Thermo Scientific ISQ User manual

ISQ
User Guide
1R120555-0003 Revision D January 2013

© 2013 Thermo Fisher Scientific Inc. All rights reserved.
ISQ, TSQ 8000, TSQ Quantum, TRACE 1300, TRACE 1310, TRACE GC, TRACE GC Ultra,
TraceFinder, and FOCUS GC are trademarks, and Xcalibur is a registered trademark of Thermo Fisher
Scientific in the United States.
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registered trademark of E.I. du Pont de Nemours and Company in the United States and other countries.
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, May 2010; Revision B, March 2012; Revision C, December 2012
Software version: Thermo Foundation 2.0 SP1, Thermo Xcalibur 2.2 SP1
For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific ISQ User Guide iii
C
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
About Your System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Safety Symbols and Signal Words . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Hydrogen Safety Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Using Hydrogen with ISQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Hydrogen Connection Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Purchasing Hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Properly Storing Hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii
Hydrogen Safety Codes, Standards and References . . . . . . . . . . . . . . . . . . . .xix
Hazardous Substances Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xx
Biological Hazard Warning Note. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xx
Venting Toxic Gases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xxi
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xxi
Chapter 1 Confirming Your GC/MS System is Working . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Checking Power to the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Verifying the Carrier Gas Flow Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Checking Your Carrier Gas Tank Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Checking the Vacuum and Temperature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Chapter 2 Changing the Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Replacing the Factory Installed Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Connecting the Column to the Transfer Line . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Chapter 3 Tuning the ISQ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Accessing ISQ Autotune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Tuning the ISQ Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Chapter 4 Creating a Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
Creating a Method for the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Creating a Method for the ISQ Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . 37
Contents

Contents
iv ISQ User Guide Thermo Scientific
Creating a Method for the GC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Creating a method for the TRACE 1300 or TRACE 1310 . . . . . . . . . . . . . . 43
Creating a Method for the TRACE GC Ultra . . . . . . . . . . . . . . . . . . . . . . . . 50
Creating a Method for the FOCUS GC . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Chapter 5 Running a Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61
Preparing Your Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Running a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Chapter 6 Exploring Your Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
Chapter 7 Optimizing Your Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .85
Changing the Chromatographic Separation. . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Finding the Best Way to Make an Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Improving the Way You Prepare Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Changing the Scan Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Narrowing the Mass Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Adjusting the Transfer Line Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Modifying an Automatic Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Chapter 8 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
No Ions Present in Scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Checking the ISQ System Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
How to Know When Your System Needs Maintenance . . . . . . . . . . . . . . . . . 107
Investigating Baseline Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Investigating Peak Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Investigating Results Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Reconfiguring Your Instrument. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

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
• re-calibration
•changesandrepairs
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.
• Polaris Q, ITQ, and Ion Trap Series standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001,
IEC 61010-2-081:2001
• DSQ II standards: EMC EN 61326-1:1997 + A1:1998 + A2:2001. Safety EN 61010-1:2001
• Direct Probe Controller (DPC) standards: EMC EN 61326-1:2006. Safety IEC 61010-1:2001,
IEC 61010-2-081:2001
• ISQ and 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
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.
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 the device.

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
l’union européenne et ce produit devrait être collecté ou recyclé par celles-ci. Davantage d'informations sur la
conformité de Thermo Fisher Scientific à ces directives, les recycleurs dans votre pays et les informations sur les
produits Thermo Fisher Scientific qui peuvent aider la détection des substances sujettes à la directive RoHS sont
disponibles sur www.thermoscientific.com/rohsweee.

Thermo Scientific ISQ User Guide ix
P
Preface
This guide contains detailed information about how to use the Thermo Scientific ISQ™ single
quadrupole GC-MS system. The ISQ system is designed to stay cleaner, longer, to maximize
your instrument’s uptime and improve your lab’s productivity. The need to break vacuum,
cool off your system, and spend hours cleaning, reassembling, and restoring the system is
gone. The heated ion volume, lens stack, and ion optics path in the ISQ system ensure that
the system stays cleaner longer, but when the system no longer meets your analytical needs,
restoring performance is quick and easy. The ExtractaBrite source incorporates a cartridge that
contains the repeller, source lenses, and RF lens, all of which can be removed from the
instrument while still under vacuum. What once took hours, or even an entire day, is now
accomplished in minutes.
About Your System
Gas chromatography/mass spectrometry (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 through the use of an optional autosampler, and then separated for
presentation to the MS. The MS will then generate a mass spectrum of the GC eluent and its
components, which can be used for qualitative identification, as well as accurate and precise
quantification of the individual compounds present in the sample.
Contents
•About Your System
•Related Documentation
•System Requirements
•Safety and Special Notices
•Hydrogen Safety Precautions
•Hazardous Substances Precautions
•Contacting Us

Preface
Related Documentation
xISQ User Guide Thermo Scientific
Related Documentation
ISQ includes Help and 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
•ISQ and TSQ 8000 Direct Probe System User Guide PN 1R120505-0006
To view product manuals
Go to Start > All Programs > Foundation 2.0 > Manuals > ISQ.
To open Help
• From the ISQ window, choose Help > ISQ Help.
• If available for a specific window or dialog box, click Help or press the F1 key for
information about setting parameters.
For more information, visit www.thermoscientific.com.

Preface
System Requirements
Thermo Scientific ISQ User Guide xi
System Requirements
Your ISQ data system must meet these minimum requirements.
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:
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
System Requirements
Hardware • 2.4 GHz processor with 4 GB RAM
•DVD/CD-ROMdrive
• Resolution display 1280 × 1024 (XGA)
• 250 GB hard drive or larger
•NTFSformat
Software • Microsoft™ Windows™ 7 SP1 Operating System (32-bit and 64-bit)
• Microsoft Windows XP SP3
• Microsoft Office™ 2007 or 2010 (32-bit only)
• Thermo Foundation 2.0 SP1 (Thermo Scientific software)
• Xcalibur™ 2.2 SP1 or later
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.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.

Preface
Safety and Special Notices
xii ISQ User Guide Thermo Scientific
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.
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.

Preface
Hydrogen Safety Precautions
Thermo Scientific ISQ User Guide xiii
Hydrogen Safety Precautions
Hydrogen is a colorless, odorless, highly flammable gas with the molecular formula H2.
Hydrogen gas presents a hazard as it is combustible over a wide range of concentrations: at
ambient temperature and pressure, this ranges from about 4% to 74.2% by volume.
Hydrogen has a flash point of - 423 °F (- 253 °C) and an auto-ignition temperature of
1,040 °F (560 °C). It has a very low ignition energy and the highest burning velocity of any
gas. If hydrogen is allowed to expand rapidly from high pressure, it can self-ignite. Hydrogen
burns with a flame that can be invisible in bright light.
Before you begin using hydrogen, you should conduct a risk assessment based on the quantity
of hydrogen to be used and the conditions of your laboratory. You should ask yourself:
“What hydrogen hazards associated with this project are most likely to occur?”
“What hydrogen hazards associated with this project have the potential to result in the
worst consequences?”
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.
Symbol Descriptor
WARNING - FIRE HAZARD: The use of hydrogen as a carrier gas is dangerous. Hydrogen
is potentially explosive and must be used with extreme care. Any use of hydrogen gas must
be reviewed by appropriate health and safety staff and all installations of hydrogen systems
must be performed to applicable codes and standards. Thermo Fisher Scientific assumes
no liability for the improper use of hydrogen as a carrier gas.

Preface
Hydrogen Safety Precautions
xiv ISQ User Guide Thermo Scientific
• Try to reduce or eliminate the higher risks by using the proper ventilation to remove
hydrogen gas before an ignitable concentration can accumulate. You should also consider
purging the hydrogen to further reduce hazards and ensure anyone who will be working
with hydrogen has basic hydrogen safety training.
• As with laboratory safety in general, be sure to wear safety glasses, laboratory coats, gloves,
etc. Typically there are no specific requirements for gaseous hydrogen, other than eye
protection when working with a compressed gas. If working with liquid (cryogenic)
hydrogen, insulated gloves and protective shoes should be worn in addition to eye
protection.
• You should post “No Smoking” and “No Open Flames” signs to identify hydrogen
sources and cylinders. Maintain, inspect and leak-test all hydrogen sources regularly.
• All hydrogen shutoff valves should be clearly marked and permanent hydrogen piping
should be labeled as such at the supply or discharge point and at regular intervals along its
length. Where hydrogen gas piping passes through a wall, the piping should be labeled on
both sides of the wall.
• There should also be contingency plans in place should an incident occur.
• The site emergency response team, as well as the local fire department, should know the
location of all hydrogen storage tanks.

Preface
Hydrogen Safety Precautions
Thermo Scientific ISQ User Guide xv
Using Hydrogen with ISQ
To use hydrogen with the ISQ instrument, you must always shut off the GC carrier gas before
venting or turning off the ISQ instrument. There are three hydrogen safety screws on the ISQ
instrument that must be in place. These are attached to your instrument at the factory.
Make sure all the covers and panels of the ISQ instrument are firmly attached before powering
on the ISQ instrument. If you vented the system, make sure the vent valve is tightly closed
before powering on the system. Make sure all fittings, ferrules, and o-rings are sealed prior to
powering on the system.
Figure 1. Hydrogen Safety Screws on the ISQ Instrument
Right Top Cover
Screw
Front Panel
Screw
Left Top
Cover Screw

Preface
Hydrogen Safety Precautions
xvi ISQ User Guide Thermo Scientific
Hydrogen Connection Guidelines
Use the following guidelines to safely connect hydrogen to your system:
•Piping—Hydrogen must be delivered to equipment using appropriate piping and be
done in such a way as to pose essentially no hazard to end-users. Piping systems for the
delivery of hydrogen should be designed and installed by a person qualified by specific
training and experience with hydrogen piping systems.
Stainless steel is usually recommended because it is a safe, cost-effective material. Piping
of black iron or copper must not be used, as the pipe can become brittle with age.
Elastomeric/plastic tubing of various plastics and polymers should not be used, unless the
tubing is approved for use with hydrogen. If elastomeric/plastic tubing is used for
hydrogen gas delivery, the tubing should be tested for hydrogen permeability to minimize
leakage.
The hydrogen piping system must be flexible enough to endure routine thermal
expansion and contraction. The system should also include considerations for the most
severe condition of temperature and pressure expected during service. Piping and
supports must be able to withstand static loading introduced by such things as ice and
snow; and dynamic loading from high wind and earthquake.
Caution should be used if burying hydrogen piping. Proper controls should be used to
protect against damage and corrosion, and also to prevent Hydrogen from entering a
building if there is any leakage.
•Fittings—All fittings must be of the proper type approved or designed for use with
hydrogen gas. Use as few fittings as possible to minimize the potential for leaks. After
installation, ensure that leak testing is carried out prior to system use, and on a regular
basis.
There must be no PTFE tape or other things like plumber's putty used to enhance a seal, as
this actually is a detriment to a good seal. Ideally the best installation would use stainless
steel tubing with appropriate gas-tight fittings.
Welding is usually preferred for joints in hydrogen piping systems since welding provides
a better connection and reduces the potential for leaks compared to mechanical fittings.
Soft solder joints are not permitted for hydrogen systems (due to the low melting point of
soft solder and its potential for brittle failure at cryogenic temperatures). Brazed joints are
permitted, but such joints should be protected against the possibility of external fire.
Tubing connections should be clamped to barbed or press-fit type connections. Hose
clamps or jubilee clamps must not be used.
•Valves—All valves must be suitable for hydrogen service and for the specific operating
conditions. Valves, including regulators, must not be used for hydrogen, unless they are
designed and identified for such a use. Ball valves are often chosen because of their
superior leak tightness through the valve seat. Pneumatic operators are usually chosen for
remotely operated valves so that potential ignition sources (electricity) are remote from
the valve.

Preface
Hydrogen Safety Precautions
Thermo Scientific ISQ User Guide xvii
Manual shutoff valves should be provided near each point of use, within immediate reach.
If a hydrogen cylinder or hydrogen generation system is located within immediate reach,
a separate point-of-use shutoff valve is usually not necessary.
Line regulators that have their source away from the point of use should have a manual
shutoff valve near the point of use.
An emergency gas shutoff device in an accessible location outside the use area should be
provided in addition to the manual point-of-use valve in each educational and
instructional laboratory space that has a piped gas supply system.
If necessary, the piping system should have uninterruptible pressure relief. The pressure
relief system should be designed to provide a discharge rate sufficient to avoid further
pressure increase and should vent to a safe location outside or to a ventilation system
exhaust.
Purchasing Hydrogen
Use the following guidelines when purchasing hydrogen:
• Hydrogen Generator—Because it minimizes the amount of hydrogen present and reduces
the degree of hazard, a hydrogen generator (also called an electrolyzer) is the safest way to
purchase hydrogen in the quantity used in GC/MS.
However, to minimize the degree of hazard, the hydrogen generator must only be
operated in a non-explosive environment because hydrogen buildup can be ignitable.
This means that your ventilation system for the room or lab hood must maintain an air
exchange rate that is at least two orders of magnitude greater than the maximum
hydrogen production rate of the hydrogen generator. Be sure to follow the manufacturers'
directions about proper use and maintenance of the regulator.
To prevent the possibility of releasing hydrogen, the hydrogen generator should be set to
shut down if:
−There is a loss of flow to the ventilation system
−A hydrogen detector alarms at 25% of the lower flammable limit of hydrogen in air.
The oxygen exhausted by the electrolyzer should be vented to the outside as well.
• Hydrogen Cylinder—Hydrogen can be delivered in standard laboratory gas bottles or
cylinders. These cylinders have a limited amount of hydrogen in them and are a safe way
to transport and store hydrogen. However, compressed hydrogen gas cylinders, like all
compressed gas cylinders, must be secured in an upright position, ideally with a
non-combustible chain or cable. If the cylinder falls over, the valve can be knocked off
and the pressurized cylinder can take off like a rocket, which leads to the release of
hydrogen and possibly an explosion, severe injury, or death. Never crack a hydrogen
cylinder valve to remove dust or dirt from fittings prior to attaching a regulator, as there is
a risk of self-ignition.

Preface
Hydrogen Safety Precautions
xviii ISQ User Guide Thermo Scientific
Properly Storing Hydrogen
Storing and handling compressed hydrogen gas and cryogenic liquid hydrogen present
potential health and safety hazards. Using proper storage and handling techniques is essential
to maintaining a safe work environment.
Use the following guidelines when storing hydrogen:
• Store spare hydrogen gas cylinders outside and away from doors, windows, building air
intake vents, structures, and vehicle routes. This precaution applies when the hydrogen is
or is not in use. Indoor storage of spare hydrogen cylinders has special requirements,
which is beyond the scope of this document. Documentation for each vessel should
include a description of the vessel, a list of available drawings or other documents, the
most recent inspection results, and the responsible person's name.
• Prevent spare cylinders from toppling by wrapping them with chains. The chains should
also be protected against corrosion and excessive heat.
• Separate spare hydrogen cylinders from oxidizing gases (such as oxygen) with a 5 ft
(1.5 m) tall fire barrier with a half-hour fire rating or place the cylinders at least 20 ft
(6 m) apart.
• When moving hydrogen cylinders:
−Remove the regulator and replace the cylinder valve cap before moving.
−Move cylinders on cylinder carts or with other appropriate transport devices.
−Never roll or drop a cylinder and never lift a cylinder by its protective cap.
• Bulk hydrogen systems include either gaseous or liquid hydrogen in fixed installations; in
some gas systems a semi-permanent trailer (tube trailer) can be used. Storage vessels for
compressed hydrogen gas or liquid hydrogen should be designed, constructed, tested, and
maintained in accordance with applicable codes and standards. Bulk hydrogen systems
represent a level of complexity again which is beyond the scope of this document;
however some general guidelines are provided.
• The bulk hydrogen storage system should not be located beneath electric power lines,
close to other flammable gases/liquids, or close to public areas. It should be readily
accessible to authorized personnel and delivery equipment, but protected from physical
damage or tampering.
• As liquid hydrogen systems also have a cryogenic hazard, additional safety considerations
for the use of cryogenic liquids may be necessary.

Preface
Hydrogen Safety Precautions
Thermo Scientific ISQ User Guide xix
Hydrogen Safety Codes, Standards and References
The following list of safety codes, standards and references is in no way an exhaustive list. In
fact, there may be federal, state or local codes that apply to your specific location. Check with
all appropriate agencies with jurisdiction before installing or using a hydrogen system.
• Air Products Safetygram #4 Gaseous Hydrogen
• ANSI/AIAA standard for hydrogen safety guidelines is AIAA G-095-2004, Guide to
Safety of Hydrogen and Hydrogen Systems
• ASME B31.1, Power Piping Code
• ASME B31.3, Process Piping Code
• ASME B31.8, Gas Transmission and Distribution Systems
• BCGA Code Of Practice CP4 Industrial Gas Cylinder Manifolds and Gas Distribution
Pipework
• BCGA Code Of Practice CP33 The Bulk Storage of Gaseous Hydrogen at Users'
Premises
• CGA G-5, Hydrogen
• CGA G-5.4, Standard for Hydrogen Piping Systems at Consumer Locations
• CGA G-5.5, Hydrogen Vent Systems
• CGA G-5.6, Hydrogen Pipeline Systems
• CGA G-5.8, High Pressure Hydrogen Piping Systems at Consumer Locations.
• FM Global Property Loss Prevention Data Sheets 7-50: Compressed Gases in Cylinders
• FM Global Property Loss Prevention Data Sheets 7-91: Hydrogen
• IGC Doc 121/04/E, Hydrogen Transportation Pipelines System Design Features
• NASA
• NSS 1740.16 Safety Standard For Hydrogen And Hydrogen Systems Guidelines for
Hydrogen System Design, Materials Selection, Operations, Storage, and Transportation
• NFPA 52, Vehicular Fuel Systems Code
• NFPA 55, Standard for the Storage, Use, and Handling of Compressed Gases and
Cryogenic Fluids in Portable and Stationary Containers, Cylinders, and Tanks, 2005
Edition
• NFPA 68, Standard on Explosion Protection by Deflagration Venting
• NFPA 70, National Electrical Code

Preface
Hazardous Substances Precautions
xx ISQ User Guide Thermo Scientific
• NFPA 497, Recommended Practice for the Classification of Flammable Liquids, Gases,
or Vapors and of Hazardous (Classified) Locations for Electrical Installations in Chemical
Process Areas
• NFPA 13, Standard for the Installation of Sprinkler Systems
• NFPA 45, Standard on Fire Protection for Laboratories Using Chemicals
• NFPA 55, Standard for the Storage, Use, and Handling of Compressed Gases and
Cryogenic Fluids in Portable and Stationary Containers, Cylinders, and Tanks
• NFPA 68, 2007 Standard on Explosion Protection by Deflagration Venting
• NFPA 69, Standard on Explosion Prevention Systems
• NFPA 91, Standard for Exhaust Systems for Air Conveying of Vapors
• NFPA 255, Standard Method of Test of Surface Burning Characteristics of Building
Materials
• OSHA 29CFR1910.103 1910.103 Hydrogen
Hazardous Substances Precautions
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.
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.