.
Save the tune file for the EI Qualification Test by changing the
emission current to 350 µA in the AutoTune tune file and save
it as EI.dsqtune.
f.
Select OK to return to the Tune window.
9
Inject 1 µL of a 1 pg/µL solution of octafluoronaphthalene using
*EI.meth as the instrument method.
10
Review the results.
a.
Look at the background subtracted spectrum in Qual Browser.
b.
Archive the chromatogram and spectrum.
c.
Use the Signal-to-noise Calculator (accessible from a
shortcut on the desktop) to display a mass chromatogram for
the range 271.5-272.5.The minimum Signal-to-Noise Ratio
should be:
d.
11
•
25:1– 70 L/s pump
•
50:1– 250 L/s pump
•
50:1– 200/200 L/s pump
Archive the signal-to-noise result.
Repeat the octafluoronaphthalene injection.
If the instrument does not pass after several injections, check for
leaks especially at the transfer line union.
68 | User’s Guide, Revision B
NOTE: To add Tools to
the Home Page select
Tools | Add Tools. The
location is
\Xcalibur\System\Programs
\SigNoise.exe.
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ____________________________________________________________ 1.17 Running EI Qualification Tests
Troubleshooting Tips
Comparing the factory test RAW files to your files. Look for any discrepancies
in your methods, or instrument readbacks by selecting View | Report |
Status log, Tune Method, and Instrument Method in Qual Browser.
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Chapter 1, Getting Connected
1.18 Running CI Qualification Tests ___________________________________________________________ TRACE DSQ or FOCUS DSQ
1.18 Running CI Qualification Tests
Tools Needed
• CI ion volume (PN 119650-0230)
• I/R tool and guide bar
• Syringe, 10 µL, 70 mm needle (PN 365 001 03)
• Test mix, octafluoronaphthalene and benzophenone
(PN 120150-TEST)
Frequency
Day 2 (If Applicable)
If the Mass Spectrometer has the CI (chemical ionization) upgrade option, you
must run CI Qualification Tests.
1
2
Load the appropriate CI method.
a.
Select Instrument Setup from the Xcalibur home page.
b.
Select File | Open to load the appropriate factory instrument
method.
c.
Navigate to \Xcalibur\Examples\Methods. Method files are
organized by several GC configurations, so you can choose
either the *PCI.meth for positive ion CI or *NCI.meth for
negative ion CI.
Prepare for the instrument for CI mode.
a.
Install a clean CI Ion Volume using the I/R Tool and the Inlet
Valve found on the Mass Spectrometer.
b.
Open the Tune window and select Instrument | CI Reagent
Gas to display the CI Reagent Gas Flow screen.
c.
Check the Reagent Gas On option.
d.
Enter 2.5 mL/min in the Reagent Gas Flow box or use the
slider to set the flow in the Reagent Gas Flow box.
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TRACE DSQ or FOCUS DSQ____________________________________________________________1.18 Running CI Qualification Tests
e.
Click the Apply button and then the OK button to return to
the Tune window. Now, you’ll see the Automatic Tune
window changed from EI mode to CI mode.
Figure 1-28 Tune Window - CI Mode
f.
3
Wait at least 30-min for the Ion Volume to heat up and bakeout.
Check the Reagent Gas spectrum.
a.
Select Experiment | Full Scan and scan from m/z 10 to 90.
b.
Verify that the Reagent Gas spectrum is similar to Figure 1-29
Positive Ion CI Spectrum (2.5 mL/min Methane).
Figure 1-29 Positive Ion CI Spectrum (2.5 mL/min Methane)
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1.18 Running CI Qualification Tests ___________________________________________________________ TRACE DSQ or FOCUS DSQ
4
c.
If it doesn’t, see if the Ion Volume is inserted correctly (adjust
it with the I/R Tool) or if the filament is properly aligned with
the electron lens hole (shut down the instrument and use a
needle to bend the filament wire to the center of the electron
lens hole.)
d.
Archive the Reagent Gas spectrum.
Check the Calibration Gas Spectrum.
a.
Select Experiment | Full Scan and scan from m/z 60 to 700.
b.
Select Instrument | Calibration | PICI to turn the PICI
Calibration Gas on.
c.
Verify that the Calibration Gas Spectrum is similar to Figure
1-30 Positive Ion Calibration Gas CI Spectrum (2.5 mL/min
Methane).
Figure 1-30 Positive Ion Calibration Gas CI Spectrum (2.5 mL/min Methane)
d.
If it doesn’t, see if the Ion Volume is inserted correctly (adjust
it with the I/R Tool) or if the filament is properly aligned with
the electron lens hole (shut down the instrument and use a
needle to bend the filament wire to the center of the electron
lens hole.)
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TRACE DSQ or FOCUS DSQ____________________________________________________________1.18 Running CI Qualification Tests
5
Select File | Open | Tune and select the autotune.dsqtune file.
Change the:
6
•
Electron energy to 120 eV
•
Emission current to 50 µA
•
Lens 2 to approximately 2 V closer to 0 V
Begin PICI tests.
a.
Select Tune | Automatic Tune to display the Automatic Tune
CI screen.
b.
Make the selections illustrated in Figure 1-31 CI Automatic
Tune - PICI Tests.
Figure 1-31 CI Automatic Tune - PICI Tests
c.
Select the Calibration Masses button to display the
Calibration Masses screen.
d.
Enter these masses 218.986, 413.978, and 501.971 for the
mass calibration.
e.
Click OK to return to the Tune window.
f.
Save the PICI auto-tune file as PICI.dsqtune for the
Installation Qualification test.
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1.18 Running CI Qualification Tests ___________________________________________________________ TRACE DSQ or FOCUS DSQ
7
8
g.
Archive the Calibration Gas Spectrum.
h.
Close the Tune window.
Perform the PICI Installation Qualification test.
a.
Go to Xcalibur | Sequence Setup and open the preset method
*PCI.meth.
b.
Inject 1 µL of a 10 pg/µL solution of benzophenone using the
preset instrument method *PCI.meth.
c.
Go to Qual Browser to review the results, by looking at the
background subtracted spectrum.
d.
Archive the chromatogram and spectrum.
e.
Select the Signal-to-noise Calculator (accessible from a
shortcut on the desktop) to display a mass chromatogram for
the range 182.5—183.5. The minimum Signal-to-Noise Ratio
should be 10:1.
f.
Archive the signal-to-noise ratio.
g.
Repeat the benzophenone injection.
Begin Negative CI Installation Qualification tests.
a.
Go to the Tune window and open the autotune.dsqtune file.
b.
Select the
negative-ion button to change to negative ion
mode. You can confirm this by viewing the Tune window.
74 | User’s Guide, Revision B
NOTE: To add tools to
the Home Page select
Tools | Add Tools. The
location is
\Xcalibur\System
\Programs\SigNoise.exe.
Chapter 1, Getting Connected
TRACE DSQ or FOCUS DSQ____________________________________________________________1.18 Running CI Qualification Tests
Figure 1-32 Tune Window - Negative CI Mode
c.
Select Instrument | CI Reagent Gas to display the CI Reagent
Gas screen.
d.
Select the option CI Reagent Gas On to turn the CI reagent
gas on.
e.
Select Tune | Automatic Tune to display the Automatic Tune
(CI) screen and enter the Prefilter settings displayed in Figure
1-33 Automatic Tuning - Negative CI Tests.
f.
Select the Change Masses button to enter these m/z values
282.9855, 311.9871, 413.9775, 451.9743 into the Calibration
Masses screen:
Figure 1-33 Automatic Tuning - Negative CI Tests
g.
Save the NICI auto-tune file as NCI.dsqtune for the
Installation Qualification test.
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1.18 Running CI Qualification Tests ___________________________________________________________ TRACE DSQ or FOCUS DSQ
h.
9
Close the Tune window.
Perform the NCI Installation Qualification test.
a.
Inject 1 µL of a 1 pg/µL solution of octafluoronaphthalene
using the preset *NCI.meth instrument method.
b.
Go to Qual Browser to review the results by looking at
background subtracted spectrum.
c.
Archive the chromatogram and spectrum.
d.
Use the Signal-to-noise Calculator (accessible from a
shortcut on the desktop) to display a mass chromatogram for
the range 271.5—272.5. The minimum S/N should be 500:1.
e.
Archive the signal-to-noise ratio.
f.
Repeat the octafluoronaphthalene injection.
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TRACE DSQ or FOCUS DSQ_______________________________________________________________ 1.19 Installing Upgrade Options
1.19 Installing Upgrade Options
Tools Needed
Option dependent
Frequency
Installation Day 2
Once you have finished installing and testing the basic TRACE DSQ or
FOCUS DSQ system, install any additional options. Upgrade options may
include:
Y
Autosampler(s): With a TRACE GC, the serial connection to the AI/AS
3000 or AS 2000 should be connected to the GC.
With a Focus GC or other type of autosampler, connect the serial
connection to COM 2 on the computer.
Y
Direct Sample Probe (DIP or DEP)
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Chapter 1, Getting Connected
1.20 Providing Basic Training ________________________________________________________________ TRACE DSQ or FOCUS DSQ
1.20 Providing Basic Training
Tools Needed
None
Frequency Day 2
Now that the system is running to factory specifications, show the customer
how to use the Xcalibur software.
1
2
3
4
Demonstrate Instrument Configuration.
a.
Start Instrument Configuration from the desktop.
b.
Show how to add, configure, and delete components.
Demonstrate the Roadmap View in the Xcalibur Home Page.
a.
Start the Xcalibur Home Page from the desktop.
b.
Show how to use the Roadmap View.
c.
Show how to view the instrument status.
Demonstrate Instrument Setup.
a.
Start Instrument Setup from the Home Page.
b.
Show how to setup a GC method.
c.
Show how to setup a Mass Spectrometer method.
d.
Show how to setup an autosampler method (if applicable).
Demonstrate the TRACE DSQ Tune window.
a.
Start Tune from Instrument Setup.
b.
Show how to open Tune files.
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TRACE DSQ or FOCUS DSQ_________________________________________________________________ 1.20 Providing Basic Training
5
6
7
c.
Show how to look at an air/water spectrum.
d.
Show how to look at a calibration gas spectrum.
e.
Show how to run an Automatic Tune.
f.
Show how to run Diagnostics.
Demonstrate the Sequence View in the Xcalibur Home Page.
a.
Set up a new sequence.
b.
Run a sample.
Demonstrate the Qual Browser.
a.
Open a *.raw file.
b.
Add a cell to view a spectrum.
c.
Explain how to use push-pins.
d.
Explain background subtraction.
e.
Demonstrate how to change the chromatogram range and
mass.
Remind the customer to use Chapter 2, Getting Started, pp. 81 to
reinforce all that you have demonstrated today.
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Chapter 1, Getting Connected
1.20 Providing Basic Training ________________________________________________________________ TRACE DSQ or FOCUS DSQ
80 | User’s Guide, Revision B
Getting
Started
This chapter provides GC/MS instructions using
Xcalibur 1.4 software.
In This Chapter
2.1 Using Desktop Icons, pp. 83
2.2 Configuring Instruments for Use, pp. 84
Analyze
•
Detect
•
Measure
•
Control™
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Chapter 2, Getting Started _________________________________________________________________ TRACE DSQ or FOCUS DSQ
Upgrades
Periodically visit our website, http://www.thermo.com, for the latest releases on
application notes, new manuals, software and firmware updates, and information
on new features.
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Chapter 2, Getting Started
TRACE DSQ or FOCUS DSQ_____________________________________________________________________ 2.1 Using Desktop Icons
2.1 Using Desktop Icons
NOTE: You might find it
helpful to copy this page
and keep it out to use as a
quick reference template
while you’re getting used
to Xcalibur.
After the instrument is connected, it’s a good idea to get acquainted with how
your software is organized on the desktop. Xcalibur desktop icons can help
you quickly get to where you want to go.
Desktop Icon
What it Does...
Launches the Xcalibur Instrument Configuration program. Use this
program to set up and inform Xcalibur which devices are connected to
the data system.
Launches the Xcalibur Home Page program.
Launches the DSQ Tune Window. HINT: When running Xcalibur, you
can also use the Q icon located in your Windows task bar.
Launches the DSQ Autotune Tune Edit program. This program is a
replicate of the Show Manual Tune View command, which is located in
the DSQ Tune Window. Use this to create and edit tune files.
Launches the Xcalibur Signal-to-noise Calculator. This program allows
the Signal-to-Noise to be calculated for specific ranges within *.raw
files.
Launches the MS Word based signal-to-noise Instructions. Use this for
help in using the Signal-to-noise Calculator.
Launches a MS Word based document. Merlin is a Microsoft Word
Template, designed to help you create reports. It automatically loads
the Merlin.dot file and automatically applies the styles to your text.
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Chapter 2, Getting Started
2.2 Configuring Instruments for Use __________________________________________________________ TRACE DSQ or FOCUS DSQ
2.2 Configuring Instruments for Use
1
Select the Xcalibur Instrument Configuration icon
Windows desktop.
2
Configure the mass spectrometer (MS).
a.
from the
Double-click the TRACE DSQ icon located in the Available
Devices column to move it to the Configured Devices panel.
Select the TRACE DSQ even if you have a FOCUS DSQ.
Figure 2-1 MS Instrument Configuration
b.
Double click the TRACE DSQ icon from in the Configured
Devices panel or click the Configure button to display the
Instrument Configuration screen.
c.
Use the tabs on the Instrument Configuration screen to
select options to display on the Instrument Setup and Tune
windows.
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NOTE: Select the Help
button to use the online
help for more detailed
instructions.
Chapter 2, Getting Started
TRACE DSQ or FOCUS DSQ___________________________________________________________ 2.2 Configuring Instruments for Use
d.
Configure General tab options:
Figure 2-2 Instrument Configuration: General
•
The default setting for Remote Start Active High is unchecked.
This starts the GC with an active high signal instead of active low.
•
Demonstration Mode is used to start the instrument in
demonstration mode. This mode is useful if no instrument is
connected, but you would like to demonstrate the software. But
don’t select this to run your first sample.
•
Specify the Pressure Units to display in the Tune window and
the Status tab.
•
Specify the Tune Path for Xcalibur to automatically retrieve
stored tune files. Use the Browse button to quickly navigate to
the folder storing your tune files. The factory default is Xcalibur |
System | DSQ | Tune.
e.
[Optional] Configure CI Gas tab options, if you have the CI
option installed.
Figure 2-3 Instrument Configuration: CI Gas
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Chapter 2, Getting Started
2.2 Configuring Instruments for Use __________________________________________________________ TRACE DSQ or FOCUS DSQ
f.
•
CI Gas option: check to activate CI gas options.
•
CI Gas Type: select a gas type. Select this option to
activate chemical ionization gas controls. Options include:
Ammonia, CO2, Isobutane, Methane, and Other. Other
refers to any gas type not listed in this list. When Other is
selected, the flow module is set to a pressure of 0.3–7.4
psig against a fixed flow restrictor. If a specific gas is
selected, the CI flow module outputs a calibrated flow for
that gas in mL/min.
•
Action when Software is closed and CI Gas is on: When
Xcalibur software is closed, these options determine what
happens if CI gas is on. You can choose to turn it off, leave
it on, or receive a prompt at the time the software is closed
asking if you want to turn the CI gas off. If you choose to
leave the CI gas on, it remains on until you restart the
software. However, as soon as you restart the software,
the CI gas is turned off.
[Optional] Configure PPINICI tab options.
Figure 2-4 Instrument Configuration: PPINICI
•
Check the PPINICI option, if you have the PPINICI option
installed on your mass spectrometer.
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TRACE DSQ or FOCUS DSQ___________________________________________________________ 2.2 Configuring Instruments for Use
g.
Configure Source Saver tab options.
Figure 2-5 Instrument Configuration: Source Saver
h.
•
Enable Cal Gas Source Saver: Check this option to enable
the instrument to turn off the filament and cal gas if left
unattended with the cal gas on. If the cal gas is not on,
source saver will not turn off the filament.
•
Timeout (minutes): Enter the time in minutes that the
instrument must wait after the last user action in tune
before turning off the filament and cal gas.
[Field Engineers Only] Configure Service tab options.
Figure 2-6 Instrument Configuration: Service
NOTE: Please do not
adjust these settings. Only
factory-trained Field
Engineers are qualified to
set the options in the
Instrument Configuration
Service tab.
•
Enable Manual Calibration: Select this option to display
the Manual Calibration menu item in Tune. This allows
the field engineer to manually calibrate the coarse mass
calibration and resolution for troubleshooting. We do not
recommend using manual calibration values for normal
operation because the calibration will not be accurate for
changing scan rates and the manual resolution calibration
makes resolution values in tune files meaningless.
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Chapter 2, Getting Started
2.2 Configuring Instruments for Use __________________________________________________________ TRACE DSQ or FOCUS DSQ
3
•
Enable DC/RF Gain Adjustment: Select this option to
display the DC/RF Gain menu item in Tune.
•
Rod DC: Select A or B. This should be set in the factory
and never change unless the DC Driver PCB, RF
subsystem, or quadrupole mass filter is changed. If
changed, calibrations for both positive and negative ions
must be performed. The terms A and B refer to the
selection of which DC polarity is applied to each
quadrupole rod pair for each ion polarity.
Configure the gas chromatograph (GC).
a.
Move the GC from the Available Devices panel to the
Configured Devices panel.
Figure 2-7 GC Instrument Configuration
b.
Select the GC icon in the Configured Devices panel, then
click the Configure button to display the GC Configuration
screen.
c.
Make these selections on the General tab:
•
Serial Port = COM 1.
•
Set the preferred pressure units.
•
Click the Get button to retrieve the GC configuration
through the serial port to Xcalibur.
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TRACE DSQ or FOCUS DSQ___________________________________________________________ 2.2 Configuring Instruments for Use
4
d.
Verify the settings on the Inlet tab match the GC configuration.
e.
Verify the settings on the Detectors and Data tab match the
GC configuration.
f.
Verify the settings on the Auxiliary and Oven Options tab
match the GC configuration and Aux 1 Present has the MS
Transfer Line selected.
g.
Click OK, if no problems are detected and return to the
Instrument Configuration screen.
Configure the autosampler (AS).
a.
Move the AS icon from the Available Devices panel to the
Configured Devices panel.
Figure 2-8 AS Instrument Configuration
b.
Double-click the AS icon in the Configured Devices panel,
then click the Configure button to display the autosampler
Configuration screen.
c.
Enter autosampler parameters in the AS Configuration
screen. The autosampler is usually connected to a COM port
on the computer (with a Focus GC) or through the GC (with a
TRACE GC and an AI/AS 3000 or AS 2000.) A 10 µL syringe is
standard.
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Chapter 2, Getting Started
2.2 Configuring Instruments for Use __________________________________________________________ TRACE DSQ or FOCUS DSQ
5
Set up the GC handshaking parameters by referring to the GC
manuals for configuration instructions.
Table 2-1 GC Handshaking Parameters
6
Remote Start In
High to Low
Inhibit Ready In
When High
End of Run Out
High to Low
Start of Run Out
High to Low
GC Ready Out
When Low
Prep Run Out
When Low
Click the
windows desktop short-cut to display the Xcalibur
home page.
Instrument Status
Figure 2-9 Xcalibur Home Page
7
Test the AS, GC, and MS communication to Xcalibur.
a.
Check the Instrument Status in the Status tab of the Info View.
All instruments should report Ready to Download. If not,
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TRACE DSQ or FOCUS DSQ___________________________________________________________ 2.2 Configuring Instruments for Use
consult the troubleshooting section of the instrument’s
appropriate manual.
NOTE: The MS may take
up to 1-min to initialize.
b.
Okay, if you’re ready to run your first sample, go to Chapter 3,
Running Your 1st Sample, pp. 93.
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Chapter 2, Getting Started
2.2 Configuring Instruments for Use __________________________________________________________ TRACE DSQ or FOCUS DSQ
92 | User’s Guide, Revision B
Running
st
Your 1
Sample
In This Chapter
3.1 Calibrating and Tuning the Instrument, pp. 95
3.2 Setting Up Methods, pp. 98
3.3 Running Methods, pp. 102
3.4 Analyzing the Data: Compounds With a Known
Retention Time, pp. 109
3.5 Analyzing the Data: Compounds With a Known
Ion Pattern, pp. 119
3.6 Analyzing the Data: Peak Height and Area, pp.
122
3.7 Analyzing the Data: Signal-to-Noise Ratio, pp.
124
Analyze
•
Detect
•
Measure
•
Control™
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Chapter 3, Running Your 1st Sample_________________________________________________________ TRACE DSQ or FOCUS DSQ
After your instruments are configured for use with Xcalibur you’re ready to run
your first sample. In just three easy steps you’ll be running your first sample using
octafluoronaphthalene, which comes with your instrument, as your test
compound.
NOTE: These
instructions are
written with Trace GC,
and AI/AS 3000
assumptions.
However, making the
necessary
modifications and/or
omissions will still
help you accomplish
each step.
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ______________________________________________________ 3.1 Calibrating and Tuning the Instrument
3.1 Calibrating and Tuning the Instrument
Before you run a sample, it’s wise to calibrate and tune the instrument using
the Tune window.
1
Open the Tune program using one of these methods:
NOTE: Select online help
for Tune Window
information.
2
•
Click the
•
Select the
from the MS method editor or,
shortcut from the Windows desktop.
Check the instrument’s basic operation by selecting Diagnostics |
Run Test to display the Diagnostics screen.
Figure 3-1 Tune Window Diagnostic Screen
3
a.
Click on the Test buttons to run each test.
b.
Select the Print Diagnostics Report button to print the
results from all the tests you ran.
c.
Close the Diagnostics.
Check the last Tune Report.
a.
Select Tune | View Tune Report to view the last tune report
and determine when the instrument was last calibrated. Select
the Print button if you want to have hard-copy handy.
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3.1 Calibrating and Tuning the Instrument _____________________________________________________ TRACE DSQ or FOCUS DSQ
b.
4
Close the Tune Report.
[Optional] Perform a Full Automatic Tune if you have just performed
maintenance or your standard operating procedure requires it.
It’s not necessary to calibrate and tune the instrument more than
once every week. However, the number and type of samples you run
determine how often you must tune your instrument.
a.
Select Tune | Automatic Tune to display the Automatic Tune
screen.
Figure 3-2 Automatic Tune Screen - Full
96 | User’s Guide, Revision B
NOTE: How often you
tune your instrument is
determined by the number
and type of samples you
run. Please refer to B.4
Automatic Tune Flow
Chart, pp. 141.
Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ______________________________________________________ 3.1 Calibrating and Tuning the Instrument
5
[Optional] Perform a manual Tune if needed for other applications.
The tuning parameters generated during automatic tune work well for
most applications, but you may find the Manual Tune options
suitable for other applications.
a.
Select Tune | Show Manual Tune View to manually set the
tune parameters in the tabs indicated in Figure 3-3.
Manual Tune Tabs
Figure 3-3 Tune | Show Manual Tune Tabs
b.
Select File | Exit to close the Tune window.
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Chapter 3, Running Your 1st Sample
3.2 Setting Up Methods_____________________________________________________________________ TRACE DSQ or FOCUS DSQ
3.2 Setting Up Methods
After your instrument is calibrated and tuned, you’re ready to set up the
instrument methods using Instrument Setup. Instrument methods are
created and modified in the Instrument Setup window and saved as *meth
files. Method files are stored in the \Xcalibur\Methods\. folder. In this
example, you will enter the method parameters for the Mass Spectrometer,
GC, and the AS.
1
2
Load an instrument method.
a.
Select Instrument Setup from the Xcalibur Home Page to
display Instrument Setup window.
b.
Select File | Open and navigate to Xcalibur\Methods.
Alternatively, navigate to Examples\Methods and then the
folder matching your GC instrument configuration.
c.
Choose1 an *_EI_FullScan.meth. This is the full scan method
file that was used to validate that your instrument met factory
specifications and saved for you to acquire a test sample.
Review MS method parameters by selecting the MS instrument
icon from the Instrument Setup window.
Figure 3-4 Trace DSQ Right_PTV_EI_FullScan.meth Parameters
1.In this example, we went to \Xcalibur\Examples\Methods\Trace Right PTV Methods and
selected RIGHT_PTV_EI_Fullscan.meth.
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ_____________________________________________________________________ 3.2 Setting Up Methods
This method acquires m/z 200–300. It starts 2.5-min after the GC
injection to allow the solvent to elute from the GC column.
3
Review the GC method parameters by selecting the GC instrument
icon from the Instrument Setup window.
Figure 3-5 Trace GC Method Parameters
This method holds the GC at 40 °C for 1-min, ramps it at 30 °C/min to
250 °C, and holds it there for 10-min. The injector is 220 °C operated
in splitless mode. The column flow is 1.0 mL/min. The transfer line
temperature is 250 °C.
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Chapter 3, Running Your 1st Sample
3.2 Setting Up Methods_____________________________________________________________________ TRACE DSQ or FOCUS DSQ
4
[Optional] Review AS method parameters by selecting the AS
instrument icon.
If you’re using an AI/AS 3000 you can enter the parameters shown in
Figure 3-6. For other autosamplers, there are several basic settings
for all autosamplers for sampling/injection and washes. All other
parameters can be left at their default values.
Sampling/Injection:
•
Sample Volume = 1 µL (This is the sample volume that will be
injected.)
•
Air Volume = 1 µL (Draw air after the sample volume to make
sure no solvent is in the needle. Having no solvent in the needle
and using a pre-injection dwell time of 1-second will give you a
hot needle injection. AI/AS 3000 is always 1 µL.)
•
Plunger strokes = 10 (Also called pull-ups or bubble elimination
strokes. This is the number of times the plunger is pulled up and
down while in the sample vial. The plunger volume should be set
larger than the sample volume to say 4 µL.)
•
Pre-injection dwell time = 1 s (Also called Injection Delay. This
gives time for the needle to heat up in the injector before the
sample is injected. This hot needle injection helps all analytes to
vaporize at the same time.)
•
Post-injection dwell time = 1 s (Also called the Pull-Out Delay.
This time allows residual solvent in and on the needle to
evaporate. If set too long, chromatographic peak tailing can
result.)
Washes:
•
Pre Injection Washes = A, 2 cycles (This will wash the syringe
with solvent vial A before drawing the sample for the injection.
This makes sure the syringe is wet and it is clean prior to drawing
up the sample. If required, the volume should be set to the size
of the syringe, 10 µL.)
•
Sample Rinses = 1 (Also called Sample Cleans. This is how many
times your sample is drawn into the syringe and discarded before
the injection is made. Using at least one means the syringe will
be rinsed once with your sample.)
•
Post Injection Washes = B, 6 cycles (This will wash the syringe
with solvent vial B after the injection is made. This will remove
any residual analytes or solvent from the syringe. It is a good idea
to use a different vial for pre and post injection washes. This way,
the pre injection solvent vial A will stay cleaner.)
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ_____________________________________________________________________ 3.2 Setting Up Methods
Figure 3-6 AI/AS 3000 Method Parameters
This method injects 1 µL of Iso-octane.
d.
5
Fill the AS solvent vials A and B with a suitable rinse solvent
such as Iso-octane.
Save the instrument method for use in the next step.
Method files have the *.meth extension and are by default saved to
the Xcalibur | Methods folder. But, you can save method files to any
folder you prefer.
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Chapter 3, Running Your 1st Sample
3.3 Running Methods _______________________________________________________________________ TRACE DSQ or FOCUS DSQ
3.3 Running Methods
After setting up the methods in Instrument Setup, you’re ready to run the
method in Sequence Setup.
1
Create a sequence to run in the Sequence Setup window to record
sample details and determine how you want to acquire the data.
a.
Select
or
from the home page to display the
Sequence Setup window.
Figure 3-7 Sequence Setup Window - Untitled
Sequence Setup works just like a spreadsheet, with each row
representing a single sample and each column an item of information
required for a sample.
Column descriptions are in Table 3-1, Sequence Setup Columns,
pp.103. Additional columns are available by choosing Change |
Column Arrangement, such as Comment.
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ________________________________________________________________________3.3 Running Methods
Table 3-1
Sequence Setup1 Columns
Item
Description
Sample Type
Type of sample, selected from the following:
• Unknown (the normal choice for qualitative
analysis; all other types are only normally
used for quantitative analysis)
• Blank
• QC (quality control)
• Standard Clear
• Standard Update
• Start Bracket
• End Bracket
• Standard Bracket
File Name
Name of the file where to save the sample data.
Sample ID
An identifier unique to the sample. This field can
also be used to import a barcode identifier.
Path
The path to the raw file that Xcalibur creates for
the sample data. Xcalibur creates this file with
extension.raw. Double-click on this field to select
a directory.
Inst Meth
The path and file name of the Instrument Method
to be used for acquisition.
Proc Meth
The path and file name of the processing method
used to process the data after acquisition.
Position
The sample’s vial number. The format of the entry
depends on the configured autosampler. AI/AS
3000 and AS 2000 use simple integers.
Inj Vol
Not used in this editor, but used instead in the AS
method editor.
Level
Used with Standard and QC samples to enter the
sample’s concentration level.
1.More information about recording samples are in the Xcalibur
Online Help or the Xcalibur Getting Productive: Qualitative Analysis
manual or the Getting Productive: Quantitative Analysis manual.
b.
Start entering information in the blank row at the bottom of the
list to add a new sequence.
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3.3 Running Methods _______________________________________________________________________ TRACE DSQ or FOCUS DSQ
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c.
Begin entering the sample information for the file name and
path (right-click in the field to display the drop-down menu,
choose Browse, to select the file.)
Figure 3-8 Sequence Setup - Sample Information
•
To insert a row within a list of samples you
have already entered, right-click anywhere
in the row below which the new sample is
to be inserted and choose Edit | Insert
Row to display the Insert Row screen.
2
Save the sequence, by selecting File | Save. Enter an appropriate
name such as OFN.sld.
3
Run the sequence by clicking on the row number you wish to run
(this highlights the row).
Figure 3-9 Sequence Setup - Running A Sequence
104 | User’s Guide, Revision B
NOTE: Press F2 on your
computer to edit text
already in a cell. Press F2
two times to see an edit
dialog box.
Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ________________________________________________________________________3.3 Running Methods
a.
Select Action | Run Sequence to display the Run Sequence
screen.
Figure 3-10 Sequence Setup - Run Sequence Screen
b.
Select Start When Ready.
c.
Press the Change Instruments button to display the Change
Instruments screen and set up your instruments for an
automatic injection or a manual injection. See the topic If
You’re Doing Automatic Injections..., pp. 3-106 or topic If
You’re Doing Manual Injections..., pp. 3-107 for instructions.
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Chapter 3, Running Your 1st Sample
3.3 Running Methods _______________________________________________________________________ TRACE DSQ or FOCUS DSQ
If You’re Doing Automatic Injections...
An autosampler performs automatic injections and you instruct Xcalibur when
to make the injection.
Figure 3-11 Sequence Setup—Change Instruments In Use Screen (automatic
injections)
1
Configure the Change Instruments In Use screen for automatic
injections:
a.
Make Yes display for each instrument (AS, GC, MS) listed in the
In Use fields (Fig. 3-11).
However, if Yes is not listed, then click on the blank field to
toggle Yes on.
2
b.
Make Yes display in the Start Instrument field for the AS. This
makes the autosampler start as soon as all devices are ready.
c.
Select OK to return to the Run Sequence screen.
Prepare the injection.
a.
Open and transfer the 100 pg octafluoronaphthalene
sample— that is in the GC/MS Test Kit (PN 120150-TEST)—
into an autosampler vial (vials are supplied with the
autosampler.)
b.
Load the sample vial into position 1 of the autosampler.
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TRACE DSQ or FOCUS DSQ________________________________________________________________________3.3 Running Methods
3
Start the Run, by selecting OK from the Run Sequence screen (Fig.
3-10).
If You’re Doing Manual Injections...
Manual injections are necessary for those not having an autosampler or not
wishing to use it to run this method.
Figure 3-12 Sequence Setup-Change Instruments In Use Screen (manual
injections)
1
2
Configure the Change Instruments In Use screen for manual
injections:
a.
Make Yes display for the GC and MS instruments listed in the
In Use fields.However, if Yes is not listed, then click on the
blank field to toggle Yes on.
b.
Make sure the GC and MS instruments Start Instrument
fields are empty (Fig. 3-12).
c.
Make sure the AS (if listed) does not say Yes in both the In
Use or Start Instrument fields.
d.
Select OK to return to the Run Sequence screen.
Open the 100 pg octafluoronaphthalene sample—that is in the GC/
MS Test Kit (PN 120150-TEST).
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3.3 Running Methods _______________________________________________________________________ TRACE DSQ or FOCUS DSQ
3
Select OK from the Run Sequence screen(Fig. 3-10) to start the run.
4
Monitor the Status View until the instrument is “Waiting for Contact
Closure.”
5
Prepare the injection.
6
7
a.
Draw 1 µL of the 100 pg octafluoronaphthalene sample into
the supplied syringe. Be sure there are no bubbles in the
syringe.
b.
Draw in 1 µL of air.
Make the injection and start the GC.
a.
Carefully, insert the needle into the injector port.
b.
Wait one-second and push the plunger.
c.
Quickly, press the Start button located on the GC.
d.
Remove the syringe.
Watch the data, while the sequence is running.
This is a good time to watch the data by selecting from one of the
two views:
a.
Click the Real Time Plot icon to view the Chromatogram and
Spectrum acquisition in real time. When the run is finished this
screen goes blank.
b.
Select the Acquisition Queue tab to view the list of the
samples you have selected to run. Green items mean the
sequence is running.
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TRACE DSQ or FOCUS DSQ________________________________3.4 Analyzing the Data: Compounds With a Known Retention Time
3.4 Analyzing the Data: Compounds With a
Known Retention Time
When you’re ready to analyze your data, use the Xcalibur browsers (Qual,
Quan, and Library) to view the data file results.
NOTE: See the online
Help for additional
instruction or see: Getting
Productive: Qualitative
Analysis, Getting
Productive: Quantitative
Analysis, Getting
Productive: Processing
Setup and Analysis of
Quantitation Data, Getting
Productive: Creating and
Searching Libraries, and
Getting Productive:
Designing and Generating
Custom Reports with
Merlin.
Reviewing Cursor Actions in Browsers
Before you begin using the Browsers, let’s review some of the cursor actions
and effects within the chromatogram and spectrum cells:
Y
A click picks a point on the cell
Y
A line dragged parallel to any axis picks a range
Y
A line dragged in any diagonal direction selects an area
The effect of these actions depends on one of these cell states:
Y
Inactive
Y
Active and unpinned— each cell has a pin icon in its top right corner.
Only one of the cells can be active at any one time. The active cell is
highlighted with a gray border.
Y
Active and pinned — pinning fixes the active status of a cell.
1
Unpin an active cell, by clicking once on the pin icon.
2
Make a cell active, by clicking anywhere within the cell.
Xcalibur highlights the cell with a gray border. Click on its pin icon if
you want to fix it as the active cell. Cursor actions in an active cell
cause the cell to be scaled according to the dimensions of the
dragged line or area (see Table 3-2, Cursor Actions In Active and
Unpinned Cells, pp.110).
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Chapter 3, Running Your 1st Sample
3.4 Analyzing the Data: Compounds With a Known Retention Time _______________________________ TRACE DSQ or FOCUS DSQ
Table 3-2 Cursor Actions In Active and Unpinned Cells
Cursor Action
Effect
Drag parallel to X-axis
Rescale graph showing selected X range only,
same Y range
Drag parallel to Y-axis
Rescale graph showing selected Y range only,
same X range
Dragged area
Rescale graph showing both the selected X and Y
ranges
The same actions in the unpinned or inactive cell have a very different
effect. In this case, the cursor actions affect the active, pinned cell
(see Table 3-3, Cursor Actions In An Inactive Or Unpinned Cell,
pp.110).
Table 3-3 Cursor Actions In An Inactive Or Unpinned Cell
Pinned cell
Cursor action
Effect
spectrum
Click in a
chromatogram cell
The spectrum cell displays the mass
spectrum at that retention time.
spectrum
Drag across a time
range in a
chromatogram cell
The spectrum cell displays the averaged
mass spectrum from that retention time
range.
chromatogram
Click in a spectrum
cell
The chromatogram cell displays the mass
chromatogram of the selected mass. If the
Plot Type is TIC or Base Peak, it is changed
to Mass Range.
chromatogram
Drag across an m/z
range in a spectrum
cell
The chromatogram cell displays the mass
range chromatogram of the selected mass
range. If the Plot Type is TIC or Base Peak,
it is changed to Mass Range.
Important points to note are:
Y
The cursor action is always applied to the pinned cell
Y
Within an active cell, cursor actions rescale the plot
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ________________________________3.4 Analyzing the Data: Compounds With a Known Retention Time
Using Qual Browser you can answer the question, “Does this sample contain
compound ‘X’? X being the octafluoronaphthalene (OFN) you used in the
previous topic. Then we will determine the peak height, area, and signal-tonoise ratio.
In this example, we used the \Xcalibur\Data\100pgEI.raw file you just
acquired (Step 6, Make the injection and start the GC., pp. 3-108), which has a
retention time of approximately 3.7-min. If you did not acquire this sample,
you can use the sample file located in Xcalibur\Data\Factory Test Data\
100pgEI.raw.
Let’s assume that you have previously carried out a GC run with a pure
sample of the compound you are interested in, compound 'X', and
consequently you know the retention time.
1
Open Qual Browser and select the *.raw file that contains the data
for the sample you want to work on.
a.
Select Qual Browser from the Home page.
b.
Choose File | Open and navigate to Xcalibur\Data and open
the sample file 100pgEI.raw or a *.raw file containing the data
you’re interested in.
Figure 3-13 100pgEI.raw
Don’t be surprised if the Qual Browser window looks different than
Figure 3-13. The default layout can be changed and saved.
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Chapter 3, Running Your 1st Sample
3.4 Analyzing the Data: Compounds With a Known Retention Time _______________________________ TRACE DSQ or FOCUS DSQ
2
Display a Chromatogram and a Mass Spectrum in the same
window.
If you want to identify the compound that is eluting at approximately
3.69-min, look at the mass spectrum recorded at that time in the
chromatogram.
a.
Click the Insert Cell
toolbar button to display a new cell
containing the same information as the existing cell.
Figure 3-14 Displaying Two Chromatograms
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TRACE DSQ or FOCUS DSQ________________________________3.4 Analyzing the Data: Compounds With a Known Retention Time
b.
Select the lower cell and then right-click your mouse to display
the context sensitive menu.
Figure 3-15 Qual Browser Chromatogram Context Menu
c.
Choose View | Spectrum from this menu to change the view
from chromatogram to spectrum. The lower cell now displays
spectral data.
Notice that the lower cell now displays a graph of Relative
Abundance vs. m/z; that is, a mass spectrum. Initially, you’ll see the
first mass spectrum.
3
Zoom in on the Time Period of Interest.
Although the full TIC chromatogram is currently displayed in the
upper cell, only the retention time around three or four minutes is of
particular interest. Therefore, zoom in on that part of the
chromatogram and view it in more detail.
There are two ways of doing this; using Mouse functions or using
Range functions.
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Chapter 3, Running Your 1st Sample
3.4 Analyzing the Data: Compounds With a Known Retention Time _______________________________ TRACE DSQ or FOCUS DSQ
Using Mouse Functions
Y
Click the pin icon that is located in the top right corner of the
chromatogram cell so it is green (pinned).
Y
Position the cursor at the starting time you are interested in, at a
position close to or on the baseline.
Y
Click and drag the cursor parallel to the time axis to the end of the
period required. Notice that a line is drawn on the screen as you do
this. As the cell redisplays, notice only that part of the chromatogram
within the line you have just drawn.
Figure 3-16 Chromatogram Using Mouse Functions
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ________________________________3.4 Analyzing the Data: Compounds With a Known Retention Time
Using Range Functions
Y
Right-click on the chromatogram to display the context-sensitive menu
and choose Ranges to display the Chromatogram Ranges screen.
Y
Enter the time range of interested in the Time Range field such 3.4 to
4.0-min.
Figure 3-17 Chromatogram Ranges Screen Using Range Functions
Y
4
Click OK to return to Qual Browser.
View the mass spectrum for a specific chromatogram retention time.
Currently, a selected chromatogram time period is displayed in one
cell and a mass spectrum in another cell. This step describes how to
select a particular retention time on the chromatogram and view the
corresponding mass spectrum.
a.
Locate the pin icon shown in the top right corner of the mass
spectrum cell and click on it. The icon changes from unpinned
to pinned
.
b.
Move the cursor over the chromatogram until it is
positioned at the retention time you are interested in and click
on it to view the mass spectrum for the desired retention
time.
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Chapter 3, Running Your 1st Sample
3.4 Analyzing the Data: Compounds With a Known Retention Time _______________________________ TRACE DSQ or FOCUS DSQ
5
Subtract the Background Contamination from the spectrum.
Peaks eluting from a GC column can contain low levels of
contamination due to material bleeding from the matrix of the
column. This material will have its own mass spectrum that will be
superimposed on that of the sample compound. The mass spectrum
of a chromatogram peak can therefore be made up of mass peaks
resulting from the sample compound plus mass peaks resulting from
background contamination.Therefore, to obtain a mass spectrum for
the compound alone (that can be used in a library search), subtract
the mass spectrum of the background contamination.
a.
Make sure that the mass spectrum cell is pinned.
b.
Choose Actions | Subtract Spectra | 2 Ranges.
You can choose between subtracting the background from either one
side of the peak you are interested in or from both sides. To get the
best results you will usually want to subtract from both sides, so
choose two Ranges.
c.
Move the cursor into the chromatogram cell and position it
slightly to one side of the peak you are interested in.
d.
Click and drag the cursor away from the peak, making sure
to stop before reaching the next discernible peak on the
chromatogram. Notice a line drawn on the screen as you do
this.
e.
Repeat to mark the opposite side of the peak.
In general, after background subtraction, most of the larger mass
peaks in the mass spectrum will be unchanged; these are “true”
peaks, due to the sample compound. Common contamination peaks
are at m/z 207, and 281. The removal of such contamination peaks will
help you to obtain a more accurate result from a library search.
6
Use the spectrum to perform a Library Search.
When you have a clean mass spectrum, you can use it to search the
NIST library, to determine the nature of the compound.
a.
Right-click in the mass spectrum cell and choose Library |
Search from the context-menu.
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TRACE DSQ or FOCUS DSQ________________________________3.4 Analyzing the Data: Compounds With a Known Retention Time
Figure 3-18 Library Search Pull-down Menu
b.
If you have the optional NIST library installed look for the
results:
4
1
2
3
1
Chemical Structure Cell
3
Library Spectrum Cell
2
Difference Spectrum Cell
4
Hit List Cell
Figure 3-19 Library Search Results window
c.
Look in the hit list cell (4) for the most likely compounds, in
decreasing order of match probability. If octafluoronaphthalene
is not one of the top hits, you may not have the optional NIST
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Chapter 3, Running Your 1st Sample
3.4 Analyzing the Data: Compounds With a Known Retention Time _______________________________ TRACE DSQ or FOCUS DSQ
library. Check which libraries are available for search by
selecting the Library Options pull-down menu.
For each compound in the hit list, Xcalibur displays a chemical
structure (1), a library spectrum (3) to compare with your spectrum,
and a difference spectrum (2); that is, the library spectrum subtracted
from your spectrum.
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ____________________________________3.5 Analyzing the Data: Compounds With a Known Ion Pattern
3.5 Analyzing the Data: Compounds With a
Known Ion Pattern
NOTE: See the online
Help for additional
instruction or see: Getting
Productive: Qualitative
Analysis, Getting
Productive: Quantitative
Analysis, Getting
Productive: Processing
Setup and Analysis of
Quantitation Data, Getting
Productive: Creating and
Searching Libraries, and
Getting Productive:
Designing and Generating
Custom Reports with
Merlin.
Using Qual Browser you can answer the question, “Does this sample contain
compound “x”? X being the octafluoronaphthalene (OFN) you used in the 3.3
Running Methods, pp. 102. Then we will determine the peak height, area, and
signal-to-noise ratio.
In this example, we used the Xcalibur\Data\100pgEI.raw file you just
acquired (Step 6, Make the injection and start the GC., pp. 3-108), which has a
retention time of approximately 3.7-min.
In this example, let’s assume that you already have some knowledge of the
mass spectrum of the compound of interest, compound 'X', and
consequently you know the characteristic ions present in its mass spectrum.
For the purposes of this example, m/z 272 represents an ion, perhaps the
molecular ion of the compound, and therefore this ion represents a “marker”
for the compound.
1
2
Open Qual Browser.
a.
Set up the cells so you have only one cell, a chromatogram. You
can delete other cells by pinning them and selecting Delete
Grid Row
from the toolbar.
b.
Reset the time range to the full range by selecting Zoom
Reset
from the toolbar.
Add a mass range chromatogram.
a.
Select the chromatogram cell and then right-click your mouse
to display the context sensitive menu.
b.
Choose Ranges from this menu to display the Chromatogram
Ranges screen.
c.
Add another plot by clicking the check box under Type.
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Chapter 3, Running Your 1st Sample
3.5 Analyzing the Data: Compounds With a Known Ion Pattern ___________________________________ TRACE DSQ or FOCUS DSQ
Figure 3-20 Qual Browser—Chromatogram 1
d.
Select Mass Range from the Plot Type field.
Figure 3-21 Qual Browser—Chromatogram 2
e.
Enter the mass range in the Range(s) field. In this example,
enter 272.
f.
Click OK to return to Qual Browser, where the chromatogram
cell now shows a mass TIC and a chromatogram for the
selected mass, m/z 272.
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ____________________________________3.5 Analyzing the Data: Compounds With a Known Ion Pattern
Figure 3-22 Displaying a TIC And Mass Range Chromatogram
The result in this example shows that the peak at retention time 3.69min is of particular interest, because it includes m/z 272, the
molecular ion from octafluoronaphthalene.
3
View the mass spectrum.
Having identified a particular retention time of interest, you can
investigate the peak further by looking at the mass spectrum. Follow
the same procedure you did in the previous section for adding a
spectrum cell.
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Chapter 3, Running Your 1st Sample
3.6 Analyzing the Data: Peak Height and Area __________________________________________________ TRACE DSQ or FOCUS DSQ
3.6 Analyzing the Data: Peak Height and
Area
In a chromatogram, the area of an isolated peak is directly proportional to the
amount of material present; for peaks that overlap, height may give a more
accurate determination. Determining the area and/or height of a peak is
therefore an important feature of quantitation.
1
Zoom in on the part of the chromatogram that is of particular interest
(3.4–4.0-min.)
a.
Right-click on the chromatogram and choose Peak
Detection | Toggle Detection in All Plots from the context
menu. Individual peaks are shown shaded and the extent of
each peak shown by blocks on the baseline.
Figure 3-23 Qual Browser—Peak Detection
b.
Right-click on the chromatogram and choose Display
Options to display the Display Options screen.
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TRACE DSQ or FOCUS DSQ___________________________________________________3.6 Analyzing the Data: Peak Height and Area
Figure 3-24 Qual Browser—Labels
c.
Select the Labels tab.
d.
Select both the Area and Height check boxes.
e.
Click on OK to return to the chromatogram.
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Chapter 3, Running Your 1st Sample
3.7 Analyzing the Data: Signal-to-Noise Ratio___________________________________________________ TRACE DSQ or FOCUS DSQ
3.7 Analyzing the Data: Signal-to-Noise
Ratio
The signal-to-noise ratio is a good measure of the performance of the
system, because it defines the smallest amounts of compound that can be
detected and quantified.
If the signal-to-noise ratio is low, true peaks (signals) resulting from the
presence of very small amounts of material can be lost in the background
noise.
Low signal-to-noise ratios can result from:
Y
Poor column quality
Y
A dirty ion source
Y
Poor quality carrier gas
Y
Inadequate sample cleanup (extraction)
Y
Poor chromatography techniques
There are two ways to determine the Signal-to-noise ratio of a peak. The first
uses Qual Browser and the second uses the Signal-to-Noise Calculator. Note
that in Xcalibur version 1.3 and earlier, the Qual Browser method is not always
accurate. This is because you cannot select the region of the chromatogram
from which to calculate noise.
Using Qual Browser...
1
2
Display the Signal-to-noise label on the chromatogram.
a.
Using Xcalibur, right-click on the chromatogram and choose
Display Options from the context menu to display the Display
Options screen.
b.
Select the Labels tab.
c.
Select the Signal-to-noise checkbox.
d.
Click on OK to return to the chromatogram.
Choose the baseline noise range.
a.
Click on the Peak Detection Settings tab
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in the Info bar.
Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ___________________________________________________ 3.7 Analyzing the Data: Signal-to-Noise Ratio
b.
Pin the chromatogram cell by clicking in the top right corner.
c.
Click on the chromatogram plot on which you wish to measure
the Signal-to-noise. It will turn grey.
d.
Check Manual Noise Region in the Info bar.
e.
Enter a noise range near the peak such 4.0–5.0-min. Avoid
choosing a region with a peak in it.
f.
Choose Apply. The RMS (root mean square) Signal-to-noise
is calculated and displayed.The noise range you chose is
shown by a red line in the chromatogram.
Using the Signal-to-Noise Calculator...
1
Use the Signal-to-noise Calculator.
Alternatively, you can use the Signal-to-noise calculator, which is
provided with all versions of Xcalibur.
a.
Run the Signal-to-noise Calculator by double-clicking the icon
the desktop. You can also run it from
\Xcalibur\System\Programs\Signoise.exe if the icon is not
available.
b.
Choose File | Open and select the 100pgEI.raw file.
c.
Select Chromatogram | Ranges.
Figure 3-25 Signal-to-noise Calculator
d.
Select Mass Range for Plot Type.
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Chapter 3, Running Your 1st Sample
3.7 Analyzing the Data: Signal-to-Noise Ratio___________________________________________________ TRACE DSQ or FOCUS DSQ
e.
Enter 272 for Range(s).
f.
Select OK to display the Signal-to-noise ratio.
Figure 3-26 Signal-to-noise Calculator
g.
Select different regions of the baseline for the noise range if
necessary. Choose Chromatogram | Automatic Noise Range
to disable the automatic range made. Choose Chromatogram
| Specify Noise Range and click and drag the noise range you
want (for example, 4.0–5.0 min). Avoid choosing a region with
a peak in it.
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Chapter 3, Running Your 1st Sample
TRACE DSQ or FOCUS DSQ___________________________________________________________________ 3.8 Automating Processing
3.8 Automating Processing
When you’re ready to automate your processing please read the following
Xcalibur books for instructions:
Y
Getting Productive: Quantitative Analysis
Y
Getting Productive: Processing Setup and the Analysis Of Quantitation
Data
Y
Getting Productive: Creating and Generating Custom Reports with
Merlin
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Chapter 3, Running Your 1st Sample
3.8 Automating Processing __________________________________________________________________ TRACE DSQ or FOCUS DSQ
128 | User’s Guide, Revision B
Appendix A Preinstallation
Checklists
In This Chapter
A.1 Preinstallation Checklist, pp. 130
A.2 Installation Checklist, pp. 131
This appendix provides checklists for both the TRACE
DSQ or FOCUS DSQ preinstallation and the field
service installation. Do not write on the copies
presented in this chapter. Rather, make duplicate
copies whenever you need a checklist or report.
Analyze
•
Detect
•
Measure
•
Control™
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Appendix A, Preinstallation Checklists
A.1 Preinstallation Checklist _________________________________________________________________ TRACE DSQ or FOCUS DSQ
A.1 Preinstallation Checklist
The customer should have met all the requirements listed on this checklist
prior to your arrival. Ask the customer to give you their copy of the
Preinstallation Checklist and check each item. Detailed information matching
the items on this checklist are in your Preinstallation Guide. Preinstallation
Guides are given to the customer by the sales person taking the order.
R
1. Entrance Requirements: delivery doors are at least 102 cm (40 in.)
wide?
R
2. Workbench Space, Weight and Stability Requirements:
workbench is at least 2 m (6 ft) across, supports a 119 kg (262 lb) load,
and is sturdy and free from vibration?
R
3. Lighting Requirements: work area is properly lit?
R
4. Power Requirements: acceptable power source available and
nearby?
R
5. Wall Outlets & Voltage Requirements: wall outlets meet system
voltage current specifications?
R
6. Environment Requirements:
R a. Temperature: room temperature is 15-31 °C (59-88 °F)?
R b. Humidity: relative humidity is between 40 and 80%, with no
condensation?
R c. Install a temperature and humidity monitor
R d. Particulate Matter: air quality is free of excess particulate
matter?
R e. Electrostatic Discharge: work area is free of electrostatic
discharge?
R f. Exhaust System: suitable exhaust system available?
R
7. Gas Equipment Requirements: is the necessary gas equipment
available?
R
8. Solvent Requirements: are the recommended solvents available?
R
9. Telephone Requirements: a telephone is located near the
workbench?
130 | User’s Guide, Revision B
Appendix A, Preinstallation Checklists
TRACE DSQ or FOCUS DSQ____________________________________________________________________ A.2 Installation Checklist
A.2 Installation Checklist
Two-Day Schedule At A Glance
30 Days before
R
R
Call customer:
R
Is Preinstallation checklist complete?
R
Are there any questions?
R
Is there anything additional I need to bring?
Step 1.1 Get the right tools
Day 1
Morning
R Step 1.2 Verify site conforms to specifications
R
Step 1.3 Unpack the instruments
Afternoon
R Step 1.4 Connect the Gas lines
R
Step 1.5 Install the Data System
R
Step 1.6 Install the GC
R
Step 1.7 Install the Mass Spectrometer
R
Step 1.8 Start the Instrument
R
Step 1.9 Confirm Readbacks
R
Step 1.10 Run Diagnostics
R
Step 1.11 Check RF DIP Calibration
R
Step 1.12 Check RF Gain Calibration
R
Step 1.13 Check Air/Water Spectrum
R
Step 1.14 Leak check
R
Step 1.15 Check the Initial Tune
R
Step 1.16 Stabilize the instruments
Day 2
Morning
R Repeat steps 1-8 to 1.14
Afternoon
R Step 1.17 Run an EI Qualification Test
R
Step 1.18 Run a CI Qualification Test
R
Step 1.19 Install Upgrade Options
R
Step 1.20 Provide basic training
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Appendix A, Preinstallation Checklists
A.2 Installation Checklist____________________________________________________________________ TRACE DSQ or FOCUS DSQ
132 | User’s Guide, Revision B
Appendix B Additional
Helps
In This Chapter
B.1
B.2
B.3
B.5
B.6
Analyze
•
Detect
•
Assembling Swagelok Fittings, pp. 134
Using a Swagelok Tee or Cross, pp. 137
Adjusting the RF Null, pp. 138
Adjusting the RF Dip Calibration, pp. 142
Reinstalling the Data System, pp. 143
Measure
•
Control™
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Appendix B, Additional Helps
B.1 Assembling Swagelok Fittings ___________________________________________________________ TRACE DSQ or FOCUS DSQ
B.1 Assembling Swagelok Fittings
Tools Needed:
• Swagelok Fitting
• Wrench set (open end), 5/16-in., 7/16-in., 1/2-in.,
9/16-in.
Frequency:
Fixing leaks
Building Swagelok compression fittings and connecting tees and crossings
are essential to a leak-free system.
A Swagelok Fitting is a compression fitting that has four components—a
Swagelok Nut, a Back Ferrule, a Front Ferrule, and an Inlet.
The completed assembly is comprised of five-pieces when the Swagelok
Ferrule and Nut assembly is affixed to Tubing. Two ferrules merge when the
nut is tightened, forming a safe and leak-free seal between the tubing and the
inlet body.
1
Place a Swagelok nut on the end of the tubing.
The threads on the nut should face the open end of the tubing as
shown in Figure B-1 Swagelok Ferrule and Nut Assembly.
Swagelok Nut Front Ferrule
Tubing
Inlet Body
Back Ferrule
Figure B-1 Swagelok Ferrule and Nut Assembly
2
Place a Swagelok back ferrule over the tubing with the smaller side
facing the open end of the tubing.
134 | User’s Guide, Revision B
NOTE: Do not put tape on
the threads of a Swagelok
fitting.
Appendix B, Additional Helps
TRACE DSQ or FOCUS DSQ____________________________________________________________ B.1 Assembling Swagelok Fittings
3
Place a Swagelok front ferrule over the tubing with the smaller side
facing the open end of the tubing.
4
Push the ferrules down into the Swagelok nut.
5
Insert the tubing into the Swagelok inlet as far as it will go as shown
in Figure B-2 Swagelok and Inlet Connection.
Inlet Body
Tubing Ferrule and Nut Assembly
Figure B-2 Swagelok and Inlet Connection
6
Slide the nut over the inlet and tighten until finger-tight.
7
Pull the tubing out from the nut very slightly (1/16-in.)
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Appendix B, Additional Helps
B.1 Assembling Swagelok Fittings ___________________________________________________________ TRACE DSQ or FOCUS DSQ
8
While holding the inlet tight with a backup wrench, tighten the nut
3/4-turn past finger-tight as shown in Figure B-3 Tightening
Swagelok Fittings.
You can make a mark on the nut before you tighten it. This helps
ensure that you have turned the nut a 3/4-turn.
Figure B-3 Tightening Swagelok Fittings
136 | User’s Guide, Revision B
Appendix B, Additional Helps
TRACE DSQ or FOCUS DSQ___________________________________________________________ B.2 Using a Swagelok Tee or Cross
B.2 Using a Swagelok Tee or Cross
Tools Needed:
• Ruler or measuring tape
• Swagelok Fittings
• Swagelok Plugs
• Tubing Cutter
Frequency:
Fixing leaks
To use a single gas source for more than one inlet or detector module, you
must use a Swagelok tee or cross to properly split the gas flow.
1
Cut the tubing.
With a tubing cutter, cut the tubing where the tee or cross will go.
2
Connect the tubing to the tee or cross with a Swagelok fitting.
Refer to instruction B.1 Assembling Swagelok Fittings, pp. 134.
3
Measure and cut.
Measure the distance from the tee or cross to the inlets or detectors,
and cut the tubing in the appropriate lengths.
4
5
Connect the tubing to the tee or cross ends with Swagelok fittings.
Install Swagelok Plugs.
Install Swagelok Plugs instead of an Inlet Body on any open ends
located on a tee or cross that are not connected with tubing.
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Appendix B, Additional Helps
B.3 Adjusting the RF Null ___________________________________________________________________ TRACE DSQ or FOCUS DSQ
B.3 Adjusting the RF Null
Use this procedure only if an RF Null adjustment is necessary. To adjust the
RF Null you adjust the R5 potentiometer located behind the heatsink of the
RF generator PCB. This procedure should only be performed by factory
trained Field Engineers.
WARNING
Personal Injury
Electrical Shock Hazard
This procedure requires the safety covers to be removed and
an adjustment made inside while the instrument is running.
This procedure should only be performed by factory trained
Field Engineers.
CAUTION
Instrument Damage
Improperly adjusting the RF Null will permanently damage the
RF system. This procedure should only be performed by
factory trained Field Engineers.
1
Run the Rod DC Test in continuous mode.
a.
Open the Tune window Diagnostic screen by selecting Tune |
Diagnostics | Run Tests to display the Diagnostics screen.
Figure B-4 Tune Diagnostic Screen
b.
Uncheck all options except the Rod DC Test.
138 | User’s Guide, Revision B
Appendix B, Additional Helps
TRACE DSQ or FOCUS DSQ____________________________________________________________________ B.3 Adjusting the RF Null
c.
Select the Rod DC Test button to display the Rod DC Test
screen.
Figure B-5 Rod DC Test
d.
2
3
Select the Continuous button, to run the test continuously.
Remove the Mass Spectrometer covers in this order: front, top, and
left.
Adjust the RF Null, which is located behind the heatsink of the RF
generator PCB.
a.
Insert the potentiometer adjustment tool into the slotted screw
of the RF Null Adjustment.
b.
Slowly turn until the A and B Rod DC values are closest to the
average Rod DC readback or 50 V.
User’s Guide, Revision B
|139
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Appendix B, Additional Helps
B.3 Adjusting the RF Null ___________________________________________________________________ TRACE DSQ or FOCUS DSQ
Figure B-6 RF Null Position
4
Replace the Mass Spectrometer covers in this order: left, top, and
front.
140 | User’s Guide, Revision B
N
N
Run Automatic Tune. Select RF
Frequency Calibration, Resolution
Calibration: Positive Ions, Full
Automatic Tune, Leak Check
Will the instrument be
used for Negative CI?
Wait for the source temperature
and vacuum to stabilize, and for
contaminants to pump away.
Has the instrument
recently been vented
and/or cleaned?
Start
N
Run Automatic Tune. Select RF
Frequency Calibration, Resolution
Calibration: Positive Ions and
Negative Ions, Full Automatic
Tune, Leak Check
Y
N
Do the ions in the Tune
window appear
calibrated?
Y
Install a clean EI ion volume in the
source. Allow source temperature
to stabilize. Run Automatic Tune,
selecting Detector Gain Calibration,
Resolution Calibration: Positive Ions,
Full Automatic Tune, Leak Check
N
N
N
Has the detector gain
been calibrated within
the past week of
operation?
Y
Run Automatic Tune, selecting
Detector Gain Calibration,
Resolution Calibration: Positive
Ions, Full Automatic Tune, Leak
Check
Did the Automatic Tune
pass all tests
Run Automatic Tune, selecting
Detector Gain Calibration,
Maintenance and Leak Check
Follow the diagnostic and
troubleshooting procedures in the
Hardware Manual.
Y
N
Y
Shutdown the instrument. Clean the
ion source, lenses and prefilter.
Replace the filament if the wire is
badly pitted or too thin. Confirm that
the detector and quadrupoles are
free of dust and fibers and the
source ceramic is aligned with the
baffle wall before starting the
instrument.
Is a clean EI ion volume
properly installed?
Was the instrument
tuned?
Are the results
acceptable?
Success
Run Automatic Tune, selecting
Maintenance and Leak Check
Y
Y
Y
Appendix B, Additional Helps
TRACE DSQ or FOCUS DSQ______________________________________________________________ B.4 Automatic Tune Flow Chart
B.4 Automatic Tune Flow Chart
Refer to this chart to determine when to use various tuning features.
User’s Guide, Revision B
|141
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Appendix B, Additional Helps
B.5 Adjusting the RF Dip Calibration__________________________________________________________ TRACE DSQ or FOCUS DSQ
B.5 Adjusting the RF Dip Calibration
Use this instruction to adjust the RF Dip Calibration readback, however, make
sure you run this calibration after the heaters and vacuum have stabilized.
1
2
Make sure the heaters and vacuum status readbacks have
stabilized.
Open the Automatic Tune screen from the Tune window.
a.
Select Tune | Automatic Tune to display the Automatic Tune
screen.
Figure B-7 Xcalibur 1.4 Automatic Tune Screen
b.
Select the RF Frequency Calibration option.
c.
Select the Maintenance option.
d.
Uncheck all other options.
e.
Click OK to adjust the RF Dip Calibration automatically and
return to the Tune window.
142 | User’s Guide, Revision B
Appendix B, Additional Helps
TRACE DSQ or FOCUS DSQ_____________________________________________________________ B.6 Reinstalling the Data System
B.6 Reinstalling the Data System
Use this procedure only if installing a new computer or replacing a hard drive.
1
Follow the instructions on the Xcalibur CD.
a.
Insert the Xcalibur CD into your computer.This should
automatically display the Xcalibur Setup screen (Figure B-8).
If it doesn’t, use windows to run the XInstall.exe from the CD.
Figure B-8 Xcalibur Data System Setup Screen
b.
NOTE: Click the Readme
button located on the
Setup Screen to read
important new information
about this option.
2
3
Select the Installation Help button file to display the
Instructions.doc file and then send it to your printer. Follow
the instructions to install the data system software.
Install any optional upgrade software.You should now install any
optional software like libraries. Follow the instructions provided with
these options.
Configure the instruments.
Follow the instructions listed in 2.2 Configuring Instruments for Use,
pp. 84.
User’s Guide, Revision B
|143
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Appendix B, Additional Helps
B.6 Reinstalling the Data System ____________________________________________________________ TRACE DSQ or FOCUS DSQ
144 | User’s Guide, Revision B
Index
A
Available Devices panel 88
Accessory plug 40
Action when Software is closed and CI Gas is on
B
86
Actions | Subtract Spectra | 2 Ranges 116
adjusting
RF dip 142
RF gain 138
Advanced 62
Advanced Calibration screen 62
Air Volume 100
air/water check 56
air/water spectrum, typical 57
Ammonia 86
Apply button 71
Area 123
AS 2000 Communication 90
AS Configuration screen 89
AS instrument icon 100
automatic injections 105
automatic range
disable 126
Automatic Tune 62
Automatic Tune CI screen 73
Automatic Tune screen 62, 96, 142
Autosampler
configuration 89
autosampler Configuration screen 89
autotune.dsqtune 73
Aux 1 Present 89
Auxiliary and Oven Options tab 89
Available Devices 84
Background Contamination 116
background spectrum 60
background spectrum, typical 61
background subtracted spectrum 74
baseline noise range 124
benzophenone 74
Browse button 85
C
cables
remote start,transfer line,ethernet 40
Cal_tune.dsqtune 62
calibration gas spectrum 54, 61, 67, 72, 74, 79
calibration gas spectrum, CI 72
calibration gas spectrum, EI 61
Calibration Masses button 73
Calibration Masses screen 73, 75
calibration, RF dip 51
calibration, RF gain 53
carrier gas
quality 124
carrier gas connection 27
Carrier Gas Supply Line 30
Category 5 Ethernet cable 32
cell states 109
cells
pinned 110
unpinned 109
Change | Column Arrangement | Comment 102
User’s Guide, Revision B
| 145
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Index ______________________________________________________________________________________Trace DSQ and Focus DSQ
Change Instruments In Use screen 106, 107
Change Masses button 75
chemical ionization 28
Chemical Structure Cell 117
Chromatogram 110, 112
zooming in on period of interest 113
chromatogram 68, 74, 76, 115
Chromatogram | Automatic Noise Range 126
Chromatogram | Ranges 125
Chromatogram | Specify Noise Range 126
Chromatogram Ranges Screen 115, 119
chromatography techniques 124
CI calibration gas spectrum 72
CI Gas 85
CO2, isobutane, ammonia,methane, other 86
Type 86
CI Gas tab 85
CI Ion Volume 70
CI Qualification Test 70
CI Reagent Gas
connecting 28
CI Reagent Gas Flow 64, 65
CI Reagent Gas Flow screen 70
CI Reagent Gas On 75
CI spectrum, typical 71
CO2 86
Column 42, 43
column 99
installation 34
poor quality 124
Column Characterization 36
Column Measuring Tool 42
Compounds
known ion pattern 119
Configuration screen 84
Configure button 84
Configured Devices 84
Configured Devices panel 88
Continuous button 139
conventions, typographical 18
146 |
User’s Guide, Revision B
cursor
actions,effects, active, inactive, unpinned, pinned
109
active 109
pinning 109
D
damage 24
data system setup 31
DC/RF Gain menu item 88
Delete 119
Delete Grid Row 119
Demonstration Mode 85
Detected RF 54
Detectors and Data tab 89
Diagnostic screen 51, 53, 138
tune window 49
diagnostics 47, 49
Diagnostics | Run Test 95
Diagnostics screen 95, 138
Difference Spectrum Cell 117
Display Options 122, 124
Display Options screen 124
DSQ Features 13
E
EI calibration gas
turning on 61
EI Qualification Test 66, 68
EI.DSQ Tune 68
electron lens hole 72
Enable Cal Gas Source Saver 87
Enable DC/RF Gain Adjustment 88
Enable Manual Calibration 62, 87
Ethernet cable 32
Experiment | Full Scan 71
F
features 14, 15
Ferrule 42
Fil/Mult/Dyn Off. 63
filament 60, 63, 72
Trace DSQ and Focus DSQ ______________________________________________________________________________________ Index
Focus
GC 89
Focus GC 15
Focus GC User’s Manual 35
Fore Pressure 47
Full Automatic Tune 61
G
gas chromatograph
configuration 88
gas connections
carrier 27
gas lines 30
GC 66
Column Eval,column characterization,column
characterization 36
leak check 37, 64
setup 33
GC Column 41
GC injection 99
GC instrument configuration 98
GC parameters
setting up 90
GC serial cable 32
GC/MS Test Kit 106, 107
General tab 85, 88
H
heaters readback 142
heaters status readback 142
heatsink 138, 139
Height 123
Hit List Cell 117
I
I/R Tool 70
In Use field 106, 107
Injector
connection 34
Inlet Valve 70
Insert Cells 112
Inst Meth 103
Installation Qualification test 73, 75
installation spec, EI 66
Instructions.doc 143
Instrument | CI Reagent Gas 70
Instrument | Fil/Mult/Dyn On 60
Instrument | System On 60
Instrument Configuration 62, 143
Instrument Configuration screen 84, 89
Instrument method 70
instrument method 101
Instrument Setup 70, 98
Instrument Setup window 98
Instrument Status Tabs 47
Ion Gauge 47
Ion Offset 62
Ion Source 65
ion source
dirty 124
Ion Source Temperature 65
Ion Volume 41, 71
Ion Volume Tool 41
Isobutane 86
Iso-octane 101
K
Keypad button 34
K-factor 36
L
Labels tab 123, 124
Leak check
carrier gas supply line 30
reagent gas supply line 30
leak check 56
gas lines 30
leak check, GC 37, 64
leaks
troubleshooting 56
library
Qual Browser 116
Library Options 118
Library Search 116
Library Spectrum Cell 117
User’s Guide, Revision B
|147
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Index ______________________________________________________________________________________Trace DSQ and Focus DSQ
M
Manual Calibration 62
Manual Calibration menu item 87
Manual Calibration screen 62
manual injections 105
Manual Noise Region 125
Mass Range 120
Mass Range Chromatogram 121
Mass Spectrum 112
Methane 28, 86
methane CI spectrum, typical 71
missing items 24
Mouse
functions 113, 114
MS covers 44
MS method editor 95
MS Transfer Line 41, 89
N
NCI Installation Qualification test 76
NCI method 76
Negative CI Installation Qualification test 74
negative ion CI 70
Negative Ions 62
negative-ion button 74
noise range 125
O
octafluoronaphthalene 76, 106, 107, 108
octafluoronaphthalene (OFN) 68, 76
octafluoronaphthalene injection 76
optional software 143
options 14, 15
Oven temperature 37, 41, 65
P
path 103
peak 116
peak detection
signal-to-noise ratio 124
Peak Detection Settings 124
148 |
User’s Guide, Revision B
Peaks
eluting 116
heights
areas 122
PICI Calibration Gas 72
PICI Installation Qualification test 74
PICI tests 73
PICI.dsqtune 73
pinned 115
Plot Type 120
Plunger strokes 100
position 103
positive ion CI 70
Post Injection Washes 100
Post-injection dwell time 100
power
data system 31
TRACE DSQ 44
PPINICI tab 86
Pre Injection Washes 100
preferred pressure units 88
Prefilter 62
Pre-injection dwell time 100
Pressure Units 85
Print Diagnostics Report button 95
Q
Qual Browser 74, 76, 111, 115, 120
cursor actions (table) 110
determining peak areas 122
determining peak heights 122
library search 116
Library Search Results window (figure) 117
signal-to-noise ratio 124
subtracting background contamination from a
spectrum 116
qualification test, EI 66
quantitation 122
R
R5 138
Range
functions 113, 115
Trace DSQ and Focus DSQ ______________________________________________________________________________________ Index
Ranges 119
subtracting spectra 116
Read This First 11
Readme button 143
Reagent Gas Flow 70
Reagent Gas On 70
Reagent Gas spectrum 71
Reagent Gas Supply Line 30
recording samples 103
Relative Abundance vs. m/z 113
Remote Start Active High 85
Resolution Calibration 62
Restore button 62
retention 121
retention time 115
RF dip calibration
setup
RF dip 51
RF Dip Calibration readback 142
RF gain adjustment 138
RF gain calibration 53
RF Gain Calibration button 54
RF Gain Calibration screen 54
RF Gain Calibration Test 54
RF generator PCB 138, 139
RF Modulation 54
RF Null adjustment 138
RIGHT_SSL_EI_Fullscan.meth 98
RMS 125
Rod DC 88
Rod DC readback 139
Rod DC Test 138
Rod DC Test button 139
Rod DC Test Fails 52
Rod DC Test screen 139
Rod DC values 139
root mean square 125
Rotary-Vane Pump 38
Run Sequence screen 105, 106, 107, 108
Run Tests 49, 51, 53, 138
S
S/N 76
sample ID 103
Sample Probe upgrade option 40
Sample Rinses 100
Sample Volume 100
Samples
type 103
sampling/injection 100
second Rotary-Vane Pump 40
Septum 42, 43
Sequence
setup columns 103
sequence
running 104, 105
saving 104
Sequence Setup
Inst Meth 103
path 103
position 103
sample type 103
sample ID 103
vial number 103
Sequence Setup window 102
Serial Port 88
Service Personnel 87
Service tab 87
setup
check air/water 56
check initial tune 60
data system 31
GC 33
RF gain 53
running diagnostics 49
starting up 45
training 78
unpacking 24
shipping damage 24
Show Manual Tune View 97
signal-to-noise
low ratios 124
measurement 124
ratio 124
Signal-to-Noise Calculator 68, 74
signal-to-noise ratio
EI 68
PCI 74
software training 78
User’s Guide, Revision B
|149
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Index ______________________________________________________________________________________Trace DSQ and Focus DSQ
solvent
elute 99
solvents
rinse 101
Source Saver tab 87
specifications 14, 15
spectrum 68, 74, 76, 110
air/water 57
background 61
calibration gas CI 72
calibration gas EI 61
methane CI 71
subtracting background contamination 116
Start Instrument field 107
starting up 45
Status tab 85
Subtract Background Contamination 116
Swagelok fittings
inlet 135
nut 134
plugs 137
Swagelok and inlet connection 135
T
Target RF 54
Temperature Settings screen 48
TIC 121
Time Period of Interest 113
Time Range field 115
Timeout 87
tools
adding 74
training 78
Transfer Line 43
Transfer Line Cable 33
Transfer Line Nut 42
transfer line union 68
troubleshooting 69
150 |
User’s Guide, Revision B
Tune 83, 87, 95
automatic, full 96
manual calibration 87
Tune | View Tune Report 95
Tune desktop icon 46
Tune Path 85
Tune Window 95
Tune window 56, 63, 68, 73, 74, 76, 85, 97, 142
Turbo Pump 47
Type 119
typographical conventions 18
U
unpacking 24
unpinned 115
upgrades 82
V
Vacuum Compensation 44
vacuum status readback 142
vial number 103
View | Spectrum 113
W
Waiting for Contact Closure 108
washes 100
website 82
X
Xcalibur CD 143
Xcalibur Instrument Configuration icon 84
Xcalibur Setup screen 143
Xcalibur software training 78
XInstall.exe 143
Z
Zoom 122
Zoom Reset 119
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