Thermo Scientific TSQ 8000 Evo User manual

TSQ 8000 Evo
Mass Spectrometer
User Guide
1R120586-0002 Revision C December 2015

© 2015 Thermo Fisher Scientific Inc. All rights reserved.
TSQ, TRACE 1300, TRACE 1310, TriPlus, and TraceFinder are trademarks, and Xcalibur is a registered
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registered trademark of McAfee, Inc. in the United States and other countries. Vespel is a registered trademark
of E.I. du Pont de Nemours and Company in the United States and other countries.
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.
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, July 2014; Revision B, February 2015; Revision C, December 2015.
Software version: Thermo Foundation 3.1 SP1, Xcalibur 4.0 or later
For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific TSQ 8000 Evo 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 a GC-MS/MS System. . . . . . . . . . . . . . . . . . . . . . . . .xiv
Hydrogen Connection Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Purchasing Hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
Properly Storing Hydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
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 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Confirming Your Instrument is Working . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Checking Power to the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Verifying the Carrier Gas Flow Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Checking Your Carrier Gas Tank Pressure. . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Verify Collision Gas Tank Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Checking the Vacuum and Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Cleaning the Exterior of Your Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Configuring Your Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Chapter 2 Changing the Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Determining the Column Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Replacing the Factory Installed Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Connecting the Column to the Transfer Line . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 3 Tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
Accessing Auto Tune. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Contents

Contents
iv TSQ 8000 Evo User Guide Thermo Scientific
Tuning the Mass Spectrometer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Updating Tunes for New RF Lens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Chapter 4 Creating a Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
Accessing the Method Editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Creating an Autosampler Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Creating a MS Instrument Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Creating a GC Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Validating and Troubleshooting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Chapter 5 Optimizing Your Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .89
Changing the Chromatographic Separation. . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Finding the Best Way to Make an Injection . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Improving the Way You Prepare Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Changing the Dwell Time or Scan Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Narrowing the Mass Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Adjusting the Transfer Line and Ion Source Temperature . . . . . . . . . . . . . . . . . 91
Optimizing an SRM Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Optimizing an NCI Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Modifying an Automatic Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Chapter 6 Computer Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111
System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Computer Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Excluding the Xcalibur Directory from Virus Scan . . . . . . . . . . . . . . . . . . . . . 114
Chapter 7 Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .115
Diagnostics Checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
How to Know When Your System Needs Maintenance . . . . . . . . . . . . . . . . . 117
Investigating Baseline Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Investigating Peak Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Investigating Results Issues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127

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
•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 and Safety Standards
• 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 61326-1:2013. Safety: IEC 61010-1:2001,
IEC 61010-2-081:2001
• ISQ Series standards: EMC: EN 61326-1:2013. Safety: IEC 61010-1:2010 (ed. 3); IEC 61010-2-081:2015 (ed.
2); IEC 61010-2-010:2014 (ed. 3); IECEE CB SCHEME CERT NO. DE 3-30000
• TSQ 8000 Evo and TSQ Duo standards: EMC: EN 61326-1:2013. Safety: IEC 61010-1:2010 (ed. 3); IEC
61010-2-081:2015 (ed. 2); IEC 61010-2-010:2014 (ed. 3); IECEE CB SCHEME CERT NO. DE 3-30034

Low Voltage Safety Compliance
This device complies with Low Voltage Directive 2011/95/EC.
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.
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.

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
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 TSQ 8000 Evo User Guide ix
P
Preface
This guide contains detailed information about how to use your Thermo Scientific
TSQ 8000™ Evo triple-quadrupole GC/MS system. The TSQ 8000 Evo system provides the
selectivity and sensitivity of a triple-quadrupole GC/MS while also functioning as a
high-performance single quadrupole instrument. The 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 greatly reduced. The extractable source incorporates a cartridge that contains the
repeller, source lenses, and RF lens, all of which can be removed from the instrument without
breaking vacuum. What once took hours, or even an entire day, is now accomplished in
minutes.
In addition, the TSQ 8000 Evo system includes innovative Thermo Scientific software that
will help users new to triple-quadrupole GC/MS/MS systems develop selected reaction
monitoring (SRM) methods.
About Your System
Thermo Scientific systems provide the highest caliber gas chromatography/mass spectrometry
(GC/MS) instrumentation available on today’s market.
Contents
•About Your System
•Related Documentation
•System Requirements
•Safety and Special Notices
•Hydrogen Safety Precautions
•Hazardous Substances Precautions
•Contacting Us

Preface
Related Documentation
xTSQ 8000 Evo User Guide Thermo Scientific
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 triple-quadrupole GC/MS/MS system provides the extra selectivity required for trace
analysis of compounds in complex matrices.
Related Documentation
The TSQ 8000 Evo system includes Help and these manuals as PDF files:
•TSQ 8000 Evo Preinstallation Guide, PN 1R120586-0001
•TSQ 8000 Evo User Guide, PN 1R120586-0002
•TSQ 8000 Evo Hardware Manual, PN 1R120586-0003
•TSQ 8000 Evo Spare Parts Guide, PN 1R120586-0004
•TSQ 8000 Evo Auto SRM User Guide, PN 1R120586-0005
•Q Exactive GC, ISQ Series and TSQ 8000 Evo Direct Probe System User Guide, PN
1R120505-0006
To view product manuals
Open the desktop folder Manuals.
To open Help
• From the TSQ Series window, choose Help > TSQ Series 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.
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.

Preface
System Requirements
Thermo Scientific TSQ 8000 Evo User Guide xi
System Requirements
Your 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
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.
System Requirements
Hardware • 4.6 GHz processor with 16 GB RAM
• CD/R-Rom or DVD drive
• 1000 GB or hard drive
• Video card and monitor capable of 1680 ×1050 resolution
• Quad core processor
Software • Microsoft™ Windows™ 7 SP1 Operating System (64-bit)
• Microsoft Office™ 2013
• Thermo Foundation 3.1 SP1 (Thermo Scientific software)
•Xcalibur™4.0
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 TSQ 8000 Evo User Guide Thermo Scientific
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.
RADIOACTIVE HAZARD: Indicates that exposure to radioactive material
could or might occur.

Preface
Hydrogen Safety Precautions
Thermo Scientific TSQ 8000 Evo User Guide xiii
Hydrogen Safety Precautions
Hydrogen is a colorless, odorless, highly flammable gas with the molecular formula H2and an
atomic weight of 1.00794, making it the lightest element. 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?”
• 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.
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 TSQ 8000 Evo User Guide Thermo Scientific
• 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.
Using Hydrogen with a GC-MS/MS System
To use hydrogen with the mass spectrometer, you must always shut off the GC carrier gas
before venting or turning off the mass spectrometer. There are three hydrogen safety screws on
the mass spectrometer that must be in place. These are attached to your instrument at the
factory.
Figure 1. Hydrogen Safety Screws on the Mass Spectrometer
Before powering on the GC-MS/MS system, ensure that:
Left Top
Cover Screw
Right Top
Cover Screw
Front Panel
Screw

Preface
Hydrogen Safety Precautions
Thermo Scientific TSQ 8000 Evo User Guide xv
• All the covers and panels of the GC-MS/MS system are firmly attached.
• The vent valve is tightly closed if you vented the system.
• All fittings, ferrules, and o-rings are sealed.
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.

Preface
Hydrogen Safety Precautions
xvi TSQ 8000 Evo User Guide Thermo Scientific
•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.
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.

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Hydrogen Safety Precautions
Thermo Scientific TSQ 8000 Evo User Guide xvii
•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.
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.

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Hydrogen Safety Precautions
xviii TSQ 8000 Evo User Guide Thermo Scientific
• 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 might be necessary.

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Hydrogen Safety Precautions
Thermo Scientific TSQ 8000 Evo 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 might 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

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Hazardous Substances Precautions
xx TSQ 8000 Evo 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.