Orbitrap Tribrid Series

Getting Connected Guide

80000-97025 Revision A June 2018

© 2018 Thermo Fisher Scientific Inc. All rights reserved.

Fusion, ID-X, Lumos, and Orbitrap ID-X are trademarks, and Orbitrap Fusion, Orbitrap Fusion Lumos,
Thermo Scientific, Tribrid, and Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the
United States.

The following are registered trademarks in the United States and other countries: COMBICON is a registered
trademark of Phoenix Contact GmbH & Co. Microsoft and Windows are registered trademarks of Microsoft
Corporation. Teflon is a registered trademark of E.I. du Pont de Nemours & Co.

The following are registered trademarks in the United States and possibly other countries: Nalgene is a
registered trademark of Nalge Nunc International Corporation. Oerlikon Leybold Vacuum is a registered
trademark of OC Oerlikon Corporation AG. Rheodyne is a registered trademark of IDEX Health & Science,
LLC. SOGEVAC is a registered trademark of Oerlikon Leybold Vacuum. Swagelok is a registered trademark of
Swagelok Company. Tygon is a registered trademark of the division of Saint-Gobain Performance Plastics
Corporation.

Chemyx is a trademark of Chemyx Inc. MX Series II is a trademark of IDEX Health & Science, LLC.
All other trademarks are the property of Thermo Fisher Scientific Inc. 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.
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: Rev A, June 2018

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

 Regulatory Compliance
Thermo Fisher Scientific performs complete testing and evaluation of its products to ensure full compliance with
applicable North American and European regulations. Your system meets the applicable requirements in the
electromagnetic compatibility (EMC) and product safety standards described in this section.

Unauthorized changes that you make to your system will void regulatory compliance and may defeat the built-in
protections for your instrument. Some examples of unauthorized changes include using replacement parts or adding
components, options, or peripherals that Thermo Fisher Scientific has not qualified and authorized. Unauthorized
changes can also result in bodily injury and/or damage to your system and laboratory.

Ensure continued compliance with regulatory standards:

• Follow all installation instructions provided in the documentation that comes with your system.
• Order replacement parts (as specified in the instrument manual) and additional components, options, and periph-
erals directly from Thermo Fisher Scientific or an authorized representative.

Regulatory compliance results for the following Thermo Scientific™ mass spectrometers:
• Orbitrap Fusion Lumos
• Orbitrap Fusion and Orbitrap ID-X

Orbitrap Fusion Lumos

Low Voltage Directive 2014/35/EU
This device complies with Low Voltage Directive 2014/35/EU and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.

EMC Directive 2014/30/EU and other EMC test standards

This device was tested by TÜV Rheinland of North America and complies with the following EMC standards:
47 CFR 15, Subpart B, Class A: 2015 EN 61000-3-2: 2006 + A1 + A2 EN 61000-4-5: 2006
CISPR 11: 2009 + A1 EN 61000-3-3: 2008 EN 61000-4-6: 2009
ICES-003: 2014 EN 61000-4-2: 2009 EN 61000-4-8: 2010
EN 55011: 2009 + A1 EN 61000-4-3: 2006 + A1 + A2 EN 61000-4-11: 2004
EN 61326-1: 2013 EN 61000-4-4: 2004 + A1
Orbitrap Fusion and Orbitrap ID-X
Low Voltage Directive 2014/35/EU
This device complies with Low Voltage Directive 2014/35/EU and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.

EMC Directive 2014/30/EU and other EMC test standards

This device was tested by TÜV Rheinland of North America and complies with the following EMC standards:
47 CFR 15, Subpart B, Class A: 2012 EN 61326-1: 2013 EN 61000-4-4: 2004 + A1
CISPR 11: 2009 + A1 EN 61000-3-2: 2006 + A1 + A2 EN 61000-4-5: 2006
AS/NZS CISPR 22: 2009 + A1 EN 61000-3-3: 2008 EN 61000-4-6: 2009
ICES-003: 2012 EN 61000-4-2: 2009 EN 61000-4-8: 2010
EN 55011: 2009 + A1 EN 61000-4-3: 2006 + A1 + A2 EN 61000-4-11: 2004

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 the device.

Notice on the Proper Use of

Thermo Scientific Instruments
In compliance with international regulations: This instrument must be used in the manner specified by Thermo Fisher
Scientific to ensure protections provided by the instrument are not impaired. Deviations from specified instructions on
the proper use of the instrument include changes to the system and part replacement. Accordingly, order replacement
parts from Thermo Fisher Scientific or one of its authorized representatives.
 WEEE Directive
2012/19/EU

Thermo Fisher Scientific is registered with B2B Compliance (B2Bcompliance.org.uk) in the UK and with the
European Recycling Platform (ERP-recycling.org) in all other countries of the European Union and in Norway.

If this product is located in Europe and you want to participate in the Thermo Fisher Scientific Business-to-Business
(B2B) Recycling Program, send an email request to [email protected] with the following information:
• WEEE product class
• Name of the manufacturer or distributor (where you purchased the product)
• Number of product pieces, and the estimated total weight and volume
• Pick-up address and contact person (include contact information)
• Appropriate pick-up time
• Declaration of decontamination, stating that all hazardous fluids or material have been removed from the product

For additional information about the Restriction on Hazardous Substances (RoHS) Directive for the European Union,
search for RoHS on the Thermo Fisher Scientific European language websites.

IMPORTANT This recycling program is not for biological hazard products or for products that have been medically
contaminated. You must treat these types of products as biohazard waste and dispose of them in accordance with
your local regulations.
 C

Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Viewing the Product Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Viewing Online User Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Providing Documentation Feedback. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi
Model Differences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Chapter 1 Connecting the Forepump for the Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . .1

Connecting the Forepumps to the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . 1
Connecting the Forepumps to the Lab Exhaust System . . . . . . . . . . . . . . . . . . . . 3
Locking the Workbench Wheels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Chapter 2 Connecting the Nitrogen and Helium Gases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5

Gas Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Connecting the Instrument Gas Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Chapter 3 Connecting the API Source and Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . .9

Installing the API Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Setting Up the Fume Exhaust Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Connecting the Solvent Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Chapter 4 Installing the Syringe Pump and Modular Valve. . . . . . . . . . . . . . . . . . . . . . . . . . .13

Chapter 5 Connecting the Cables and Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Chapter 6 External Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17

Contact Closure Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Communication Connectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Appendix A Installation Kits and Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Syringe Pump and Modular Valve Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide vii

Contents

MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27

viii Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 P

Preface
The Orbitrap Tribrid Series Getting Connected Guide is intended for the following Thermo
Scientific™ mass spectrometers (MSs):
• Orbitrap Fusion™ (also known as Fusion™)
• Orbitrap Fusion Lumos™ (also known as Lumos™)
• Orbitrap ID-X™(also known as ID-X™)

This guide describes how to install the MS system in your laboratory and connect any external
liquid chromatography (LC) devices. External devices include those that are controlled from
or are independent of Thermo Scientific mass spectrometry applications, such as the Thermo
Xcalibur™ data system. For a list of hardware differences for this MS series, see Model
Differences.

Also, because this guide uses drawings of various connections and component parts to help
illustrate procedures, be sure to start from , no matter where it appears.

IMPORTANT Thermo Fisher Scientific field service engineers access internal components
by opening the top cover. Ensure that the instrument location allows for a vertical
clearance of at least 92 cm (36 in.) above the instrument. For additional clearance
guidelines, refer to the Preinstallation Requirements Guide.

Contents
• Accessing Documentation
• Providing Documentation Feedback
• Special Notices, Symbols, and Cautions
• Model Differences
• Contacting Us

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide ix

Preface

Accessing Documentation
The Orbitrap Tribrid Series MS includes complete documentation.
• Viewing the Product Manuals
• Viewing Online User Documentation

For system requirements, refer to the release notes on the software DVD.

Viewing the Product Manuals

The Thermo Fisher Scientific service engineer installs the instrument control applications and
the instrument manuals on the data system computer.

 To view the product manuals

From the Microsoft™ Windows™ taskbar, choose Start > All Apps (Windows 10) or
All Programs (Windows 7) > Thermo Instruments > model x.x, and then open the
applicable PDF file.

Viewing Online User Documentation

Visit the Thermo Fisher Scientific website for product manuals and more.

 To view user documentation from the Thermo Fisher Scientific website

1. Go to thermofisher.com.
2. Point to Services & Support and click Manuals on the left.
3. In the Refine Your Search box, search by the product name.
4. From the results list, click the title to open the document in your web browser, save it, or
print it.
To return to the document list, click the browser Back button.

Providing Documentation Feedback

 To suggest changes to the documentation or to the Help

Complete a brief survey about this document by clicking the button below.
Thank you in advance for your help.

x Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 Preface

Special Notices, Symbols, and Cautions

Make sure you understand the special notices, symbols, and caution labels in this guide. Most
of the special notices and cautions appear in boxes; those pertaining to safety also have
corresponding symbols. Some symbols are also marked on the instrument itself and can
appear in color or in black and white. For complete definitions, see Table 1.
Table 1. Notices, symbols, labels, and their meanings
Notice, symbol, or label Meaning
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
product.
Note Highlights information of general interest.
Tip Highlights helpful information that can make a task easier.
Caution: Read the cautionary information associated with this
task.

Chemical hazard: Observe safe laboratory practices and

procedures when handling chemicals. Only work with volatile
chemicals under a fume or exhaust hood. Wear gloves and other
protective equipment, as appropriate, when handling toxic,
carcinogenic, mutagenic, corrosive, or irritant chemicals. Use
approved containers and proper procedures to dispose of waste
oil and when handling wetted parts of the instrument.
Heavy object: The Orbitrap Tribrid Series MS, excluding its
workbench, weighs over 227 kg (500 lb). Never try to detach
and move the instrument from its workbench; you can suffer
personal injury or damage the instrument.
Pinch point: Keep hands away from the specified areas.

Risk of eye injury: Eye injury can occur from splattered

chemicals, airborne particles, or sharp objects. Wear safety
glasses when handling chemicals or servicing the instrument.

Trip obstacle: Be aware of cords, hoses, or other objects located

on the floor.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide xi

Preface

Model Differences
This table lists the required number of forepumps and the available options for the
Orbitrap Tribrid Series MSs.

Instrument Number of Available options

forepumps
Advanced
EASY-IC EASY-ETD 1M Orbitrap UVPD
peak
ion source ion source resolution laser module
determination
Orbitrap Fusion Lumos 2     

Orbitrap Fusion 1   

Orbitrap ID-X 1 

xii Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 Preface

Contacting Us
Contact Email Telephone QR Codea

U.S. Technical Support [email protected] (U.S.) 1 (800) 532-4752

U.S. Customer Service [email protected] (U.S.) 1 (800) 532-4752

and Sales

Global Support  To find global contact information or customize your request

1. Go to thermofisher.com.
2. Click Contact Us, select the country, and then select the type of support
you need.
3. At the prompt, type the product name.
4. Use the phone number or complete the online form.

 To find product support, knowledge bases, and resources

Go to thermofisher.com/us/en/home/technical-resources.

 To find product information

Go to thermofisher.com/us/en/home/brands/thermo-scientific.
Note To provide feedback for this document, go to surveymonkey.com/s/PQM6P62 or send an email message to
Technical Publications ([email protected]).
a
You can use your smartphone to scan a QR Code, which opens your email application or browser.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide xiii

Preface

xiv Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 1

Connecting the Forepump for the Vacuum System

To connect the forepump or forepumps to the Orbitrap Tribrid Series MS and the lab exhaust
system, follow these procedures.

Contents
• Connecting the Forepumps to the Mass Spectrometer
• Connecting the Forepumps to the Lab Exhaust System
• Locking the Workbench Wheels

CAUTION In addition to reading the forepump’s operating and maintenance instructions,

follow the instructions for adding and changing the oil.

Connecting the Forepumps to the Mass Spectrometer

Before you begin, lift up and remove the workbench’s front panel. To determine which
instrument requires two forepumps, see Model Differences.

CAUTION Possible pinch points. Be aware where you place your hands when you
remove or attach the workbench’s front panel.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 1

1 Connecting the Forepump for the Vacuum System
Connecting the Forepumps to the Mass Spectrometer

 To attach the vacuum hose assembly

Two-pump MS System Single-pump MS System

Using a centering ring and a swing

clamp, connect a 90-degree
1 plumbing elbow to the MS’s back
vacuum port with the open end
facing toward the side, not the
floor (as shown). Then, using a
center ring and swing clamp from
the vacuum hose assembly,
connect the hose to the elbow.
Using the stainless steel clamp, connect the short
tubing on the vacuum hose assembly to the
vacuum port located under the workbench (front,
left corner).

4 Using a hose clamp, a hose adapter, a centering ring, and a

swing clamp, connect the other end of the vacuum hose to
the plumbing elbow on the forepump.

3 Using a centering ring and a swing clamp, attach the

plumbing elbow to the forepump’s inlet port.

2 (Optional) Place each forepump on an oil tray. Then,

move them under the MS.

IMPORTANT For optimal performance of the forepumps, place them as follows:

• For a two-forepump MS system, place the forepumps under the workbench.
• For a single-forepump MS system, place the forepump under the workbench or
within 2.4 m (8 ft) of the instrument.
• Prevent the forepump from overheating by ensuring that there is sufficient air
clearance around each forepump.

2 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 1 Connecting the Forepump for the Vacuum System
Connecting the Forepumps to the Lab Exhaust System

Connecting the Forepumps to the Lab Exhaust System

Most atmospheric pressure ionization (API) applications contribute to solvents accumulating
in the forepump. Choose an exhaust system that can accommodate the periodic purging of
these solvents. The frequency of the purging depends on the throughput of the system—never
operate the pump continuously with the gas ballast valve open.

CAUTION
• Run the exhaust hose at floor level for at least 2 m (79 in.). This hose acts as a trap for
exhaust fumes that would otherwise recondense in the forepump oil.
• Maintain the exhaust pressure from atmospheric pressure minus 15 mbar to
1.15 bar absolute (0.15 bar relative).
• Although Thermo Fisher Scientific recommends that you periodically open the gas
ballast valve for at least 30 minutes (on the side of the pump) to purge the
accumulated solvents, opening the valve might allow a large volume of volatile solvent
waste to enter the fume exhaust system.
• The forepump exhaust is a health hazard. The dedicated exhaust system must be
actively vented and be able to accommodate the periodic purging of the accumulated
solvents in the forepump.

 To connect the forepumps to the exhaust system

(Orbitrap Fusion Lumos MS)

If you removed the workbench’s front

panel (as shown), reattach it.

Connect one end of the exhaust tubing to the forepump exhaust

ports. Then, secure the other end to the lab exhaust system.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 3

1 Connecting the Forepump for the Vacuum System
Locking the Workbench Wheels

Locking the Workbench Wheels

After you position the forepumps and workbench, lock the workbench wheels.

 To lock the workbench wheels

1. Lift up the workbench’s front panel to remove it, and set it aside.

CAUTION Possible pinch points. Be aware where you place your hands when you
remove or attach the workbench’s front panel.

2. Lock the front wheels by moving the locking levers forward to the upright position.
The locking levers have three positions. To fully unlock the roll and swivel movements,
push the levers back to the third position (almost horizontal).
3. Reattach the front panel when you are ready.

4 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 2

Connecting the Nitrogen and Helium Gases

Connections and gas delivery systems might vary. You are responsible for supplying any
additional fittings or connections necessary during installation. If your system includes
additional devices that require their own gas connections, refer to those instruments’ manuals.

Contents
• Gas Specifications
• Connecting the Instrument Gas Lines

Gas Specifications
Make sure that the ultra-high-purity (UHP) and high-purity (HP) supply gases are delivered
with the necessary pressure and purity as listed in Table 2.
Table 2. Summary of the required gases for the Orbitrap Tribrid Series MS
Required Typical daily
Type Recommended purity Function
pressure consumptiona
Helium UHP (99.999%)—Has less than 275 ±70 kPa 9.22 L Linear ion trap damping gas
1.0 ppm each of water, oxygen, (40 ±10 psi) (0.325 ft3) and collision gas
and total hydrocarbons.
Nitrogen UHP (99.999%)—Has less than 345 ±70 kPa 46 L (1.62 ft3) Venting gas, ion routing
3.0 ppm each of water, oxygen, (50 ±10 psi) multipole (IRM) collision
and total hydrocarbons. gas, and make-up gas and
reagent carrier gas for the IC
and ETD configurations
HP (99%) 690 ±140 kPa 11 500–26 700 L API source auxiliary gas,
(100 ±20 psi) (406–943 ft3) sheath gas, and sweep gas
a
Approximate value when operating 24 hours and 7 days a week

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 5

2 Connecting the Nitrogen and Helium Gases
Connecting the Instrument Gas Lines

Connecting the Instrument Gas Lines

CAUTION You must use either copper (provided) or stainless steel for the UHP gas lines.

CAUTION After completing these connections, route the tubing so that they are not a trip
hazard.

 To connect the gas lines to the back of the MS

(Orbitrap Fusion Lumos MS)

1 (HP nitrogen gas) Cut a length of the

Teflon™ PFA tubing and push it into the
Nitrogen In inlet. On the other end,
connect an appropriate fitting that
connects to your HP nitrogen gas supply.

2 3

(UHP nitrogen gas) Cut a length of the copper tubing, (UHP helium gas) Repeat Step 2 with another length
attach the 1/8 in. ID Swagelok™-type nut and ferrule of copper tubing, except connect it between the
set, and then connect it to the UHP Nitrogen inlet until Helium In inlet and your UHP helium gas supply.
fingertight. On the other end, connect an appropriate
fitting that connects to your UHP nitrogen gas supply.

Note Use an open wrench to tighten the fitting on the

gas inlet another 1/8- to 1/4-turn.

Swagelok fittings, 1/8 in. ID

6 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 2 Connecting the Nitrogen and Helium Gases
Connecting the Instrument Gas Lines

IMPORTANT
• After you start using the MS, do not shut off the gases. Optimum performance
requires a continuous gas flow.
• Do not shut off the UHP nitrogen gas unless you have vented the MS.
• If you intend to use helium for sparging your LC solvents, you must have a second
tank and regulator.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 7

2 Connecting the Nitrogen and Helium Gases
Connecting the Instrument Gas Lines

8 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 3

Connecting the API Source and Waste Container

To install the Thermo Scientific API source and the solvent waste container to the
Orbitrap Tribrid Series MS, follow these procedures.

Contents
• Installing the API Source
• Setting Up the Fume Exhaust Connections
• Connecting the Solvent Waste Container

Installing the API Source

All the wiring and gas plumbing for the API source are internal. This means you can install or
remove the API source or change the ionization mode1 (H-ESI, APCI, or APPI) by changing
the spray insert—all without the use of tools. For information about the spray inserts,
optional interface kits, and switching ionization modes, refer to the API source manual.

1 APCI and APPI modes require that you purchase and install the applicable kits.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 9

3 Connecting the API Source and Waste Container
Setting Up the Fume Exhaust Connections

 To install the API source onto the MS

Install the ion sweep Unlock the source

cone on the MS. locking levers.

1 2

Align the source mounting holes with the MS pins and carefully
attach the source. Then, lock the source levers.

Setting Up the Fume Exhaust Connections

 To equip your lab with at least two fume exhaust systems

Do the following:
• Ensure that the exhaust tubing from the forepump connects to a dedicated fume
exhaust system.
The analyzer optics become contaminated if the drain/waste tubing and the exhaust
tubing from the forepump connect to the same fume exhaust system.
• Ensure that the waste container vents to a dedicated fume exhaust system—do not
vent the Tygon™ drain tube (or any vent tubing connected to the waste container) to
the same fume exhaust system that connects to the forepump.
The exhaust system for the API source must accommodate a flow rate of up to
30 L/min (64 ft3/h).

10 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 3 Connecting the API Source and Waste Container
Connecting the Solvent Waste Container

Connecting the Solvent Waste Container

The MS internally routes the solvent waste from the bottom of the API source to the back
drain/waste port.

 To connect the solvent waste container to the MS

2 Connect the tubing to the

MS’s Drain/Waste port and
(Orbitrap Fusion Lumos MS) the external vent system.

Connect the filling/venting cap to the solvent 1

waste container Then, connect the Tygon
waste tubing (1 in. ID) to the cap openings.

Note Use the provided Tygon tubing to connect the solvent waste container to a
fume exhaust system. To prevent solvent waste from backing up into the instrument,
make sure that all Tygon tubing is above the level of liquid in the waste container as
follows:
• From the MS to the solvent waste container
• From the waste container to the exhaust system

CAUTION After completing these connections, route the tubing so that they are not a trip
hazard.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 11

3 Connecting the API Source and Waste Container
Connecting the Solvent Waste Container

12 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 4

Installing the Syringe Pump and Modular Valve

To install the syringe pump and the modular divert/inject valve, follow this procedure. The
only tool required is a #2 Phillips screwdriver.

Note For instructions on how to set up the syringe pump and plumb the modular valve,
refer to the Getting Started Guide.

 To assemble and install the syringe pump and modular valve

1
3
Using the screwdriver and two of the provided
screws, attach the bottom shelf to the holder.
Center the bottom of the syringe pump on the top
angled, support bracket. Then, using your fingers or
the screwdriver, tighten the knurled, spring-type
screw into the pump.

4
Place the valve on the bottom shelf; using the (Not shown) Place the assembly on the top, left
screwdriver and two screws, attach the top shelf. surface of the MS and adjust its position as needed.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 13

4 Installing the Syringe Pump and Modular Valve

14 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 5

Connecting the Cables and Power Cords

Read and understand the following cautions before you make the electrical connections in the
next procedure. If the API source contains the optional APPI lamp, you must provide a USB
splitter to accommodate the three USB connections. See also Chapter 6, “External Devices.”

CAUTION Avoid an electric shock and equipment damage.

• Forepumps—Read the warning on the forepump. When you disconnect the
forepump’s power cord from the electrical outlet do not touch the plug’s pins for at
least 5 minutes to allow time for the voltage potential to dissipate.
• Mass spectrometer—Be aware of the following:
– The AC Output receptacle is not used at this time—do not plug the forepump
(or any other appliance) power cord into this receptacle; see step 5 on page 16.
– Before you begin the installation, place the Main Power switch in the Off (down)
position and the Electronics service switch in the Service Mode (down) position.
• Syringe pump—Make sure that the voltage selector switch is set to the appropriate
voltage (110 V or 220 V) for your country or territory.

CAUTION Safety and EMC regulations require the use of Category 5e, shielded Ethernet
communication cables, maximum 3 m (10 ft) long.

CAUTION After completing these connections, route all cables and power cords so that
they are not a trip hazard.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 15

5 Connecting the Cables and Power Cords

 To connect the MS and data system cables and power cords1

5
(Not shown) Connect both ends of the power
cords (for the computer, Ethernet switch, modular
valve, syringe pump, MS, and forepumps).

IMPORTANT Plug the power cords for the MS

and forepumps into separate, dedicated 230 Vac
electrical outlets—that is, circuits A, B, and C for a
dual-forepump system.
Connect the Ethernet cables from the
Ethernet switch to the computer’s LC/MS Note If the modular valve’s LED remains off, press
Ethernet network card and the MS. its front Remote button to exit local mode.

(Not shown) Connect the Ready Out

cable (not provided) and contact
closure cable (Start In and Ground
pins) between the MS and the external
device. Then, attach the connector
housings. See External Devices.

4
2
Connect the relay
control cable between
3 the MS (V65 Pump
Enable) and the
Connect the USB cables from the forepumps.
MS to the syringe pump and the
modular valve.

IMPORTANT Before turning on the MS, make sure to complete all of the system
connections described in this guide.

Tip For troubleshooting purposes, you might want to record which devices connect to
which ports on the Ethernet switch.

1 The back of the data system computer might not be as shown.

16 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 6

External Devices
Control of external devices (through a contact closure cable) might or might not be through
one of the Thermo Scientific mass spectrometry applications, such as the Xcalibur data
system. For instructions on how to set the external device as the start instrument for data
acquisition, refer to the Getting Started Guide.

Contents
• Contact Closure Signal
• Communication Connectors

Contact Closure Signal

The Orbitrap Tribrid Series MS can start data acquisition upon receiving a contact closure
(start) signal from an external LC device, which is typically an autosampler. Thermo Scientific
mass spectrometry applications can control external devices (for example, autosamplers,
pumps, and detectors) from several manufacturers including Thermo Fisher Scientific,
Agilent Technologies, and Waters Corporation.

When an external device is not controlled by a Thermo Scientific mass spectrometry

application, such as the Xcalibur data system, you must properly connect it to send its contact
closure (start) signal. To assemble the two-wire contact closure cable, use the contact closure
mating connector (P/N 00004-21512) supplied in the MS Setup Kit and the contact closure
cable provided with the LC device.

CAUTION The external device providing the start signal must have proper earth
grounding. Ground loops can cause problems and create a safety hazard. The
complementary metal-oxide-semiconductor (CMOS) integrated circuits that are mounted
on the internal input/output (I/O) PCB fail if they receive more than 5 Vdc or 5 mA.

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 17

6 External Devices
Communication Connectors

IMPORTANT
• Before proceeding, verify that the external device is suitable for use with the
Orbitrap Tribrid Series MS. Make sure that the signal from the external device meets
the requirement stated in the pin 4 (Start In) pin-out description (see Table 3). If it
does not meet this requirement, you cannot use it with the MS.
• To help prevent sample waste if the MS becomes unresponsive, connect a cable
between the optional LC device and the MS’s Ready Out and Injection Hold pins (see
Table 3). Then, configure the Contact Closure settings in the Method Editor. You are
responsible for providing this cable.

Communication Connectors
Use the left-side communication connectors to connect the MS to the Ethernet switch, the
syringe pump, the modular valve, and any external device.

Table 3 lists the pin-out descriptions for the connectors shown in Figure 1.

CAUTION After connecting the external device cables, attach the connector housings.

Table 3. Pin-out descriptions for the communication connectors (Sheet 1 of 3)

Pin Name Description
– Reset Resets the instrument to a power-up state.
Note Use this button only if the instrument does not
respond to the control program on the data system
computer or if you need to restart the instrument
without turning off the electronics service switch.
Peripheral Control
1 Ground Earth ground.
2 5V Provides a 5 Vdc, 500 mA output (with pin 1).

18 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 6 External Devices
Communication Connectors

Table 3. Pin-out descriptions for the communication connectors (Sheet 2 of 3)

Pin Name Description
4 Start In Receives the start signal from the contact closure
connection of a connected external device.

To activate this signal, the external device must pull the

signal either low (below 0.75 Vdc) or high (above
2.4 Vdc), depending on the polarity, for at least
100 ms by using a relay, an open-collector driver, or a
similar device that connects between pins 4 and 1.
Note In the Instrument Configuration window, set
the contact closure signal to “High-to-low edge” or
“Low-to-high edge,” whichever matches the setting
for the connected external device.
5 Ready Out Provides a relay-driven programmable output signal to
the connected external device. The relay opens when a
method starts and closes when the method finishes.

Output: Maximum 24 Vdc, 3 A

6 Injection Hold Provides a relay-driven programmable output signal to
the connected external device, such as a fraction
collector.

Output: Maximum 24 Vdc, 3 A

8 RO/IH Common (return) connection for the Ready Out and
Injection Hold pins.
Analog Input

The two analog channels connect to two separate 12-bit analog-to-digital converters (ADC)
for on-demand conversion of the input voltage. The conversion rate depends on the MS
rate.
1 Chassis Earth ground (for pins 3 and 4).
3, 4 2V Max: (Channel 2) Provides a connection for an external
+ (positive, pin 3) and device, such as an LC instrument.
– (negative, pin 4)
Input: 0–2 Vdc (voltage clamps at 5 Vdc)
5 Chassis Earth ground (for pins 7 and 8).
7, 8 10V Max: (Channel 1) Provides a connection for an external
+ (positive, pin 7) and device, such as an LC instrument.
– (negative, pin 8)
Input: 0–10 Vdc (voltage clamps at 15 Vdc)

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 19

6 External Devices
Communication Connectors

Table 3. Pin-out descriptions for the communication connectors (Sheet 3 of 3)

Pin Name Description
Other connectors
– USB (2 ports) Provides a connection for the syringe pump and
modular valve.
– Ethernet 1000 Base T Provides a connection for the Ethernet switch.

Figure 1. Communication connectors (left side of the MS)

Reset button

Peripheral Control connector

Analog Input connector

USB ports

Ethernet port

20 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 A

Installation Kits and Power Cords

The Orbitrap Tribrid Series MS ships with several kits and power cords. This appendix lists
the necessary components for the instructions in this guide. For a full list of the kits and their
contents, refer to the Hardware Manual.

Contents
• Syringe Pump and Modular Valve Assembly
• Single Mechanical Pump Kit
• Dual Mechanical Pumps Kit
• MS Setup Kit
• Power Cords

Syringe Pump and Modular Valve Assembly

Image Item Quantity Part number
Holder, L-shaped, syringe pump and modular valve 1 80000-60363

Chemyx™ Fusion 100T syringe pump with a power cord 1 00109-99-00045

and USB interface cable

Rheodyne™ MX Series II™ modular divert/inject valve 1 00109-99-00046

(six-port, two-position) with an ac adapter, power cord,
USB interface cable, and high-pressure fitting sets

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 21

A Installation Kits and Power Cords
Single Mechanical Pump Kit

Single Mechanical Pump Kit

Item Quantity Part number
Image
Forepump, Oerlikon Leybold Vacuum™ SOGEVAC™ 1 00108-01-00032
SV65BI (rated single-phase 230 Vac, 50/60 Hz)

Forepump oil tray, stainless steel, caster wheels 1 00201-99-00549

Relay control cable, single pump, 2.4 m (8 ft) long 1 80000-63139

(preassembled)
Single pump vacuum hose assembly, KF40 1 80000-60229
(preassembled; exploded view shown)

Elbow connection
Elbow, aluminum, NW40, 90 degree 2a 00108-02-00010

Centering ring with O-ring, nitrile and aluminum, 2a 00108-02-00005

NW40

Swing clamp, aluminum, NW32/40 2a 00108-02-00004

Exhaust waste connection

Tubing, Tygon, 3/4 in. (19.1 mm) OD, 0.5 in. 1 00301-22920
(12.7 mm) ID, 3 m (10 ft) long

a
Only one piece is required.

22 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 A Installation Kits and Power Cords
Dual Mechanical Pumps Kit

Dual Mechanical Pumps Kit

Item Quantity Part number
Image
Forepump, Oerlikon Leybold Vacuum SOGEVAC 2 00108-01-00032
SV65BI (rated single-phase 230 Vac, 50/60 Hz)

Forepump oil tray, stainless steel, caster wheels 2 00201-99-00549

Dual relay control cable, 2.4 m (8 ft) long 1 80100-63146

(preassembled)

Dual pump vacuum hose assembly, including the 1 80011-60077

stainless steel 45-degree elbows and connection parts
(preassembled)

Exhaust waste connection

Fitting Tee, barbed, nylon, for 0.5 in. (12.7 mm) ID 1 00103-01-00012
tubing

Tubing, Tygon, 3/4 in. (19.1 mm) OD, 0.5 in. 1 00301-22920
(12.7 mm) ID, 6 m (20 ft) long

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 23

A Installation Kits and Power Cords
MS Setup Kit

MS Setup Kit
Image Item Quantity Part number
Communications connection
Connector plug, MINI-COMBICON™, 8-pin, 2 00004-21512
26.67 mm (1.05 in.) long, rated 160 V, 8 A (contact
closure)
– Connector housing, MINI-COMBICON, 8-position 2 00004-21514
– Ethernet cables, shielded Category 5e, 2.1 m (7 ft) long 2 00302-99-00036
– Ethernet power supply (rated 100–240 Vac, 50/60 Hz, 1 00012-01-00039
0.6/0.3 A input; 18 W, 12 Vdc, 1.5 A output)
Ethernet switch, 5-port gigabit 1 00825-01-00111

Gas connections
– Ferrule, brass, back, 1/4 in. ID 2 00101-04000
– Ferrule, brass, back, 1/8 in. ID 2 00101-02500
– Ferrule, brass, front, 1/4 in. ID 2 00101-10000
– Ferrule, brass, front, 1/8 in. ID 2 00101-08500
– Swagelok-type nut, brass, 1/4 in. ID 2 00101-12500
– Swagelok-type nut, brass, 1/8 in. ID 2 00101-15500
– Tubing, precleaned copper, 1/8 in. OD, 0.030 in. thick, 1a 00301-22701
4.6 m (15 ft) long (for the UHP helium and UHP
nitrogen gases)
– Tubing, Teflon PFA, 1/4 in. (6.35 mm) OD, 0.062 in. 1 00101-50100
(1.57 mm) thick, 4.6 m (15 ft) long (for the HP
nitrogen gas)
– Fittings to connect the copper and PFA tubings to the – –
gas supplies (customer provided)
Solvent waste connection
Container, Nalgene™, 4 L heavy-duty; filling/venting cap 1 80100-20265

24 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 A Installation Kits and Power Cords
Power Cords

Image Item Quantity Part number

Drain hose adapter with O-ring (not shown) 1 70111-20971

Tubing, Tygon, 1-3/8 in. OD, 1 in. ID, 3 m (10 ft) long 1 00301-01-00020

a Your order ships with a second length of copper tubing outside of this kit.

Power Cords
Device Cord length Country or territorya Plug configuration Plug rating
Mass spectrometer 2.5 m (8 ft) North America NEMA 6-15 250 Vac, 15 A
(P/N 96000-98035)
Internationalb CEE (3-pole) 250 Vac, 16 A
(P/N 80000-63188)
Forepump 2.5 m (8 ft) North America NEMA 6-15 250 Vac, 15 A
(no separate part number)
International CEE (3-pole) 250 Vac, 16 A
(P/N 80000-63186)
Peripheral components 1.8 m (6 ft) –c – –
a
Part numbers are provided for Thermo Fisher Scientific field service use only.
b
“International” designation is for countries or territories that do not use the North American plug configuration.
c
Not specified in this guide

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 25

A Installation Kits and Power Cords
Power Cords

26 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific

 I

Index

C G
cable connections 16 gases, specifications and consumptions 5
communication connectors 20
compliance K
EMC 15
kits, installation 21
FCC iv
regulatory iii
contact closure, start instrument signal 17 M
contacting us xiii model differences xii
customer-supplied hardware 15, 18
P
D power cords 16, 25
directives procedures
regulatory iii API source, installing 10
WEEE v forepumps, connecting 1
documentation online survey x gases, connecting 6
documentation, accessing x modular valve and syringe pump, installing 13
MS and data system, connecting the cables 16
solvent waste container, connecting 11
E workbench wheels, locking 4
electrical connections, cautions 15
electromagnetic compatibility iii
EMC compliance 15
R
exhaust hose, connecting 3 regulatory compliance iii
external devices relay switch circuit, external device 19
earth ground caution 17 Reset pin, instrument 18
important notes 18
S
F safety standards iii
FCC compliance iv solvent waste system, connecting 11
forepump connections start signal
fume exhaust system cautions 3 See contact closure, start instrument signal
vacuum hose 2 symbols, meaning xi
forepumps
fume exhaust system cautions 10
gas ballast valve, opening 3
maintenance instructions 1

Thermo Scientific Orbitrap Tribrid Series Getting Connected Guide 27

Index: T

T
Thermo Fisher Scientific website, user documents x
tools 13
troubleshooting, Ethernet switch 16

V
valve, LED 16
viewing documents x

W
WEEE directive v
workbench
forepump placement 2
wheels 4

28 Orbitrap Tribrid Series Getting Connected Guide Thermo Scientific