ISQ and TSQ 8000

Direct Probe System User Guide

1R120505-0006 Revision B December 2012

© 2012 Thermo Fisher Scientific Inc. All rights reserved.

TSQ 8000, ISQ, TRACE 1300, TRACE 1310, and TraceFinder are trademarks, and Xcalibur is a registered
trademark of Thermo Fisher Scientific in the United States.

The following are registered trademarks in the United States and other countries: Microsoft, Windows, XP,
Office, and Excel are registered trademarks of Microsoft.
All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.
The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.

Release history: Revision A, October 2012; Revision B, December 2012

Software version: Thermo Foundation 2.0 SP1; Xcalibur 2.2 SP1

For Research Use Only. Not for use in diagnostic procedures.

 C

Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
About Your System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Power Ratings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Environmental Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Safety Symbols and Signal Words . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Hazardous Substances Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Biological Hazard Warning Note. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Venting Toxic Gases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi

Chapter 1 Using the Direct Probes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

How the Direct Probe System Works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Using the Probe to Analyze Cholesterol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Step 1: Set Up the Direct Probe System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Step 2: Tune and Calibrate the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . 11
Step 3: Replace the Repeller in the Ion Source Cartridge . . . . . . . . . . . . . . . . 11
Step 4: Program the Direct Probe Controller. . . . . . . . . . . . . . . . . . . . . . . . . 30
Step 5: Prepare the Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Step 6: Create an Xcalibur Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Step 7: Create a Sequence File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Step 8: Insert the Probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Step 9: Collect the Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Step 10: Remove the Probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Step 11: Analyze the Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Loading Probe Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Cleaning the Probe Shaft, Direct Probe Controller, DIP Sample Cups,
and DEP Filament. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Chapter 2 Ordering Spare Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61

Thermo Scientific ISQ and TSQ 8000 Direct Probe System User Guide iii
 Declaration
Manufacturer: Thermo Fisher Scientific

Thermo Fisher Scientific is the manufacturer of the instrument described in this manual and, as such, is responsible for
the instrument safety, reliability and performance only if:
• installation,
• recalibration, and
• changes and repairs

have been carried out by authorized personnel and if:

• the local installation complies with local law regulations,
• the instrument is used according to the instructions provided, and
• if its operation is only entrusted to qualified trained personnel.

Thermo Fisher Scientific is not liable for any damages derived from the non-compliance with the aforementioned
recommendations.
Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable domestic and international regulations. When the system is delivered to you, it meets all pertinent
electromagnetic compatibility (EMC) and safety standards as described in the next section or sections by product name.

Changes that you make to your system may void compliance with one or more of these EMC and safety standards.
Changes to your system include replacing a part or adding components, options, or peripherals not specifically
authorized and qualified by Thermo Fisher Scientific. To ensure continued compliance with EMC and safety standards,
replacement parts and additional components, options, and peripherals must be ordered from Thermo Fisher Scientific
or one of its authorized representatives.
EMC Directive 89/336/EEC
EMC compliance has been evaluated by Professional Testing.
• ITQ and Ion Trap Series standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001,
IEC 61010-2-081:2001
• Direct Probe Controller (DPC) standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001,
IEC 61010-2-081:2001
• ISQ standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001, IEC 61010-2-081:2001
• TSQ 8000 standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001, IEC 61010-2-081:2001
Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1:2001.
FCC Compliance Statement
 THIS DEVICE COMPLIES WITH PART 15 OF THE FCC RULES. OPERATION IS SUBJECT TO
THE FOLLOWING TWO CONDITIONS: (1) THIS DEVICE MAY NOT CAUSE HARMFUL
INTERFERENCE, AND (2) THIS DEVICE MUST ACCEPT ANY INTERFERENCE RECEIVED,
INCLUDING INTERFERENCE THAT MAY CAUSE UNDESIRED OPERATION.

CAUTION Read and understand the various precautionary notes, signs and symbols
contained inside this manual pertaining to the safe use and operation of this product
before using it.

Notice on Lifting and Handling of

Thermo Scientific Instruments
For your safety, and in compliance with international regulations, the physical handling of this Thermo Fisher Scientific
instrument requires a team effort to lift and/or move the instrument. This instrument is too heavy and/or bulky for one
person alone to handle safely.

Notice on the Proper Use of

Thermo Scientific Instruments
In compliance with international regulations: Use of this instrument in a manner not specified by Thermo Fisher
Scientific could impair any protection provided by the instrument.

Notice on the Susceptibility

to Electromagnetic Transmissions
Your instrument is designed to work in a controlled electromagnetic environment. Do not use radio frequency
transmitters, such as mobile phones, in close proximity to the instrument.
For manufacturing location, see the label on the instrument.

WEEE Compliance
This product is required to comply with the European Union’s Waste Electrical & Electronic Equipment (WEEE)
Directive 2002/96/EC. It is marked with the following symbol:

Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union
(EU) Member State, and these companies should dispose of or recycle this product. See www.thermoscientific.com/
rohsweee for further information on Thermo Fisher Scientific’s compliance with these Directives and the recyclers in
your country.

WEEE Konformität
Dieses Produkt muss die EU Waste Electrical & Electronic Equipment (WEEE) Richtlinie 2002/96/EC erfüllen.
Das Produkt ist durch folgendes Symbol gekennzeichnet:

Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten

getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Mehr Information
über die Einhaltung dieser Anweisungen durch Thermo Fisher Scientific, über die Verwerter, und weitere Hinweise,
die nützlich sind, um die Produkte zu identifizieren, die unter diese RoHS Anweisung fallen, finden sie unter
www.thermoscientific.com/rohsweee.
 Conformité DEEE
Ce produit doit être conforme à la directive européenne (2002/96/EC) des Déchets d'Equipements Electriques et
Electroniques (DEEE). Il est marqué par le symbole suivant:

Thermo Fisher Scientific s'est associé avec une ou plusieurs compagnies de recyclage dans chaque état membre de
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disponibles sur www.thermoscientific.com/rohsweee.
 P

Preface
This guide contains detailed information about using, maintaining, and troubleshooting the
direct probe system.

Contents
• About Your System
• Related Documentation
• System Requirements
• Power Ratings
• Environmental Requirements
• Safety and Special Notices
• Hazardous Substances Precautions
• Contacting Us

About Your System

Thermo Scientific systems provide the highest caliber gas chromatography/mass spectrometry
(GC/MS) instrumentation available on today’s market.

GC/MS represents a combination of two powerful analytical techniques: GC, which acts as a
separation technique, and MS, which acts as a detection technique. Complex mixtures of
individual compounds can be injected into the GC, either manually or by an autosampler,
and then separated for presentation to the MS. The MS will generate a mass spectrum of the
GC eluate and its components. The mass spectrum can then be used for qualitative
identification as well as accurate and precise quantification of the individual compounds
present in the sample.

A single-quadrupole GC/MS system provides speed and simplicity of operations and method
development with powerful qualitative (full scan, library search) and quantitative (SIM) data.

A triple-quadrupole GC/MS/MS system provides the extra selectivity required for trace
analysis of compounds in complex matrices.

Thermo Scientific ISQ and TSQ 8000 Direct Probe System User Guide ix
Preface
Related Documentation

WARNING Thermo Scientific systems operate safely and reliably under carefully
controlled environmental conditions. If the equipment is used in a manner not specified
by the manufacturer, the protections provided by the equipment might be impaired. If
you maintain a system outside the specifications listed in this guide, failures of many
types, including personal injury or death, might occur. The repair of instrument failures
caused by operation in a manner not specified by the manufacturer is specifically excluded
from the standard warranty and service contract coverage.

Related Documentation
The ISQ Document Set, PN 1R120555, includes these manuals as PDF files:
• ISQ Preinstallation Requirements Guide, PN 1R120555-0001
• ISQ Hardware Manual, PN 1R120555-0002
• ISQ User Guide, PN 1R120555-0003
• ISQ Spare Parts Guide, PN 1R120555-0004

Instrument Help is available from within the ISQ Autotune and Method Editor software.

The TSQ 8000 system includes Help and these manuals as PDF files:
• TSQ 8000 Preinstallation Guide, PN 1R120505-0001
• TSQ 8000 User Guide, PN 1R120505-0002
• TSQ 8000 Hardware Manual, PN 1R120505-0003
• TSQ 8000 Spare Parts Guide, PN 1R120505-0004
• TSQ 8000 Auto SRM User Guide, PN 1R120505-0005
• ISQ and TSQ 8000 Direct Probe System User Guide, PN 1R120505-0006

 To view product manuals

If you have a TSQ 8000 system, go to Start > All Programs > Thermo Instruments >
Manuals > TSQ 8000.
If you have an ISQ, go to Start > All Programs > Thermo Instruments > Manuals >
ISQ.

 To open Help

• From the TSQ 8000 or ISQ window, choose Help > TSQ 8000 Help (or ISQ
Help).
• If available for a specific window or dialog box, click Help or press the F1 key for
information about setting parameters.

x ISQ and TSQ 8000 Direct Probe System User Guide Thermo Scientific
 Preface
System Requirements

For more information, visit www.thermoscientific.com.

System Requirements
Your ISQ or TSQ 8000 data system must meet these minimum requirements.

System Requirements
Hardware • 2.4 GHz processor with 4 GB RAM
• DVD/CD-ROM drive
• Resolution display 1280 × 1024 (XGA)
• 250 GB hard drive
• NTFS format
Software • Microsoft™ Windows™ 7 SP1 Operating System (32-bit or 64-bit with
32-bit Microsoft Office™ 2010) or Microsoft Windows XP™ SP3
• Microsoft Office™ 2010 (32-bit)
• Thermo Foundation 2.0 SP1 (Thermo Scientific software)
• Xcalibur™ 2.2 SP1
• TraceFinder™ 2.1a
a
Your system will function without TraceFinder, but earlier versions of TraceFinder will not work with the
Thermo Scientific software required for this instrument.

Thermo Scientific ISQ and TSQ 8000 Direct Probe System User Guide xi
Preface
Power Ratings

Power Ratings
Mass Spectrometer (MS)
• 100-240 V ac, 50/60 Hz, 15 A max

Gas Chromatograph (GC)

• 120 V ac +6%/-10%, 50/60 Hz, 20 A max
• 230 V ac ±10%, 50/60 Hz, 10 A max

Direct Probe Controller (DPC)

• 100-230 V ac, 50/60 Hz, 2 A max

The foreline pump must be set to the line voltage that will be used at your location. Detailed
instrument specifications are in the Product Specification or Product Brochure.
Note Always make sure that, in case of emergency, it is easy to disconnect the system’s
electrical cable.

Environmental Requirements
The normal operating environment for the TSQ 8000 and ISQ mass spectrometers and the
direct probe controller must have the following characteristics:
• Indoor use only
• Altitude up to 2000 meters
• Maximum relative humidity between 5% and 95% up to 31 °C. The maximum relative
humidity decreases linearly to 67% as the temperature climbs to 35 °C.
• Voltage variations not exceeding 10% of the nominal value
• Transient overvoltages not exceeding those specified in category II of IEC 60364-4-443.

Use the following guidelines to ensure your site has the proper environmental conditions for
the system:
1. Ensure that your room temperature is 5-40 °C (41-104 °F). The analytical performance is
only confirmed for temperatures between 15-35 °C (59-95 °F). For best performance, the
operating temperature should be constant. Use the table below to calculate the amount of
heat your system will generate and ensure your air-conditioning system can handle that
amount of heat
Table 1. Heat output of system components (Sheet 1 of 2)
Heat Output (BTU
Instrument Heat Output (W)
per Hr)
ISQ, including foreline pump 4095 1200
TSQ 8000, including foreline pump 3685 1080

xii ISQ and TSQ 8000 Direct Probe System User Guide Thermo Scientific
 Preface
Safety and Special Notices

Table 1. Heat output of system components (Sheet 2 of 2)

Heat Output (BTU
Instrument Heat Output (W)
per Hr)
TRACE 1300 and TRACE 1310 6830 2000
Direct Probe Controller 819 240
Computer1 1365 400
Monitor1 85 25
AI/AS 1310 325 95
TriPlus RSH 6832 or 13663 2002 or 4003
1
Power requirements vary by manufacturer.
2
With one power module.
3
With two power modules.

2. Ensure that the relative humidity in your laboratory is between 5 and 95% with no
condensation. A temperature and humidity monitor in your laboratory helps ensure that
the climate is within these specifications.
3. Ensure that the air in your site is free of excess particulate matter.
For reference, the air should contain fewer than 100,000 particles (larger than 5 μm) per
cubic meter. If the concentration is larger than this amount, dust can accumulate on
electronic components. This accumulation reduces their ability to cool off properly and
could cause them to overheat. If your environment is particularly dusty, we recommend
that you purchase the optional dust filter for your MS.
4. Ensure that your site is free of electrostatic discharge (ESD), which may damage the
electronic components of your system. Ensure your static has been discharged before
touching internal components of the instrument. ESD can damage sensitive components,
resulting in premature failures.

Safety and Special Notices

Make sure you follow the precautionary statements presented in this guide. The safety and
other special notices appear in boxes.

Special Notices
Special notices include the following:

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal
performance of the system.

Thermo Scientific ISQ and TSQ 8000 Direct Probe System User Guide xiii
Preface
Safety and Special Notices

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Safety Symbols and Signal Words

All safety symbols are followed by WARNING or CAUTION, which indicates the degree of risk
for personal injury, instrument damage, or both. Cautions and warnings are following by a
descriptor. A WARNING is intended to prevent improper actions that could cause personal
injury. A CAUTION is intended to prevent improper actions that might cause personal injury
or instrument damage. You can find the following safety symbols on your instrument or in
this guide.

Symbol Descriptor

BIOHAZARD: Indicates that a biohazard will, could, or might occur.

BURN HAZARD: Alerts you to the presence of a hot surface that could or
might cause burn injuries.

ELECTRICAL SHOCK HAZARD: Indicates that an electrical shock could or

might occur.

FIRE HAZARD: Indicates a risk of fire or flammability could or might occur.

FLAMMABLE GAS HAZARD: Alerts you to gases that are compressed,

liquefied or dissolved under pressure and can ignite on contact with an
ignition source. This symbol indicates this risk could or might cause physical
injury.

GLOVES REQUIRED: Indicates that you must wear gloves when performing
a task or physical injury could or might occur.

HAND AND CHEMICAL HAZARD: Indicates that chemical damage or

physical injury could or might occur.

xiv ISQ and TSQ 8000 Direct Probe System User Guide Thermo Scientific
 Preface
Hazardous Substances Precautions

Symbol Descriptor

INSTRUMENT DAMAGE: Indicates that damage to the instrument or

component might occur. This damage might not be covered under the
standard warranty.

LIFTING HAZARD: Indicates that a physical injury could or might occur if

two or more people do not lift an object.

MATERIAL AND EYE HAZARD: Indicates that eye damage could or might
occur.

RADIOACTIVE HAZARD: Indicates that exposure to radioactive material

could or might occur.

READ MANUAL: Alerts you to carefully read your instrument’s

documentation to ensure your safety and the instrument’s operational
ability. Failing to carefully read the documentation could or might put you at
risk for a physical injury.

TOXIC SUBSTANCES HAZARD: Indicates that exposure to a toxic substance

could occur and that exposure could or might cause personal injury or death.

For the prevention of personal injury, this general warning symbol precedes
the WARNING safety alert word and meets the ISO 3864-2 standard. In the
vocabulary of ANSI Z535 signs, this symbol indicates a possible personal
injury hazard exists if the instrument is improperly used or if unsafe actions
occur. This symbol and another appropriate safety symbol alerts you to an
imminent or potential hazard that could cause personal injury.

Hazardous Substances Precautions

WARNING Before using hazardous substances (toxic, harmful, and so on), please read the
hazard indications and information reported in the applicable Material Safety Data Sheet
(MSDS). Use personal protective equipment according to the safety requirements.

Thermo Scientific ISQ and TSQ 8000 Direct Probe System User Guide xv
Preface
Contacting Us

Biological Hazard Warning Note

In laboratories where samples with potential biological hazards are handled, the user must
label any equipment or parts which might become contaminated with biohazardous material.

The appropriate warning labels are included with the shipment of the instrument. It is the
user’s responsibility to label the relevant parts of the equipment.

When working with biohazardous materials, you are responsible for fulfilling the following
mandatory requirements:
• Providing instructions on how to safely handle biohazardous material.
• Training operators to be aware of potential hazards.
• Providing personal protective equipment.
• Providing instructions for what to do if operators are exposed to aerosols or vapors during
normal operation (within the intended use of the equipment) or in case of single fault
situations such as a broken vial. The protective measures must consider potential contact
with the skin, mouth, nose (respiratory organs), and eyes.
• Providing instructions for decontamination and safe disposal of relevant parts.

WARNING The user or operator is responsible for the safe handling of hazardous
chemicals or biological compounds including (but not limited to) bacterial or viral
samples and the associated waste, according to international and local regulations.

Venting Toxic Gases

When analyzing toxic compounds, be aware that during the normal operation of the GC
some of the sample might be vented outside the instrument through the split and purge flow
vents; therefore, be sure to vent the exhaust gases to a fume hood. Consult local
environmental and safety regulations for instructions in exhausting fumes from your system.

Contacting Us
There are several ways to contact Thermo Fisher Scientific for the information you need.

 To find out more about our products

Go to www.thermo.com/ms for information about our products.

 To get local contact information for sales or service

Go to www.thermoscientific.com/wps/portal/ts/contactus.

xvi ISQ and TSQ 8000 Direct Probe System User Guide Thermo Scientific
 Preface
Contacting Us

 To suggest changes to documentation or to Help

• Fill out a reader survey online at www.surveymonkey.com/s/PQM6P62.

• Send an e-mail message to the Technical Publications Editor at
[email protected].

Thermo Scientific ISQ and TSQ 8000 Direct Probe System User Guide xvii
 1

Using the Direct Probes

This chapter explains how to use the direct insertion probe (DIP) and direct exposure probe
(DEP) with the ISQ and TSQ 8000 mass spectrometers.

The direct sample probes provide an alternate means of sample introduction that reduces or
eliminates sample preparation time. The technique also requires a minimal sample amount for
testing (micrograms to nanograms). This system, designed for use with a broad range of
Thermo Scientific GC-MS systems, is ideal for quickly screening samples or for any
application that does not require or allow a GC column separation.

The direct probes provide a quick, simple method for sample introduction directly into the
mass spectrometer ion source, allowing for accurate analysis of highly polar, thermally labile
solid or liquid compounds, polymers, composites, pieces of materials, or organisms. The
direct probes are compatible with all modes of ionization and mass analysis: EI, CI, Full Scan,
SIM, SRM, and MS/MS. Switching to a direct probe system takes less than three minutes and
leaves the GC interface undisturbed.

The direct probes can determine the mass spectrum of substances that cannot usually be
analyzed by gas chromatography. The samples can be thermally labile, highly active, or have
physical characteristics (for example, a boiling point) that would prohibit or limit their ability
to be analyzed by a GC system. The direct probes allow you to place a small amount of sample
on the probe’s end, which then is inserted directly into the ion source, and the sample is
vaporized or pyrolyzed directly in the source, under vacuum. The direct probes not only allow
rapid sample preparation and introduction but also provide an alternative to conventional
methods of complex sample analysis.

The DIP can be used to analyze solid or liquid samples. The DIP is used to controllably (10
to 120 °C) heat a sample up to 450 °C in a glass or aluminum crucible in the vacuum
chamber. The combination of heat and low pressure allows many compounds to enter the gas
phase where they can be ionized and detected by the mass spectrometer. This approach can be
useful when the traditional separation technique using a GC either takes too long or requires
temperatures that degrade the sample before it can be sent into the mass spectrometer as well
as to look at the volatile decomposition products of non-volatile materials, like polymers. The
process of thermal decomposition in absence of oxygen is called pyrolysis.

The DEP allows you to rapidly (from 1 to 1,000 °C/s) heat the sample applied to the
filament, and after flash vaporization or pyrolysis introduce solid or liquid samples directly
into the ion source, which is used to rapidly analyze liquids, solids, or trace components in
solid matrices.

Thermo Scientific ISQ and TSQ 8000 Direct Probe System User Guide 1
1 Using the Direct Probes

Note Unless noted otherwise, all instructions for using the direct probe controllers apply
to both the ISQ and TSQ 8000 mass spectrometers.

Contents
• How the Direct Probe System Works
• Using the Probe to Analyze Cholesterol
• Loading Probe Samples
• Cleaning the Probe Shaft, Direct Probe Controller, DIP Sample Cups,
and DEP Filament

2 ISQ and TSQ 8000 Direct Probe System User Guide Thermo Scientific
 1 Using the Direct Probes
How the Direct Probe System Works

How the Direct Probe System Works

The direct probe controller is an instrument used to generate analytically useful signals in
collaboration with the sample probe (DIP or DEP) and mass spectrometer. The main
advantage to using a probe is that it allows you to rapidly screen samples for any application
that does not require a GC column separation. Another advantage is that a probe allows you
to volatize or pyrolyze a wide range of samples directly into the ion source.

To use the direct insertion probe (DIP), it must be attached to the direct probe controller.
Once the probe is attached and you turn on the direct probe controller, the direct probe
controller automatically identifies the type of probe attached. To program a DIP, you must set
an initial temperature and hold time, a temperature ramp, and a final hold time and
temperature. The DIP allows for a maximum of two temperature ramps.

The initial temperature of the DIP can be set within the range of 30 °C to 450 °C. You can
program the temperature ramp in 10 °C increments from 10 °C/min to 120 °C/min. There is
also a maximum heating rate that will heat the DIP tip as rapidly as possible. The final
temperature must be at least 10 °C above the initial temperature if a ramp is being used. You
can set the time to hold the sample at the final temperature within a range of 0 to 900
seconds. You can also use a second ramp, but it must have a final temperature of at least 10 °C
above the final temperature used in the first ramp.

WARNING - BURN HAZARD: Keeping the DIP in the instrument at 350 °C for more
than 15 minutes will cause the probe tip to become very hot. Use caution when handling
a probe at this temperature.

To use the direct exposure probe (DEP), it must be attached to the direct probe controller.
Once the direct exposure probe is attached and you turn on the direct probe controller, the
direct probe controller automatically identifies the type of probe attached. To program a DEP,
you must set an initial current and hold time, a current ramp, and a final hold time and
current. The software used for your particular analysis is determined when you develop your
analytical method.

The initial current of the DEP can be set within a range of 0 mA to 1000 mA. You can
program the current ramp within a range of 0 mA/min to 1000 mA/s. The final current must
be greater than the initial current if a ramp is being used. You can set the time to hold the
sample at the final current within a range of 0 to 900 seconds.

WARNING - BURN HAZARD: Keeping the DEP above 750 mA for more than 15 minutes
will cause the probe tip to become very hot. Use caution when handling a probe at this
temperature.

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1 Using the Direct Probes
How the Direct Probe System Works

The direct probe system consists of the following components:

Figure 1. The Direct Probe System

Direct Probe

Direct Probe Controller

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Using the Probe to Analyze Cholesterol

Using the Probe to Analyze Cholesterol

Both the DIP Kit and the DEP Kit contain samples for analyzing cholesterol. The steps below
can also be used to set up the system for the analysis of other compounds. The cholesterol
sample is used for instrument qualification to ensure it is working properly. The process for
using the probe to analyze cholesterol on the ISQ or TSQ 8000 system is as follows:
• Initial Setup
Step 1: Set Up the Direct Probe System
Step 2: Tune and Calibrate the Mass Spectrometer
Step 3: Replace the Repeller in the Ion Source Cartridge
• Analyzing the Sample
Step 4: Program the Direct Probe Controller
Step 5: Prepare the Sample
Step 6: Create an Xcalibur Method
Step 7: Create a Sequence File
Step 8: Insert the Probe
Step 9: Collect the Data
Step 10: Remove the Probe
Step 11: Analyze the Data

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Step 1: Set Up the Direct Probe System

To set up the direct probe system:
1. Place the direct probe controller on top of or to the side of the ISQ or TSQ 8000 mass
spectrometer.
Note If your GC/MS system has an autosampler attached to it, you may have to set the
direct probe controller on the table to the left of the mass spectrometer.

2. Use the cable in the kit to connect the direct probe controller to the mass spectrometer.

a. Connect the 9-pin end of the cable to the Remote Ready connector on the back of
the direct probe controller.
Figure 2. Connecting the Cable to the Direct Probe Controller

Remote Ready Connector

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b. If you have an ISQ mass spectrometer, connect the small round end of the cable to
the Accessory Start connector on the back of the instrument.
Figure 3. Connecting the Cable to the ISQ Mass Spectrometer

Accessory
Start
Connector

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c. If you have a TSQ 8000 mass spectrometer, connect the small round end of the cable
to the Accessory Start connector on the side of the instrument.
Figure 4. Connecting the Cable to the TSQ 8000 Mass Spectrometer

Accessory Start
Connector

d. (Optional) Choose an air source to use as a probe coolant and connect it to the Air
Source connector on the back of the direct probe controller.
The air source must be dry air or nitrogen at no more than 100 psi. We recommend
80 psi for normal operation. The coolant is used with the probe to rapidly cool the
probe tip, which allows rapid sample throughput. However, it is not designed for
subambient operation, and room temperature will affect the minimum probe tip
temperature.

Note The probe tip must be able to be cooled to 35 °C for automatic cooling to
complete. Press the Start/Stop button to cancel the automatic air cooling to less than
35 °C.

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Figure 5. Connecting the Air Source to the Direct Probe Controller

Air Source Connector

e. Connect one end of the power cord to the direct probe controller and the other end
to the electrical outlet. The power cord provides the safety grounding for the unit.
Always make sure that, in case of emergency, it is easy to disconnect the electrical
cable.
Figure 6. Connecting the Direct Probe Controller to the Electrical Outlet

AC Input Connector

f. Press the top ( | ) of the power switch on the back of the direct probe controller to
power it on.
Figure 7. Powering On the Direct Probe Controller

Power Switch

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3. Connect one end of the communication cable to the end of the probe.
Figure 8. Connecting the Communication Cable to the Probe

Cable Connector
on the Probe

4. Connect the other end of the communication cable to the direct probe controller. Match
the red dot located on the cable to the red dot located on the direct probe controller and
firmly insert the cable until it locks in position.
Figure 9. Connecting the Communication Cable to the Direct Probe Controller

Cradle

Cable
Connector

5. Place the probe in the cradle of the direct probe controller.

Figure 10. Placing the Probe in the Cradle

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6. Power-on the mass spectrometer, if necessary.

Step 2: Tune and Calibrate the Mass Spectrometer

If you are using the ISQ mass spectrometer, refer to the online help of the Tune software for
information about determining if the instrument has been tuned and calibrated.

If you are using the TSQ 8000 mass spectrometer, click Auto Tune on the TSQ 8000
dashboard to tune and calibrate the instrument.

Refer to your mass spectrometer user guide for more information about tuning the
instrument.

IMPORTANT Set the repeller voltage to zero and be sure that the tune file saved and
used for the analysis has the repeller set to zero. If automatic tuning returns a non-zero
repeller value, you might have to clean the ion source. Additionally, you may create a new
tune type that does not change the repeller voltage from zero volts.

Step 3: Replace the Repeller in the Ion Source Cartridge

To use the probe with the ISQ or TSQ 8000 mass spectrometer, you must replace the repeller
inside the ion source cartridge. The repeller that comes standard on the ISQ and TSQ 8000
systems does not have a hole in it. The hole in the new repeller allows the sample that is
volatized by the probe to enter the ionization region of the ISQ or TSQ 8000 mass
spectrometer. Your Direct Insertion Probe Kit or Direct Exposure Probe Kit contains the
correct repeller to use with the probe.

To replace the standard repeller with a probe repeller:

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1. Twist off the round vacuum interlock knob located on the front of the instrument and set
it aside. As you can see, the knob covers access to a long tunnel that goes into the
instrument. This tunnel is called the vacuum interlock.
Figure 11. Removing the Vacuum Interlock Knob

Vacuum Interlock Knob

Tip To prevent leaks through the vacuum interlock, we recommend that you leave the
vacuum interlock knob attached to the instrument, except when you are removing or
inserting the ion source cartridge. After you reattach the knob, press the Evacuate button
to eliminate any air inside the vacuum interlock.

2. Get the source exchange tool out of the ISQ or TSQ 8000 Toolkit that shipped with your
instrument. It is used to remove and insert the ion source cartridge through the vacuum
interlock. The tool has a large black handle on one end and a stainless steel barrel at the
other. On the black handle is a diagram describing how to insert and remove the ion
source cartridge from the instrument using the tool. The stainless steel barrel is cut with a

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track, and the black handle moves up and over the track, depending on whether you are
removing or installing an ion source cartridge.
Figure 12. Components of the Source Exchange Tool

Alignment
Groove
Left Track
Handle of Barrel

Right Track
Usage Diagram of Barrel

3. Grasp the handle of the source exchange tool in one hand and use your other hand to pull
the metal barrel out and away from the handle so that the tool is fully extended.
4. Rotate the black handle to the right to lock it in place on the vacuum manifold.
a. With your hand around the barrel, twist the tool until the alignment groove at the
end of the barrel aligns with the left screw around the slot vacated by the vacuum
interlock knob.
Figure 13. Inserting the Source Exchange Tool

Alignment
Groove

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b. Twist and push the barrel to the right until it clicks into place under the screw at the
top of the slot.
Figure 14. Twisting the Tool Into Place

Alignment
Groove

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5. Press the blue Evacuate button on the front of the instrument. When the Evacuate light
flashes green for approximately 20 seconds and turns off, the Ready to Open light turns
solid green. At that point, the air has been evacuated from the instrument and it is safe to
open the vacuum interlock valve.
Figure 15. Evacuating the Instrument

Vacuum
Interlock
Handle

Evacuate
Button

6. Twist, then loosen the top part of the vacuum interlock handle to allow the entire handle
to move up and down. This handle controls the interior ball valve, which seals the
vacuum chamber and protects it from the outside pressure.
7. Push the handle down and then twist the top of it in the opposite direction to lock it into
place.
Figure 16. Pulling Down the Vacuum Interlock Handle

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8. Pull the handle up to open the interior ball valve.

Note If a minute has elapsed since the Ready to Open light first came on, the Ready to
Open light will turn off. You should press the Evacuate button and wait until the Ready
to Open light is lit again before opening the valve. Do not open the valve if the ready to
open light is not on. This may indicate a leak in the valve region. When a leak is detected
during the evacuate sequence, the amber evacuate LED will flash on and off.

9. Slowly push the source exchange tool into the instrument. Because you are removing the
ion volume in this step, you will go down the right side of the metal track on the barrel.
Figure 17. Pushing the Tool into the Instrument

10. Once the tool is all the way in (when the groove at the end of the barrel is covered by the
black handle) twist the handle to the left to engage the ion source cartridge and move it
onto the end of the barrel. You are essentially disconnecting the ion source cartridge from
the ion source block and moving it onto the tool.

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11. Pull the tool toward you and down the left side of the metal track on the barrel. As you
keep pulling it toward you, more and more of the barrel will be exposed.
Figure 18. Pulling the Tool Down the Left Track

12. Once you reach the end of the track (when the back line at the end of the barrel is covered
by the black handle), twist the handle to the left to lock it into place.
Figure 19. Locking the Tool in Place

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13. Pull the vacuum interlock handle down.

Note Be sure to fully extend the tool so that you do not crush the ion source cartridge
with the ball valve.
Figure 20. Pulling the Vacuum Interlock Handle Down

14. Grasp the barrel of the tool and twist it to the left so that the alignment groove moves
toward the left screw. Then pull the tool out of and away from the instrument.
Figure 21. Removing the Tool from the Instrument

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15. Replace the plug in the VPI to prevent accidental venting and excessive leaks.
16. Let the ion source cartridge cool.
17. Hold the handle of the tool with one hand and use the other hand to pull the barrel
toward you and into the handle.
Figure 22. Exposing the Ion Source Cartridge

18. Invert the ion source tool so that the barrel is pointed toward the floor.
Figure 23. Inverting the Tool

Ion Source
Cartridge

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19. Slide the source holder, which is in the ISQ or TSQ 8000 Toolkit, onto the end of the ion
source cartridge. The opening of the source holder is designed to accommodate the
handles of the ion volume.
Figure 24. Attaching the Source Holder

Wing of Ion
Volume

Ion Volume
Source Holder Handles Fit Here

20. Twist the holder to disengage the ion source cartridge from the tool.
21. Set the ion source cartridge and holder on a clean surface.
Figure 25. Removing the Ion Source Cartridge

WARNING - BURN HAZARD: The ion source cartridge may be hot.

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22. Let the ion source cartridge cool down before removing it from the source holder.
23. Disassemble the ion source cartridge by removing the locking ring first, then the repeller
spring, then the nut, insulator, and repeller (which comes out in one piece).
IMPORTANT Always wear clean, lint-free gloves when handling the ion source cartridge.

Figure 26. Ion Source Cartridge Components

Lens 2

Ion EI Ion Volume

Volume-Repeller
Insulator Ion Cartridge Sleeve

Repeller
Spring Lens 3/RF Lens
Lens 1
Ion Volume
Locking Ring

Probe
Repeller

Repeller
Nut

24. Set the components on a clean work surface.

25. Replace the standard repeller (no hole) with the probe repeller.
a. Unscrew the repeller nut.
b. Slide the insulator off the repeller.
c. Put the insulator on the probe repeller. Make sure it goes on in the correct direction.
d. Screw the repeller nut down on the probe repeller until it is snug. Make sure the
repeller is centered in the ceramic ring while tightening the nut.

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26. Insert the large flat end of the probe repeller so that it rests on top of the ion volume.
Figure 27. Inserting the Probe Repeller into the Source Sleeve

Large End of
Probe
Repeller

27. Attach the repeller spring to the probe repeller.

Figure 28. Inserting the Repeller Spring into the Sleeve

Repeller
Spring

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28. Place the locking ring on top of the repeller spring so that the probe repeller protrudes
through the center hole on the locking ring. The hooks on the sleeve fit between the
larger gaps on the locking ring.

Note Do not twist and lock the locking ring at this time.
Figure 29. Inserting the Locking Ring into the Sleeve

Larger Gaps on
Locking Ring

29. Hold the source holder and ion source cartridge in one hand and use the other hand to
hold the source exchange tool so that the barrel is facing toward the floor. The diagram on
the tool should be facing you.
IMPORTANT If you try to attach the ion source cartridge to the tool without inverting it,
the components may fall, so make sure you are working over a table. Otherwise, you may
have to stop and clean the components again.

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30. Look for a small vertical 1/8 in. line engraved on the end of the barrel. There is a similar
engraved line on the sleeve of the ion source cartridge.
Figure 30. Aligning the Tool with the Ion Source Cartridge

Groove
on End of
Tool

Groove
on the
Sleeve

31. Position the line on the tool a half inch to the left of the line on the ion source cartridge so
that the teeth of the locking ring will fit into the grooves on the end of the tool.

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32. Push the ion source cartridge up into the barrel of the tool and twist it until the engraved
lines are aligned. The ion source cartridge should easily slide into place with very little
force.
CAUTION - INSTRUMENT DAMAGE: If you push the ion source cartridge into the barrel
and it does not slide easily into position, make sure the components are assembled
correctly and have not slid out of place inside the sleeve. Using too much force when
inserting the ion source cartridge into the barrel can cause damage. The ion volume and
lenses have keying features to assure the lens spring contacts will align with the metal parts
of the lenses.

Figure 31. Reattaching the Ion Source Cartridge to the Tool

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33. Gently pull the source holder away from the ion source cartridge.
Figure 32. Removing the Source Holder

34. Turn the source exchange tool around so that the ion source cartridge is furthest away
from you.
35. Firmly grasp the black handle of the source exchange tool in one hand and use your other
hand to pull the metal barrel out and away from the handle so that the tool is fully
extended.The ion source cartridge is now hidden inside the barrel.
36. When the barrel can go no further, twist the handle to the left to lock it into position.
37. Insert the barrel end of the source exchange tool into the vacuum interlock and twist it to
the right to lock it into position.

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Figure 33. Evacuating the Instrument

Evacuate
Button

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38. Press the Evacuate button on the front of the instrument. When the Evacuate light
flashes green for approximately 20 seconds and turns off, the Ready to Open light turns
solid green. At that point, the air has been evacuated from the instrument and it is safe to
open it.
39. Pull the vacuum interlock handle up when the Ready to Open light is a solid green.
40. Twist the handle of the tool slightly to the left until it is feels like it is lodged into the
left-most track.
IMPORTANT Make sure you take the correct track on the tool or the ion volume will
disassemble inside the instrument. If that happens, the tool will get stuck and you will
have to shut down, vent the mass spectrometer, and manually remove the ion volume
through the top of the instrument.

41. Push the handle toward the instrument until the end of the handle aligns with the
engraved line at the end of the barrel. When you reach this line, the tool is all the way in
and the ion source cartridge has been placed back onto the ion source block.

CAUTION - INSTRUMENT DAMAGE: Make sure the vacuum interlock handle is all the
way up. Otherwise if you insert the tool with the handle down, you can damage the
instrument.

42. Twist the handle of the ion source tool to the right and pull it back toward you and down
the right side of the barrel’s metal track.
Figure 34. Pulling the Tool Down the Right Track

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43. Pull the vacuum interlock handle down to close the interior ball valve.
Figure 35. Pulling Down the Vacuum Interlock Handle

44. Twist the end of the vacuum interlock handle and flip the handle up so that it rests next
to the vacuum interlock knob location. Then twist the end again to hold it in place.

CAUTION - INSTRUMENT DAMAGE: Do not push the handle all the way up or you will
open the interior ball valve, which will cause you to lose vacuum and possibly damage the
instrument.

45. Remove the tool from the instrument.

46. Reattach the vacuum interlock knob.
Tip To prevent leaks in the vacuum interlock, we recommend that you leave the vacuum
interlock knob attached to the instrument, except when you are removing or inserting the
ion source cartridge. After you reattach the knob, press the Evacuate button will also
eliminate any air inside the vacuum interlock.

47. For optimal performance, wait at least 30 minutes for the ion source to heat up to the
same temperature as the inside of the instrument. Otherwise, the masses or intensities
may be different.

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Step 4: Program the Direct Probe Controller

Programming the Direct Insertion Probe

For the analysis of the cholesterol standard, which is included in your Direct Insertion Probe
Kit, you must set the initial temperature to 50 °C and hold it for 60 seconds. Then you need
to adjust the maximum heating rate to raise the temperature of the probe to 350 °C and hold
it for 40 seconds. The second temperature ramp is not used.

To program the direct probe controller:

1. Set the initial temperature:
a. Press the Method button on the direct probe controller.
b. Press the Up or Down buttons to adjust the temperature.
c. Press Next once the temperature is set and program the initial time.
2. Set the initial time by pressing the Up or Down buttons. Once the initial time is set, press
Next and program the temperature ramp.
3. Set the temperature ramp by pressing the Up or Down buttons. Once the temperature
ramp is set, press Next and program the final temperature.
4. Set the final temperature by pressing the Up or Down buttons. Once the final
temperature is set, press Next and program the final hold time.
5. Set the hold time by pressing the Up or Down buttons. Once the hold time is set, press
Next and program the second temperature ramp rate.

If the second temperature ramp rate is set to Off, press the Next button. The direct probe
controller is now programmed and should display DIP 1 ready. Otherwise, repeat
steps 3-5 to set the second temperature ramp, final temperature and hold time.
6. Save a method:
a. Press the Prog button.
b. Press the Next button to display Save Method 1.
c. Press the Up or Down buttons to change the number (1-9) of the method you are
saving.
d. Once the method number is set, press Next to save it.

Programming the Direct Exposure Probe

For the analysis of the cholesterol standard, which is included in your Direct Exposure Probe
Kit, you must set the initial current to 0 mA and hold it for 30 seconds. Then you need to use
the 20 mA/s rate to raise the current of the probe to 1000 mA and hold it for 30 seconds.

To program the direct probe controller:

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1. Set the initial current:

a. Press the Method button on the direct probe controller.
b. Press the Up or Down buttons to adjust the current.
c. Press Next once the current is set and program the initial time.
2. Set the initial time by pressing the Up or Down buttons. Once the initial time is set, press
Next and program the current ramp.
3. Set the current ramp by pressing the Up or Down buttons. Once the current ramp is set,
press Next and program the final current.
4. Set the final current by pressing the Up or Down buttons. Once the final current is set,
press Next and program the final hold time.
5. Set the hold time by pressing the Up or Down buttons. Once the hold time is set, press
Next and program the second current ramp rate.
6. Save a method:
a. Press the Prog button.
b. Press the Next button to display Save Method 1.
c. Press the Up or Down buttons to change the number (1-9) of the method you are
saving.
d. Once the method number is set, press Next to save it.

Retrieving a Method
To retrieve a previously saved method from the direct probe controller:
1. Press the Prog button to display Load Method: X (methods numbered 1-9).
2. Press the Up and Down buttons to locate a method number.
3. Press the Enter button to select the method number and retrieve the method.

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Step 5: Prepare the Sample

Preparing the sample for the Direct Insertion Probe

To prepare the cholesterol sample in the DIP Test Mix:
1. Place the sample cup holder on a level surface.
2. Insert a clean sample cup into the holder.
3. Use a syringe to inject 1 μL of the (1 ng/μL as supplied) cholesterol solution into the
sample cup.
4. Wait several minutes for the solvent to evaporate.
5. Use tweezers to place the sample cup onto the tip of the probe.

Preparing the sample for the Direct Exposure Probe

To prepare the cholesterol sample in the DEP Test Mix:
1. Place the sample filament holder on a level surface.
2. Insert a clean filament into the holder.
3. Use a syringe to place a drop of the cholesterol solution on the filament.
4. Wait several minutes for the solvent to evaporate.
5. If desired, place another drop of the (1 ng/μL as supplied) cholesterol solution on the
filament.
6. Use tweezers to place the filament onto the tip of the probe.
If the filament is already inserted into the tip of the probe, it is not necessary to take it
out: the solution can be applied to the filament while it is inserted into the tip of the
probe.

Step 6: Create an Xcalibur Method

To create an Xcalibur method:
1. Open the Xcalibur software and click the Instrument Setup icon.

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Figure 36. Creating an Xcalibur Method.

Instrument
Setup Icon

Status Pane

2. Select File | New from the main menu.

3. If you have an ISQ mass spectrometer and are analyzing the cholesterol standard that was
included with your DIP or DEP, enter the 60-400 in the Mass List or Range (amu)
column. Set the MS transfer line and the ion source temperatures to 200 °C. Select Probe

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Run Time for run completion, otherwise you must manually stop the acquisition. See
Figure 37.
Figure 37. Creating a Method for the ISQ Mass Spectrometer

4. If you have a TSQ 8000 mass spectrometer and are analyzing the cholesterol standard
that was included with your DIP or DEP, enter the following parameters. Set the MS
transfer line and the ion source temperatures to 200 °C. Enter 60-400 in the SRM, SIM

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or Scan Masses column. Be sure to select Acquisition-General from the Method Type
pull-down menu. See Figure 38.
Figure 38. Creating a Method for the TSQ 8000 Mass Spectrometer

5. If you are creating a new method and have the GC in the configuration, ensure that
vacuum compensation is on for the GC carrier flow, otherwise, the GC carrier gas flow
will be too high into the ion source. If you do not want to change the current GC
settings, you can obtain the current method from the GC using a command from the
instrument method editor menu.
6. Select File | Save from the main menu.
7. Enter the name of the cholesterol method and click Save. Xcalibur automatically adds the
.meth extension to any method file.
8. Return to the Xcalibur Home Page window.

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Step 7: Create a Sequence File

To create a sequence file:
1. Open the Xcalibur software and click the Sequence Setup icon.
Figure 39. Setting up a Sequence in Xcalibur

Sequence
Setup Icon

Note If your have devices such as an autosampler or GC configured that you are using for
the probe analysis, you may want to remove them from the instrument configuration.
Xcalibur will not start the run if a device is not connected or reporting an error, even if it
is not needed for the analysis. See your mass spectrometer user guide for instructions on
configuring your system.

2. Select File | New to open a blank sequence file.

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3. Enter the settings shown in the figure below.

Figure 40. Creating a Sequence

Sequence List

Note Filenames are not case-sensitive.

4. Select File | Save from the main menu.

5. Enter the name of the new sequence file and click Save to return to the Sequence Setup
window. Xcalibur automatically adds the .sld extension to the filename.

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Step 8: Insert the Probe

To insert the probe:
1. Twist off the round vacuum interlock knob located on the front of the instrument and set
it aside. As you can see, the knob covers access to a long tunnel that goes into the
instrument. This tunnel is called the vacuum interlock.
Figure 41. Removing the Vacuum Interlock Knob

Vacuum
Interlock
Knob

2. Lift the probe with the sample loaded at the tip. .

Figure 42. Direct Insertion Probe

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Figure 43. Direct Exposure Probe

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3. Grasp the handle of the probe in one hand and use your other hand to pull the metal
barrel out and away from the handle so that tool is fully extended.
4. With your hand around the barrel, twist the probe until the alignment groove at the end
of the barrel aligns with the left screw around the slot vacated by the vacuum interlock
knob.
Figure 44. Inserting the Probe

Alignment
Groove

5. Twist and push the barrel to the right until it clicks into place under the screw at the top
of the slot.
Figure 45. Twisting the Probe Into Place

Alignment
Groove

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6. Press the blue Evacuate button on the front of the instrument. When the Evacuate light
flashes green for approximately 20 seconds and turns off, the Ready to Open light turns
solid green. At that point, the air has been evacuated from the instrument and it is safe to
open it.
Figure 46. Evacuating the Instrument

Vacuum
Interlock
Handle

Evacuate
Button

7. Twist, then loosen the top part of the vacuum interlock handle to allow the entire handle
to move up and down. This handle controls the interior ball valve, which seals the
vacuum chamber and protects it from the outside pressure.

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Using the Probe to Analyze Cholesterol

8. Push the handle down and then twist the top of it in the opposite direction to lock it into
place.
Note If a minute has elapsed since the Ready to Open light first came on, the Ready to
Open light will turn off. You should press the Evacuate button and wait until the Ready
to Open light is lit again before opening the valve. Do not open the valve if the ready to
open light is not on. This may indicate a leak in the valve region. When a leak is detected
during the evacuate sequence, the amber evacuate LED will flash on and off.

Figure 47. Pulling Down the Vacuum Interlock Handle

9. Pull the handle up to open the interior ball valve.

10. Slowly push the probe into the instrument.

Note To keep sample cool for volatile samples, do not fully insert the probe into the ion
source until you are ready to press the Start button on either direct probe controller.

11. Once the probe is all the way in, you are ready to perform your analysis.

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Step 9: Collect the Data

To collect the data:
1. Double-click the Xcalibur software icon on your computer desktop.
2. In the Xcalibur Roadmap window, click the Sequence Setup icon
Figure 48. Setting up Sequence in Xcalibur

Sequence
Setup Icon

Note If your have devices such as an autosampler or GC configured that you are using for
the probe analysis, you may want to remove them from the instrument configuration.
Xcalibur will not start the run if a device is not connected or reporting an error, even if it
is not needed for the analysis. See your mass spectrometer user guide for instructions on
configuring your system.

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3. Load the sequence you created in Step 7: Create a Sequence File and skip to step 16
below. If you want to create a different sequence, proceed to step 4 below.

Tip If not all columns are visible on your Sequence Setup page, right-click on any of the
columns to view and add more options.

4. In the Sequence Setup window, click in the first row of the Sample Type column and
select a sample type from the drop-down menu. You should select Unknown when you
are developing an analytical method. The other types of samples require a quantitation
method.

Note To open an existing sequence, you can select File | Open from the main menu or
click the icon and browse to a sequence.

Figure 49. Entering Samples in Xcalibur

Once you select a sample type, default information automatically appears in some of the
other columns. You can also right-click on the field to clear, copy, or paste into the field,
as well as add and delete rows.
Note If you do not have some of the columns discussed here, you can add them by
selecting Change | Column Arrangement in the main menu.

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5. Click the first row in the File Name column and enter a file name for your first data file.

Note Your file name cannot contain spaces.

Figure 50. Selecting a Data File in Xcalibur

Tip You can double-click in the File Name field and browse to a raw file on your
computer.

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6. Click past the Sample ID column, which typically contains the number of the sample.
Since you are in the process of developing your method, you do not have that many
samples so you do not have to enter anything in this field. You can right-click on the field
to clear, copy, or paste a number, as well as add and delete rows.
7. Double-click the first row in the Path column and select the folder in which to store your
data files. You can also right-click on the field to clear, copy, or paste into the field, browse
to a folder on your computer, or add and delete rows.
8. Double-click the first row in the Instrument Method column and navigate to the folder
containing your instrument method. Select the instrument method and click the Open
button. You can also right-click on the field to clear, copy, or paste into the field, browse
to a folder on your computer, or add and delete rows.
Figure 51. Opening an Instrument Method

9. Click past the Processing Method column, which typically contains the path to your
processing method. You are in the process of developing your method and the processing
method is created after your method is finalized.
10. Click past the Level column, which is only used when you have a processing method.
Since you are in the process of developing your method, you do not have the processing
method defined yet.
11. Now that you have set up one row of your sequence, you can stop or you can continue
adding tasks. Click in the next row and repeat steps 2-10 for each additional task in your
sequence. Remember, you can right-click in most fields to add more rows as you go.
12. Once you have created a sequence of all your samples, select File | Save or click the
icon to save the sequence.

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13. Enter a comment and click OK.

14. Click the row you want to run and select Actions | Run This Sample from the main
menu. You can also just click the icon on the main toolbar.
Figure 52. Starting a Sample or Sequence Run in Xcalibur
.

Run Sample Run Sequence

Icon Icon

To run the whole sequence, select Actions | Run Sequence from the main menu. You can
also just click the icon on the main toolbar.
15. In the Run Sequence window, customize the way you want your sequence to run.

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Using the Probe to Analyze Cholesterol

Figure 53. Customizing a Run

a. Select the Start When Ready checkbox to run the sequence when the instruments
are ready.
b. Click the Change Instruments button and use the In Use and Start Instrument
(MS only) columns to define the instruments that are in use and the instrument that
will define the start of the sequence. Then click the OK button.

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Figure 54. Changing Instruments in Use on the TSQ 8000 System

c. In the Instrument Method group, you can browse to the sequence to be used when
the instrument starts up or shuts down.
d. Configure the After Sequence Set System group:
• On—Select this option to leave the instrument fully ready after an acquisition.
• Standby—Select this option to leave the instrument fully ready after an
acquisition.
• Off—Select this option to shut down the MS using the automatic shutdown
sequence built into the instrument firmware. This will turn off high voltages,
heaters, and vacuum pumps.
e. In the User field, you can change your user name. The user name defaults to the
name that was used to log into the computer.
f. In the Run Rows field, enter the rows to be run in the sequence. Each value must be
separated by a hyphen.
g. Select the Priority Sequence checkbox if this sequence has priority over any other
sequence. If someone else’s sequence is running in the background, this setting puts
your sequence ahead of theirs.

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h. In the Processing Actions group, select Quan, Qual, Reports, Programs or Create
Quan Summary. Since you are developing your method, you can skip this setting.
Note The Reports checkbox is only enabled when you select the Qual checkbox. The
Reports and Create Quan Summary checkboxes are only enabled when you select the
Quan checkbox.

16. Click the OK button to run the sample or sequence. and store your data on the
computer.
17. Push the Start/Stop button on the direct probe controller.

Tip Manual control is available for controlling the temperature of the Direct Insertion
Probe during a temperature program. To pause the current program’s ramp, press Enter
on the probe controller. This holds the probe at its current temperature. Now you can
manually adjust the temperature up and down between the low and high points of the
temperature ramp by pressing the Up and Down buttons on the probe controller. Press
the Start button during the paused temperature state to resume the program at the current
ramp. Note that these manual control options are not available when the ramp rate is set
to MAX.

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18. In the Save As window, select a location on your computer that you want to store your
sequence. Then click the Save button.
Figure 55. Saving a Sequence on Your System

19. Once your sequence completes, you are ready to explore your data.

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Step 10: Remove the Probe

To remove the probe:
1. Pull the probe slowly away from the instrument. Before proceeding to the next step, make
sure the probe is fully extended.
CAUTION - INSTRUMENT DAMAGE: Do not remove the probe when it is hot (above
100 °C) or you may damage the inlet valve vacuum seals. Also, make sure the probe is
fully extended before closing the ball valve to prevent damage to the ball valve and the
probe.

2. Close the ball valve by pulling down the vacuum interlock handle.
Figure 56. Pulling Down the Handle

3. Remove the probe from the vacuum interlock.

WARNING - BURN HAZARD: Keeping the probe in the instrument at 350 °C for more
than 15 minutes will cause the probe tip to become very hot. Use caution when handling
a probe at this temperature.

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4. Reattach the vacuum interlock knob.

Tip To prevent leaks through the vacuum interlock, we recommend that you leave the
vacuum interlock knob attached to the instrument, except when you are removing or
inserting the ion source cartridge. After you reattach the knob, press the Evacuate button
to eliminate any air inside the vacuum interlock.

Figure 57. Reattaching the Vacuum Interlock Knob

Vacuum
Interlock
Knob

5. Close the front door of the instrument.

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Step 11: Analyze the Data

Analyzing Data Acquired Using a Direct Insertion Probe

To analyze the data file acquired with a DIP:
Note To analyze another cholesterol sample, repeat the steps in Step 5: Prepare the
Sample and make the appropriate addition to the sequence table.

1. In the Sequence Setup window, click the Roadmap icon to return to the Xcalibur Home
Page.
2. Select Qual Browser to open the Qual Browser window. Refer to the Qual Browser
documentation to learn how to use Qual Browser techniques.
3. Select File | Open and select the raw data file you just ran. Your cholesterol sample should
look similar to the data shown in the figure below.
Figure 58. Analyzing Your DIP Data in Qual Browser

Analyzing the Data Acquired Using a Direct Exposure Probe

To analyze the data file acquired using a DEP:
Note To analyze another cholesterol sample, repeat the steps in Step 5: Prepare the
Sample and make the appropriate addition to the sequence table.

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1. At the Sequence Setup window, click the Roadmap icon to return to the Xcalibur Home
Page.
2. Select Qual Browser to open the Qual Browser window. Refer to the Qual Browser
manual to learn how to use Qual Browser techniques.
3. Select File | Open and select the raw data file you just ran. Your cholesterol sample should
look similar to the data shown in the figure below.
Figure 59. Analyzing Your DEP Data in Qual Browser

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Loading Probe Samples

Loading Probe Samples

Loading Samples into a Direct Insertion Probe
You can load liquid or solid samples into your DIP. However, before loading samples, use the
following precautions to avoid contaminating the ion source.
1. Inspect the DIP tip and the sample cup holder.
2. Clean the DIP tip prior to loading the first sample. A DIP tip can get contaminated by
handling or from previous sample runs.
Figure 60. Cleaning the Probe Tip

3. Handle sample cups with clean tweezers or wear gloves. Use one sample cup for each
sample to avoid cross-contamination. Make sure the sample cup is clean.
4. Place the sample cup holder on a level surface.
Note The sample cup holder can be used to hold several samples at one time and can
be carefully warmed on a laboratory hot plate to evaporate the solvent from liquid
samples.

5. Use clean tweezers to place a sample cup into the sample cup holder.
6. Put a liquid or solid sample into the sample cup.
a. Liquid samples may be injected directly into the sample cup. However, you may
choose to dilute your liquid sample in a solvent, in which case please wait till the
solvent evaporates before inserting the probe into the MS.
b. Put solid samples directly into the sample cup or you can dissolve solid samples in a
solvent.
c. Do not overload sample cups. If your samples are in powder form, get easily
electrostatically charged, or will be subjected to pyrolysis, it may be advantageous to
use aluminium crucibles (PN 0568761) and crimp the top of the crucible with
tweezers or pliers. This will prevent sputtering of the sample while letting the vapors
and gases to still exit the crucible. The aluminium crucibles, unlike the glass ones, do
not have a flared-up rim that prevents them from sinking into the tip. Do not push
the aluminium crucibles all the way down the sample cup holder to be able to easily
retrieve them after the analysis is finished. Excess powder type samples can
electrostatically move through the analyzer and create performance issues.

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Loading Probe Samples

d. Use small samples to help keep the system clean, thereby reducing the amount of
maintenance required. Small samples also keep the background low. In general, the
sample size should be 1 μL or less to minimize contamination of the ion source.
e. Sample along the walls may evaporate at a different temperature than sample at the
bottom, and could therefore distort the evaporation profile.
f. Avoid putting sample on the outer wall of the sample cup. This contaminates the
probe tip.

Loading Liquid Samples on the Direct Insertion Probe

To load liquid samples on the DIP:
1. Use a syringe to inject the liquid sample into a sample cup.
2. Wait for the solvent to evaporate.
3. Use a pair of clean tweezers to insert the sample cup into the probe tip. You can use an
infrared or incandescent bulb as a heat source to increase the evaporation rate of your
solvent. However, be careful not to warm the sample droplet too quickly, or the solvent
could sputter and cause sample loss.

Loading Solid Samples on the Direct Insertion Probe

To load solid samples on the DIP:
1. Put the solid sample into the sample cup and compress it into the bottom.
2. Use a pair of clean tweezers to insert the sample cup into the DIP tip.

Loading Liquid Samples on the Direct Exposure Probe

Apply liquid samples directly to the sample loop or the end of the filament on the DEP.

To load liquid samples on the DEP:

1. Use a 10 μL syringe to draw 1 or 2 μL of sample.
2. Apply the liquid onto the filament loop. The loop will support the resulting bead of
liquid.

CAUTION - INSTRUMENT DAMAGE: Allow sample solvent to evaporate completely

before inserting the DEP into the mass spectrometer.

3. Evaporate the solvent carefully, so that the sample remains deposited uniformly on the tip
of the filament wire.

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Loading Probe Samples

You can use an infrared or incandescent bulb as a heat source to increase the evaporation
rate of your solvent. However, be careful not to warm the sample droplet too quickly, or
the solvent could sputter and cause sample loss.

Loading Solid Samples on the Direct Exposure Probe

To load solid samples directly onto the filament of the DEP:
1. Load solid samples with a dry syringe needle, or use a piece of clean wire or capillary
column to collect some of the sample.
2. Lightly touch the sample to the filament being careful not to bend or damage the
filament.

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Cleaning the Probe Shaft, Direct Probe Controller, DIP Sample Cups, and DEP Filament

Cleaning the Probe Shaft, Direct Probe Controller, DIP Sample Cups,
and DEP Filament
To clean the probe shaft, direct probe controller, and sample cups:
1. After your probe has thoroughly cooled, check it for obvious residue or abrasions. You
should examine and clean your probe and sample cups often to ensure the integrity of
your experiments.
2. Clean the probe shaft.
a. Use a soft cloth to wipe the probe handle and shaft.
Figure 61. Cleaning the Probe Shaft

Probe Shaft

Handle

b. Use a soft cloth dampened in a mild detergent and water solution to remove dirt.
Never use abrasive cleaners.
c. Wipe the probe with water to remove detergent residue.
d. Allow the probe to dry completely before reusing.
3. Clean the sample cups on the DIP.
Note If you want to reuse your sample cups, clean them before reusing them. Dirty
sample cups can lead to false-positive data in subsequent runs.

a. Clean the sample cups in an ultrasonic solvent bath.

b. Dry the sample cups in a drying oven at 250 °C.
c. Store clean sample cups in a clean glass container.
d. Use clean tweezers to handle the clean sample cups and avoid contamination.
4. Clean the filament on the DEP.

CAUTION - INSTRUMENT DAMAGE: Always start and clean the probe when it is in a
vacuum, and the vacuum manifold is sufficiently pumped down.

a. Examine and clean your filament wire often to ensure the integrity of your
experiments.

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Cleaning the Probe Shaft, Direct Probe Controller, DIP Sample Cups, and DEP Filament

b. Insert the probe with the filament to be cleaned into the mass spectrometer. Press the
Clean button on the direct probe controller, which runs 1200 mA through the
filament to burn off any residues. The residues are typically removed after one or two
cleaning cycles.

CAUTION - INSTRUMENT DAMAGE: Supplying current greater than 100 mA to the

filament in the presence of air can burn out the filament.

Figure 62. Pressing the Clean Button

Clean Button

5. Clean the direct probe controller.

a. Power-off and unplug the direct probe controller.
b. Use a clean, damp cloth to wipe the direct probe controller.
c. Dry off the direct probe controller and plug it back in.
d. Power-on the direct probe controller.

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 2

Ordering Spare Parts

To order spare parts for your direct probe system, contact Customer Service or your local sales
representative.

Thermo Fisher Part

Description Qty
Number
Direct Sample Probe Controller for the ISQ, with both Direct 1R119300-0800 1
Insertion and Direct Exposure Sample Probes
Direct Probe Controller and Direct Exposure Probe 1R119300-0600 1
Direct Probe Controller and Direct Insertion Probe 1R119300-0500 1
Direct Insertion Probe (requires controller) 1R120439-0050 1
Direct Exposure Probe (requires controller) 1R120439-0060 1
Direct Probe Controller 1R119300-5000 1
Probe Repeller 1R120406-4400 1
Test Sample, DEP/DIP 1R120339-0001 1
DEP Filaments Pkg/5 119322-0001 1
DIP Sample Cups (glass crucibles with flared-up rim) Pkg/25 119329-0001 1
DEP Sample Cups (aluminum crucible, crimpable, straight) 0568761 1
Pkg/200
Fuses, T2A, low-insertion force, 250 V 76706-0200 2
Cable from Direct Probe Controller to Probe 119303-0001 1
Holder for DIP Sample Cups (fits 6) and DEP Filaments (fits 119342-0001 1
6)
9-pin Cable 119378-0032 1

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