Orbitrap Fusion Series Getting Connected Guide

Orbitrap Fusion Series Getting Connected Guide

Orbitrap Fusion Series

Getting Connected Guide

80011-97002 Revision A July 2015

© 2015 Thermo Fisher Scientific Inc. All rights reserved.

EASY-Max NG and Orbitrap Fusion Lumos are trademarks, and Orbitrap, Orbitrap Fusion, 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 the Crawford Fitting 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, July 2015

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 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.

Regulatory compliance results for the following Thermo Scientific™ products:

Orbitrap Fusion Lumos

Orbitrap Fusion

Orbitrap Fusion Lumos

EMC Directive 2004/108/EC

EMC compliance has been evaluated by TÜV Rheinland of North America.

EN 55011: 2009, A1: 2010

EN 61000-3-2: 2006, A2: 2009

EN 61000-3-3: 2008

EN 61000-4-2: 2009

EN 61000-4-3: 2006, A2: 2010

EN 61000-4-4: 2004, A1: 2010

EN 61000-4-5: 2006

EN 61000-4-6: 2009

EN 61000-4-8: 2010

EN 61000-4-11: 2004

EN 61326-1: 2013

CISPR 11: 2009, A1: 2010

ICES-003 Issue 5: 2014

CFR 47, FCC Part 15, Subpart B, Class A: 2015

Low Voltage Safety Compliance

This device complies with Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1:2010

(3rd Edition).

Orbitrap Fusion

EMC Directive 2004/108/EC

EMC compliance has been evaluated by TÜV Rheinland of North America.

EN 55011: 2009, A1: 2010

EN 61000-3-2: 2006, A2: 2009

EN 61000-3-3: 2008

EN 61000-4-2: 2009

EN 61000-4-3: 2006, A2: 2010

EN 61000-4-4: 2004, A1: 2010

EN 61000-4-5: 2006

EN 61000-4-6: 2009

EN 61000-4-11: 2004

EN 61326-1: 2013

CISPR 11: 2009, A1: 2010

ICES-003 Issue 5: 2012

CFR 47, FCC Part 15, Subpart B, Class A: 2012

Low Voltage Safety Compliance

This device complies with Low Voltage Directive 2006/95/EC and harmonized standard EN 61010-1:2010

(3rd Edition).

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.

Directive DEEE

2012/19/EU

Thermo Fisher Scientific s'est associé avec une ou plusieurs sociétés de recyclage dans chaque état membre de l’Union

Européenne et ce produit devrait être collecté ou recyclé par celle(s)-ci. Pour davantage d'informations, rendez-vous sur la page www.thermoscientific.fr/rohs .

WEEE Direktive

2012/19/EU

Thermo Fisher Scientific hat Vereinbarungen mit Verwertungs-/Entsorgungsfirmen in allen EU-Mitgliedsstaaten getroffen, damit dieses Produkt durch diese Firmen wiederverwertet oder entsorgt werden kann. Weitere Informationen finden Sie unter www.thermoscientific.de/rohs .

C

Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

Orbitrap Fusion Series Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii

Installation Kits and Power Supply Cords. . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii

Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi

Syringe Pump and Divert/Inject Valve Assembly. . . . . . . . . . . . . . . . . . . . . xvii

Power Supply Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii

Cautions and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xix

Chapter 1 Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Connecting the Forepumps to the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . 2

Connecting One Forepump to the Mass Spectrometer . . . . . . . . . . . . . . . . . . 2

Connecting Two Forepumps to the Mass Spectrometer . . . . . . . . . . . . . . . . . 3

Connecting the Forepumps to the Lab Exhaust System . . . . . . . . . . . . . . . . . . . . 5

Connecting the Forepumps to the Mass Spectrometer and Line Power . . . . . . . . 6

Chapter 2 Nitrogen and Helium Gases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Schematic of the Internal Gas Supply Lines. . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Connecting the Gas Supplies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Connecting the Helium Gas Supply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Connecting the Nitrogen Gas Supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Chapter 3 Mass Spectrometer and Data System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15

Connecting the Mass Spectrometer to the Data System Computer . . . . . . . . . . 15

Connecting to Line Power. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Locking the Workbench Wheels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Chapter 4 API Source and Solvent Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19

Installing the API Source Spray Insert . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Connecting the Solvent Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

vii

Contents

Chapter 5 Syringe Pump and Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

Installing the Syringe Pump and Divert/Inject Valve . . . . . . . . . . . . . . . . . . . . . 25

Connecting the Cables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Chapter 6 External Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29

Contact Closure Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Communication Connectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

F

Figures

Figure 1.

Orbitrap Fusion MS vacuum port connection . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Figure 2.

Vacuum hose to the forepump connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Figure 3.

Vacuum port connection (Orbitrap Fusion Lumos MS) . . . . . . . . . . . . . . . . . . . 4

Figure 4.

Vacuum hose to the forepump connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Figure 5.

Forepump and exhaust system connection (Orbitrap Fusion Lumos MS) . . . . . . 6

Figure 6.

Power entry module (forepump control) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Figure 7.

Schematic of the internal gas supplies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Figure 8.

Gas inlet ports (back of the Orbitrap Fusion Lumos MS) . . . . . . . . . . . . . . . . . 12

Figure 9.

Connector assembly for the helium tubing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Figure 10.

Ethernet switch connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Figure 11.

Power entry module (line power) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Figure 12.

MS mount assembly with the spray cone and ion sweep cone . . . . . . . . . . . . . . 20

Figure 13.

EASY-Max NG API source assembly (H-ESI mode). . . . . . . . . . . . . . . . . . . . . 21

Figure 14.

Connection for the solvent waste container (Orbitrap Fusion Lumos MS) . . . . . 22

Figure 15.

Holder with the bottom shelf installed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Figure 16.

Holder with the divert/inject valve installed between shelves. . . . . . . . . . . . . . . 26

Figure 17.

Syringe pump secured to the support bracket (bottom of holder shown) . . . . . 27

Figure 18.

Communication connectors (left side of the MS) . . . . . . . . . . . . . . . . . . . . . . . . 32

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

ix

Figures x

Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

P

Preface

The Orbitrap Fusion Series Getting Connected Guide describes how to connect the Thermo

Scientific™ Orbitrap Fusion™ Series Tribrid™ mass spectrometer (MS) to line power (ac mains power system), the data system computer, the external vacuum system, the waste exhaust system, and any external liquid chromatography (LC) devices. External devices include those that are controlled from or are independent of Thermo mass spectrometry applications, such as the Thermo Xcalibur™ data system.

Contents

Orbitrap Fusion Series Models

Related Documentation

Installation Kits and Power Supply Cords

Cautions and Special Notices

Contacting Us

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.

Orbitrap Fusion Series Models

The Orbitrap Fusion Series documentation is intended for the following instrument models:

• Orbitrap Fusion—Requires one forepump.

• Orbitrap Fusion Lumos™—Requires two forepumps.

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

xi

Preface

Related Documentation

The Orbitrap Fusion Series mass spectrometer includes complete documentation. In addition to this guide, you can also access the following documents as PDF files from the data system computer:

Orbitrap Fusion Series Preinstallation Requirements Guide

Orbitrap Fusion Series Getting Started Guide

Orbitrap Fusion Series Hardware Manual

Ion Max NG and EASY-Max NG Ion Sources User Guide

EASY-ETD and EASY-IC Ion Sources User Guide (for instruments with the ETD or

Internal Calibration configuration)

Safety and Regulatory Guide

The Orbitrap Fusion Series also ships with a printed copy of the Safety and Regulatory

Guide. This guide contains important safety information about Thermo Scientific liquid chromatography (LC) and mass spectrometry (MS) systems. Make sure that all lab personnel have read and have access to this document.

To view the product manuals

From the Microsoft™ Windows™ taskbar, do the following:

• For a Thermo Scientific mass spectrometer, choose Start > All Programs > Thermo

Instruments > model x.x, and then open the applicable PDF file.

• For an LC instrument controlled by a Thermo application, choose Start > All

Programs > Thermo Instruments > Manuals > LC Devices and so on.

To download user documentation from the Thermo Scientific website

1. Go to www.thermoscientific.com

.

2. In the Search box, type the product name and press Enter.

3. In the left pane, select Documents & Videos, and then under Refine By Category, click

Operations and Maintenance.

4. (Optional) Narrow the search results or modify the display as applicable:

• For all related user manuals and quick references, click Operator Manuals.

• For installation and preinstallation requirements guides, click Installation

Instructions.

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

Preface

• For documents translated into a specific language, use the Refine By Language feature.

• Use the Sort By options or the Refine Your Search box (above the search results display).

5. Download the document as follows: a. Click the document title or click Download to open the file.

b. Save the file.

Installation Kits and Power Supply Cords

The Orbitrap Fusion Series MS ships with several kits and power supply cords. However, for the procedures in this guide, the following kits provide the necessary components:

Single Mechanical Pump Kit (one-forepump system)

Dual Mechanical Pumps Kit

(two-forepump system)

MS Setup Kit

Syringe Pump and Divert/Inject Valve Assembly

Power Supply Cords

For a full list of the kits and their contents, refer to the Orbitrap Fusion Series Hardware

Manual.

Single Mechanical Pump Kit

Table 1. Single Mechanical Pump Kit (P/N 80100-62004) (Sheet 1 of 2)

Image

Item

Forepump, Oerlikon Leybold Vacuum™ SOGEVAC™

SV 65 BI (rated single-phase 230 Vac, 50/60 Hz)

Quantity Part number

1 00108-01-00032

Thermo Scientific

Relay control cable, single pump, 2.4 m (8 ft) long

(preassembled)

1 80000-63139

Orbitrap Fusion Series Getting Connected Guide

xiii

Preface

Table 1. Single Mechanical Pump Kit (P/N 80100-62004) (Sheet 2 of 2)

Image

Item

Single pump vacuum hose assembly, KF40

(preassembled; exploded view shown)

Quantity Part number

1 80000-60229

Elbow connection

Elbow, aluminum, NW40, 90 degree 2 a

00108-02-00010

Centering ring with O-ring, nitrile and aluminum,

NW40

Swing clamp, aluminum, NW32/40

Exhaust waste connection

Tubing, Tygon™, 3/4 in. (19.1 mm) OD, 0.5 in.

(12.7 mm) ID, 3 m (10 ft) long a

Only one piece is required

2 a

2 a

00108-02-00005

00108-02-00004

1 00301-22920

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

Preface

Dual Mechanical Pumps Kit

Table 2. Dual Mechanical Pumps Kit (P/N 80011-62006)

Image

Item

Forepump, Oerlikon Leybold Vacuum SOGEVAC

SV 65 BI (rated single-phase 230 Vac, 50/60 Hz)

Quantity Part number

2 00108-01-00032

Dual relay control cable, 2.4 m (8 ft) long

(preassembled)

1 80100-63146

Dual pump vacuum hose assembly, including the stainless steel 45-degree elbows and connection parts

(preassembled)

1 80011-60077

Exhaust waste connection

Fitting Tee, barbed, nylon, for 0.5 in. (12.7 mm) ID tubing

Tubing, Tygon, 3/4 in. (19.1 mm) OD, 0.5 in.

(12.7 mm) ID, 6 m (20 ft) long

1 00103-01-00012

1 00301-22920

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

xv

Preface

MS Setup Kit

Table 3. MS Setup Kit (P/N 80100-62003) (Sheet 1 of 2)

Image

Communications connection

Item

Connector plug, MINI-COMBICON™, 8-pin,

26.67 mm (1.05 in.) long, rated 160 V, 8 A (contact closure)

Ethernet cables, shielded Category 5e, 2.1 m (7 ft) long

Ethernet power supply (rated 100–240 Vac, 50/60 Hz,

0.6/0.3 A input; 18 W, 12 Vdc, 1.5 A output)

Ethernet switch, 5-port Gigabit

Quantity Part number

2

2

1

1

00004-21512

00302-99-00036

00012-01-00039

00825-01-00111

Gas connections

Ferrule, brass, front, 1/4 in. ID

Ferrule, brass, front, 1/8 in. ID

Ferrule, brass, back, 1/4 in. ID

Ferrule, brass, back, 1/8 in. ID

Swagelok™-type nut, brass, 1/4 in. ID

Swagelok-type nut, brass, 1/8 in. ID

Tubing, precleaned copper, 1/8 in. OD, 0.030 in. thick,

4.6 m (15 ft) long (for the ultra-high-purity [UHP] helium and UHP nitrogen gases)

Tubing, Teflon™ PFA, 1/4 in. (6.35 mm) OD, 0.062 in.

(1.57 mm) thick, 4.6 m (15 ft) long (for the high-purity

[HP] nitrogen gas)

Fittings to connect the copper and PFA tubings to the gas supplies (customer provided)

2

2

2

2

2

2

1 a

1

00101-10000

00101-08500

00101-04000

00101-02500

00101-12500

00101-15500

00301-22701

00101-50100

Solvent waste connection

Container, Nalgene™, 4 L heavy-duty; filling/venting cap 1 80100-20265

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

Preface

Table 3. MS Setup Kit (P/N 80100-62003) (Sheet 2 of 2)

Image Item

Drain hose adapter with O-ring (not shown)

Quantity Part number

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.

Syringe Pump and Divert/Inject Valve Assembly

Table 4. Syringe pump and divert/inject valve assembly

Image Item

Holder, divert valve and syringe pump, L-shaped

Quantity Part number

1 80000-60363

Chemyx™ Fusion 100T syringe pump with a power supply cord and USB interface cable

1 00109-99-00045

Rheodyne™ MX Series II™ modular divert/inject valve

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

1 00109-99-00046

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

xvii

Preface

Power Supply Cords

Table 5 lists the specifications for the various detachable power supply cords that ship with

your order.

Table 5. Power supply cord specifications

Device

Mass spectrometer

Cord length

2.5 m (8 ft)

Country or territory a

North America

(P/N 96000-98035)

International b

(P/N 80000-63188)

Plug configuration

NEMA 6-15

CEE (3-pole)

Forepump 2.5 m (8 ft) North America

(no separate part number)

NEMA 6-15

International

(P/N 80000-63186)

– c

CEE (3-pole)

Peripheral components 1.8 m (6 ft) – a c

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.

Not specified in this guide

Plug rating

250 Vac, 15 A

250 Vac, 16 A

250 Vac, 15 A

250 Vac, 16 A

Cautions and Special Notices

Make sure that you follow the cautions and special notices presented in this guide. Cautions and special notices appear in boxes; those concerning safety or possible damage also have corresponding caution symbols.

This manual uses the following types of cautions and special notices.

CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION notice is accompanied by an appropriate CAUTION symbol.

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.

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

Preface

The Orbitrap Fusion Series Getting Connected Guide contains the following caution-specific symbols (

Table 6

).

Table 6. Caution-specific symbols and their meanings

Symbol Meaning

Chemical hazard: 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 Fusion Series mass spectrometer, 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 could occur from splattered chemicals or airborne particles. Wear safety glasses when handling chemicals or servicing the instrument.

Trip obstacle: Be aware of cords, hoses, or other objects located on the floor.

Contacting Us

There are several ways to contact Thermo Fisher Scientific for the information you need. You can use your smartphone to scan a QR code, which opens your email application or browser.

Contact us Customer Service and Sales Technical Support

(U.S.) 1 (800) 532-4752 (U.S.) 1 (800) 532-4752

(U.S.) 1 (561) 688-8731 (U.S.) 1 (561) 688-8736

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

xix

Preface

Contact us Customer Service and Sales

us.customer-support.analyze

@thermofisher.com

Technical Support

us.techsupport.analyze

@thermofisher.com

To find global contact information or customize your request

1. Go to www.thermoscientific.com

.

2. Click Contact Us, select the Using/Servicing a Product option, and then type the product name.

3. Use the phone number, email address, or online form.

To find product support, knowledge bases, and resources

Go to www.thermoscientific.com/support .

To find product information

Go to www.thermoscientific.com/lc-ms .

Note To provide feedback for this document:

• Send an email message to Technical Publications ( [email protected]

).

• Complete a survey at www.surveymonkey.com/s/PQM6P62 .

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

1

Vacuum System

This chapter describes how to connect the forepump or forepumps to the Orbitrap Fusion

Series MS, the laboratory exhaust system, and line power (ac mains power system). As noted

in the Preface

, each instrument requires one or two external forepumps to maintain its internal vacuum pressure.

The Single Mechanical Pump Kit (see

Table 1 ) or Dual Mechanical Pump Kit (see

Table 2 )

contain the required components to complete these connections. For easier access to the forepump when it is under the workbench, you can order the optional forepump tray

(P/N 80000-10309).

Note

• A Thermo Fisher Scientific field service engineer must install the mass spectrometer.

• For information about the line power requirements, refer to the Orbitrap Fusion Series

Preinstallation Requirements Guide.

CAUTION In addition to reading the operating and maintenance instructions provided with the forepump, do the following:

• Prevent the forepump from overheating by ensuring that there is sufficient air clearance around the pump.

• Maintain the exhaust pressure from atmospheric pressure minus 15 mbar to

1.15 bar absolute (0.15 bar relative).

• Follow the instructions for adding and changing the oil.

Contents

Connecting the Forepumps to the Mass Spectrometer

Connecting the Forepumps to the Lab Exhaust System

Connecting the Forepumps to the Mass Spectrometer and Line Power

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

1

1

Vacuum System

Connecting the Forepumps to the Mass Spectrometer

Connecting the Forepumps to the Mass Spectrometer

IMPORTANT To ensure the best pumping performance, limit the length of the vacuum hose that connects the mass spectrometer to the forepump or forepumps to no more than

2.4 m (8 ft).

Follow the applicable procedure for your Orbitrap Fusion Series system:

Connecting One Forepump to the Mass Spectrometer

Connecting Two Forepumps to the Mass Spectrometer

Connecting One Forepump to the Mass Spectrometer

Unless otherwise noted, use the following procedure for a system that requires one forepump.

To connect the forepump to the mass spectrometer

1. Place the forepump behind the mass spectrometer.

2. Using a centering ring

and a

swing clamp , connect a plumbing elbow to the mass

spectrometer’s back vacuum port with the open end facing toward the side, not the floor

(left side in Figure 1 ).

Figure 1.

Orbitrap Fusion MS vacuum port connection

MS vacuum port

Exploded view of the connection shown to the left

To forepump

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

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Vacuum System

Connecting the Forepumps to the Mass Spectrometer

3. Using the centering ring and the swing clamp, connect the other elbow to the forepump’s

inlet port ( Figure 2 ).

Figure 2.

Vacuum hose to the forepump connection

Hose clamp

Hose adapter, KF40

Centering ring, NW40

Swing clamp, NW32/40

Vacuum hose,

1.5 in. ID

Elbow (90 degree)

Swing clamp, NW32/40

Centering ring, NW40

Forepump vacuum port flange

4. Connect the preassembled

vacuum hose assembly to the two elbows by using the

centering rings and the swing clamps from the vacuum hose assembly (

Figure 1

).

5. Move the forepump under the mass spectrometer.

Connecting Two Forepumps to the Mass Spectrometer

Unless otherwise noted, use the following procedure for a system that requires two forepumps.

To connect the forepumps to the mass spectrometer

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.

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

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1

Vacuum System

Connecting the Forepumps to the Mass Spectrometer

2. Using the stainless steel clamp, connect the short tubing on the vacuum hose assembly

to the vacuum port located under the mass spectrometer’s front, left corner (

Figure 3

).

Figure 3.

Vacuum port connection (Orbitrap Fusion Lumos MS)

The instrument vacuum port extends through the workbench (front/left corner viewed from the back of the workbench).

3. Using a centering ring and a swing clamp, connect a plumbing elbow to each forepump’s

inlet port ( Figure 4 ).

Figure 4.

Vacuum hose to the forepump connection

Vacuum hose, 1.5 in. ID

Hose clamp

Centering ring, NW40

Hose adapter, KF40

Swing clamp, NW32/40

Elbow (45 degree)

Swing clamp, NW32/40

Centering ring, NW40

Forepump vacuum port flange

4. Using the centering rings and the swing clamps from the vacuum hose assembly, connect the other ends of the vacuum hose assembly to the elbows that are on the forepumps.

5. Move the forepumps under the mass spectrometer.

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

1

Vacuum System

Connecting the Forepumps to the Lab Exhaust System

Connecting the Forepumps to the Lab Exhaust System

To properly operate the forepumps, you must connect them to an efficient fume exhaust system. Most atmospheric pressure ionization (API) applications contribute to solvents accumulating in the forepump. Although Thermo Fisher Scientific recommends that you periodically open the gas ballast valve (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. 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.

To connect the forepumps to the lab exhaust system

Secure one end of the exhaust tubing

to the forepump exhaust ports ( Figure 5 ), and then

secure the other end to the lab exhaust system.

CAUTION

• Run the exhaust hose at floor level for at least 2 m (78.7 in.). This hose acts as a trap for exhaust fumes that would otherwise recondense in the forepump oil.

• The forepump exhaust is a health hazard. Therefore, make sure that the forepump exhaust vents to an appropriate external exhaust system.

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

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1

Vacuum System

Connecting the Forepumps to the Mass Spectrometer and Line Power

Figure 5.

Forepump and exhaust system connection (Orbitrap Fusion Lumos MS)

Vacuum hoses

Exhaust ports

Exhaust tubing (connects to the lab exhaust system)

(Workbench shown without the front panel.)

Connecting the Forepumps to the Mass Spectrometer and Line Power

This section describes how to connect the forepumps’ relay control cable and power supply cables.

To connect the forepumps to the mass spectrometer and line power

1. Connect the relay control cable

as follows:

• Connect the 4-pin connector (the end labeled Power Module) to the SV65 Pump

Enable connector located on the right side of the mass spectrometer (

Figure 6

).

The mass spectrometer uses this cable to remotely turn the forepumps on and off.

• Connect the DE9 connectors (the end labeled Roughing Pump) to the forepumps.

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

Thermo Scientific

1

Vacuum System

Connecting the Forepumps to the Mass Spectrometer and Line Power

Figure 6.

Power entry module (forepump control)

SV65 Pump Enable connector

(forepump on/off control)

AC Output receptacle

(reserved for future use)

Power In receptacle

(230 Vac)

2. Connect the power supply cords to the forepumps, and then plug the cords into two separate, dedicated 230 Vac electrical outlets.

CAUTION Do not plug the power supply cord into the mass spectrometer’s auxiliary

AC Output receptacle. This receptacle is not used at this time.

3. If you removed the workbench’s front panel, reattach it.

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

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

CAUTION Avoid an electric shock. Read the warning on the forepump. Take care when you disconnect the forepump’s power supply cord from the electrical outlet. After disconnecting the power supply cord, do not touch the plug’s pins for at least 5 minutes to allow time for the voltage potential to dissipate.

Orbitrap Fusion Series Getting Connected Guide

7

1

Vacuum System

Connecting the Forepumps to the Mass Spectrometer and Line Power

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

2

Nitrogen and Helium Gases

This chapter describes how to connect the Orbitrap Fusion Series MS to the laboratory gas supplies. Connections and gas delivery systems might vary. You are responsible for supplying any additional fittings or connections necessary during installation.

The MS Setup Kit contains the required components to complete these connections (see

Table 3 ).

Note

• Make sure that the lab already has the gas supply lines installed, properly terminated, and ready to connect to the mass spectrometer. For additional information about the required gases, refer to the Orbitrap Fusion Series Preinstallation Requirements Guide.

• If your system includes additional devices that require their own gas connections, refer to the applicable instrument manuals.

Contents

Schematic of the Internal Gas Supply Lines

Connecting the Gas Supplies

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

9

2

Nitrogen and Helium Gases

Schematic of the Internal Gas Supply Lines

Schematic of the Internal Gas Supply Lines

Figure 7

shows a schematic drawing of the gas lines in the Orbitrap Fusion Series MS where

Reagent ion source represents the optional EASY-IC or EASY-ETD ion source.

Figure 7.

Schematic of the internal gas supplies

Helium open split inlet

Ion-routing multipole

Vent valve

Gas block

Reagent ion source

API source

Linear ion trap

Source PCB

Regulator

UHP nitrogen gas inlet

UHP helium gas inlet

(Back of the MS)

HP nitrogen gas inlet

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

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Nitrogen and Helium Gases

Connecting the Gas Supplies

Connecting the Gas Supplies

The Orbitrap Fusion Series MS requires ultra-high-purity (UHP) helium gas, high-purity

(HP) nitrogen gas, and UHP nitrogen gas. The instrument can use large amounts of gas during daily operation. Make sure that the gases are delivered with the necessary pressure and purity as listed in

Table 7 .

Table 7. Summary of the required gases for the Orbitrap Fusion Series MS

Type

Helium

Recommended purity

UHP (99.999%)—Has less than

1.0 ppm each of water, oxygen, and total hydrocarbons.

Nitrogen HP (99%)

Required gas pressure

275 ±70 kPa

(40 ±10 psi)

Typical daily consumption a

9.22 L

(0.325 ft

3

)

Function

Linear ion trap and damping gas collision gas

UHP (99.999%)—Has less than

3.0 ppm each of water, oxygen, and total hydrocarbons.

690 ±140 kPa

(100 ±20 psi)

345 ±70 kPa

(50 ±10 psi)

11 500–26 700 L

(406–943 ft

3

)

API source

auxiliary gas ,

sheath gas , and sweep gas

46 L (1.62 ft

3

) Venting gas, ion routing multipole (IRM) collision

gas, and make-up gas and reagent carrier gas

for the IC and ETD configurations a

Approximate value when operating 24 hours and 7 days a week

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

Use the following procedures to connect the required gas lines to the back of the mass

spectrometer ( Figure 8 ).

Connecting the Helium Gas Supply

Connecting the Nitrogen Gas Supplies

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

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2

Nitrogen and Helium Gases

Connecting the Gas Supplies

Figure 8.

Gas inlet ports (back of the Orbitrap Fusion Lumos MS)

HP nitrogen gas inlet

UHP helium gas inlet UHP nitrogen gas inlet

Connecting the Helium Gas Supply

Use the following procedure to connect the UHP helium gas supply to the instrument.

To connect the UHP helium supply to the mass spectrometer

1. Cut an appropriate length of the precleaned, 1/8 in. OD, copper tubing.

2. On one end of the tubing, connect an appropriate fitting for the gas supply, and then connect this end of the tubing to the UHP helium gas supply.

3. On the other end of the tubing, connect the 1/8 in. ID Swagelok-type nut, followed by

the two-piece, 1/8 in. ID ferrule set ( Figure 9 ). Then, connect this end of the tubing to

the Helium In gas inlet.

Figure 9.

Connector assembly for the helium tubing

Back ferrule

Gas tubing Front ferrule

Swagelok-type nut

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

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Nitrogen and Helium Gases

Connecting the Gas Supplies

Note

• After you start using the mass spectrometer, do not shut off the helium gas. Optimum performance requires a continuous flow of the helium.

• If you intend to use helium for sparging your LC solvents, you must have a second tank and regulator.

Connecting the Nitrogen Gas Supplies

Use the following procedure to connect the HP and UHP

1

nitrogen gas supplies to the instrument.

To connect the HP nitrogen supply to the mass spectrometer

1. Cut an appropriate length of the 1/4 in. OD Teflon PFA tubing.

2. On one end of the tubing, connect an appropriate fitting for the gas supply, and then connect this end of the tubing to the HP nitrogen gas supply.

3. Push the other end of the tubing into the Nitrogen In gas inlet ( Figure 8 ).

To connect the UHP gas supply to the mass spectrometer

1. Cut an appropriate length of the precleaned, 1/8 in. OD, copper tubing.

2. On one end of the tubing, connect an appropriate fitting for the gas supply, and then connect this end of the tubing to the UHP nitrogen gas supply.

3. On the other end of the tubing, connect the 1/8 in. ID Swagelok-type nut, followed by

the two-piece, 1/8 in. ID ferrule set ( Figure 9 ). Then, connect this end of the tubing to the UHP Nitrogen In gas inlet ( Figure 8 ).

IMPORTANT After you start using the mass spectrometer, do not shut off the UHP nitrogen gas unless you have vented the mass spectrometer. Optimum performance requires a continuous flow of the nitrogen gas.

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

Thermo Scientific

1

IC and ETD configuration systems only

Orbitrap Fusion Series Getting Connected Guide

13

2

Nitrogen and Helium Gases

Connecting the Gas Supplies

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

3

Mass Spectrometer and Data System

This chapter describes how to connect the Orbitrap Fusion Series MS to the data system computer and how to connect the instrument and computer to line power (ac mains power system).

The MS Setup Kit contains the required components to complete these connections (see

Table 3 ).

Contents

Connecting the Mass Spectrometer to the Data System Computer

Connecting to Line Power

Locking the Workbench Wheels

Connecting the Mass Spectrometer to the Data System Computer

The data system for the Orbitrap Fusion Series MS includes a computer, monitor, and

Ethernet switch. You can also add a printer. The mass spectrometer communicates with the data system computer through an Ethernet network.

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

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

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3

Mass Spectrometer and Data System

Connecting the Mass Spectrometer to the Data System Computer

To connect the mass spectrometer to the data system computer

Do the following:

• Connect one Ethernet cable from a port on the Ethernet switch to the Ethernet port on the left side of the mass spectrometer (

Figure 10 ).

• Connect the second Ethernet cable from a port on the Ethernet switch to the

Ethernet network card in the data system computer ( Figure 10 ).

The Ethernet network card is located at the back of the computer and labeled

LC/MS.

Figure 10. Ethernet switch connections

MS communication connectors (left side)

Data system computer

Ethernet port

Ethernet switch

Ethernet network card

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

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

3

Mass Spectrometer and Data System

Connecting to Line Power

Connecting to Line Power

This section describes how to connect the Ethernet switch, the computer, and the mass spectrometer to line power.

To connect the Ethernet switch and computer to line power

1. Connect a power supply cord into the Ethernet power supply.

2. Connect the Ethernet power supply from the Ethernet switch to an electrical outlet.

The Power LED indicator turns green when the switch receives power.

3. Connect a power supply cord into the computer and then to an electrical outlet.

4. Turn on the computer.

To connect the mass spectrometer to line power

1. Turn off the mass spectrometer’s Main Power switch (

Figure 11 ).

Figure 11. Power entry module (line power)

Electronics service switch

Thermo Scientific

Power In receptacle

(230 Vac)

Main Power switch

2. Place the electronics service switch in the Service Mode (down) position.

3. Connect the mass spectrometer’s power supply cord from the Power In receptacle to a

230 Vac electrical outlet.

IMPORTANT Do not turn on the mass spectrometer until after you complete all of the system connections described in this guide.

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

Orbitrap Fusion Series Getting Connected Guide

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3

Mass Spectrometer and Data System

Locking the Workbench Wheels

Locking the Workbench Wheels

After you complete the installation, you can lock the front caster wheels to prevent the workbench from moving.

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.

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

4

API Source and Solvent Waste Container

This chapter describes how to install the

electrospray (ESI)

or

atmospheric pressure chemical ionization (APCI) spray insert into the Thermo Scientific EASY-Max NG™ API source

( Figure 13

) and how to connect the solvent waste container to the drain/waste port on the back of the Orbitrap Fusion Series MS.

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 mode

1

(H-ESI, APCI, or APPI) by changing the spray insert—all without the use of tools.

The MS Setup Kit contains the required components for the solvent waste connection (see

Table 3 ).

Contents

Installing the API Source Spray Insert

Connecting the Solvent Waste Container

Thermo Scientific

1

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

Orbitrap Fusion Series Getting Connected Guide

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4

API Source and Solvent Waste Container

Installing the API Source Spray Insert

Installing the API Source Spray Insert

The EASY-Max NG API source ships with a H-ESI spray insert. For APCI mode, you can order the optional APCI Source Installation Kit (P/N 80000-62060), which includes the

APCI spray insert. For APPI mode, you can order the optional APPI Interface Kit

(P/N OPTON-30185) and use either the H-ESI or APCI spray insert, as applicable. For more information about the spray inserts, refer to the Ion Max NG and EASY-Max NG Ion

Sources User Guide.

To install the spray insert

1. For H-ESI and APCI modes, make sure that the ion sweep cone is installed over the mass

spectrometer’s spray cone ( Figure 12 ).

Note Not all ion sweep cones are compatible with all mass spectrometers.

Figure 12. MS mount assembly with the spray cone and ion sweep cone

Spray cone

Ion sweep cone

(offset orifice)

2. Attach the API source (

Figure 13 ) to the front of the mass spectrometer.

For instructions and information about the available ionization techniques, refer to the

Ion Max NG and EASY-Max NG Ion Sources User Guide.

3. To switch the ionization mode, refer to the Ion Max NG and EASY-Max NG Ion Sources

User Guide.

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

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4

API Source and Solvent Waste Container

Installing the API Source Spray Insert

Figure 13. EASY-Max NG API source assembly (H-ESI mode)

Spray insert (H-ESI mode)

Heater assembly

Grounding union holder

(H-ESI mode)

Heater/vaporizer tube

API source housing

Orbitrap Fusion Series Getting Connected Guide

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4

API Source and Solvent Waste Container

Connecting the Solvent Waste Container

Connecting the Solvent Waste Container

The Orbitrap Fusion Series MS internally routes the solvent waste from the bottom of the

API source to the back drain/waste port (

Figure 14 ).

During the initial installation of the mass spectrometer, a Thermo Fisher Scientific field service engineer installs the solvent waste system.

Figure 14. Connection for the solvent waste container (Orbitrap Fusion Lumos MS)

Drain/Waste port with attached adapter

Tygon waste tubing

(1 in. ID)

Tygon tubing

(1 in. ID) to the external vent system

Filling/venting cap

Solvent waste container

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

4

API Source and Solvent Waste Container

Connecting the Solvent Waste Container

CAUTION

Use these guidelines for the API source drain:

• Use the Tygon tubing provided with the solvent waste container to connect the solvent waste container to a fume exhaust system.

• To prevent solvent waste from backing up into the mass spectrometer, make sure that all Tygon tubing is above the level of liquid in the waste container as follows:

– From the mass spectrometer to the solvent waste container

– From the waste container to the exhaust system

Equip your lab with at least two fume exhaust systems:

• The analyzer optics become contaminated if the drain/waste tubing and the exhaust tubing from the forepump connect to the same fume exhaust system. Route the exhaust tubing from the forepump 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. Vent the waste container to a dedicated fume exhaust system. The exhaust system for the API source must accommodate a flow rate of up to 30 L/min (64 ft

3

/h).

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

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

23

4

API Source and Solvent Waste Container

Connecting the Solvent Waste Container

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

5

Syringe Pump and Divert/Inject Valve

This chapter describes how to install the Thermo Scientific syringe pump and modular divert/inject valve and how to connect these components to the Orbitrap Fusion Series MS and line power (ac mains power system).

The Syringe Pump and Divert/Inject Valve Assembly

contains both of these components and

their accessories (see Table 4

).

Note For instructions on how to set up the syringe pump and plumb the divert/inject valve, refer to the Orbitrap Fusion Series Getting Started Guide.

Contents

Installing the Syringe Pump and Divert/Inject Valve

Connecting the Cables

Installing the Syringe Pump and Divert/Inject Valve

This section describes how to assemble and install the syringe pump and the modular divert/inject valve system onto the mass spectrometer. These instructions require a #2 Phillips screwdriver only.

Follow these procedures:

1.

To attach the modular valve to the holder

2.

To attach the syringe pump to the holder

3.

To attach the syringe pump/valve assembly to the mass spectrometer

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

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5

Syringe Pump and Divert/Inject Valve

Installing the Syringe Pump and Divert/Inject Valve

To attach the modular valve to the holder

1. Using a #2 Phillips screwdriver and two of the provided screws, secure the bottom shelf to the holder (

Figure 15

).

The top and bottom shelves are identical.

Figure 15. Holder with the bottom shelf installed

Bottom shelf for the valve

Screw

2. Hold the divert/inject valve on the bottom shelf with one hand, and with the other hand install the top shelf above the valve by using a #2 Phillips screwdriver and the other two provided screws (

Figure 16

).

Figure 16. Holder with the divert/inject valve installed between shelves

Top shelf

Valve between top and bottom shelves

Screw

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

Thermo Scientific

5

Syringe Pump and Divert/Inject Valve

Installing the Syringe Pump and Divert/Inject Valve

To attach the syringe pump to the holder

1. Center the bottom of the syringe pump on the top angled, support bracket ( Figure 17

).

Figure 17. Syringe pump secured to the support bracket (bottom of holder shown)

Angled support bracket for the pump

Knurled, spring-type screw

Syringe pump

Cable management channel

2. Using either your fingers or a #2 Phillips screwdriver, tighten the knurled, spring-type screw into the bottom of the syringe pump.

To attach the syringe pump/valve assembly to the mass spectrometer

1. Place the syringe pump/valve assembly on the top, left surface of the mass spectrometer.

The weight of the assembly holds it in place on the instrument.

2. Adjust the assembly’s position, as needed.

Orbitrap Fusion Series Getting Connected Guide

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5

Syringe Pump and Divert/Inject Valve

Connecting the Cables

Connecting the Cables

The syringe pump and divert/inject valve each require two cables, one for their input power and the other for signal communication between the component and the mass spectrometer.

The divert/inject valve and syringe pump connectors are on the back of these components.

The mass spectrometer communication connectors are on the left side of the instrument

( Figure 18

).

To connect the cables

1. Connect the two USB interface cables as follows:

• Connect a USB cable from the syringe pump to the USB port on the mass spectrometer.

• Connect a USB cable from the valve to the USB port on the mass spectrometer.

Note If the API source contains the optional APPI lamp, install a USB splitter into one of the instrument’s USB ports to accommodate the three USB connections.

2. Connect the syringe pump to line power as follows: a. Turn off the syringe pump’s power switch. b. Make sure that the voltage selector switch is set to the appropriate voltage (110 V or

220 V) for your country or territory. c.

Connect the syringe pump’s power supply cord from the pump to an electrical outlet.

3. Connect the divert/inject valve to line power as follows:

• Connect the ac adapter’s output cord to the valve’s input connector (24 Vdc).

• Connect the power supply cord from the ac adapter to an electrical outlet.

If the LED on the front of the valve remains off, press the front Remote button to exit local mode.

4. Place the cords in the cable management channel ( Figure 17

).

CAUTION After you complete these connections, route the ac adapter and cables so that they are not a trip hazard.

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

6

External Devices

This chapter provides information on how to control an external device that connects to the

Orbitrap Fusion Series MS through a contact closure cable. Control of external devices 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 Orbitrap Fusion Series Getting Started Guide.

Contents

Contact Closure Signal

Communication Connectors

Contact Closure Signal

The Orbitrap Fusion 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. This cable connects the contact closure pins on the mass spectrometer to your 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 V or 5 mA.

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

29

6

External Devices

Communication Connectors

IMPORTANT

• Before proceeding, verify that the external device is suitable for use with the

Orbitrap Fusion 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 8 ). If it

does not meet this requirement, you cannot use it with the mass spectrometer.

• You are responsible for providing the cable that connects the Ready Out and Injection

Hold pins (see Table 8

) to an optionally connected LC device. To help prevent sample waste if the mass spectrometer becomes unresponsive, connect this cable and configure the Contact Closure settings in the Method Editor.

To connect the contact closure cable

1. Connect the contact closure cable to the Start In

and Ground pins on the left side of the mass spectrometer (

Figure 18

).

2. Connect the other end of the cable to the external device according to its manual.

Communication Connectors

Use the left-side communication connectors to connect the Orbitrap Fusion Series MS to the

Ethernet switch, the syringe pump, the divert/inject valve, and any external device.

Table 8 lists the pin-out descriptions for the left-side communication connectors shown in

Figure 18 .

Table 8. Pin-out descriptions for the communication connectors (Sheet 1 of 3)

Pin

Name

Reset

Description

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

2

Ground

5V

Earth ground

Provides a 5 Vdc, 500 mA output (with pin 1).

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Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

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6

External Devices

Communication Connectors

Table 8. Pin-out descriptions for the communication connectors (Sheet 2 of 3)

Pin

4

Name

Start In

Description

Receives the start signal from the contact closure connection

of a connected external device.

5 Ready Out

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.

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.

6

8

Injection Hold

RO/IH

Output: Maximum 24 Vdc, 3 A

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

Output: Maximum 24 Vdc, 3 A

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 mass spectrometer rate.

1 Chassis Earth ground (for pins 3 and 4)

3, 4 2V Max:

+ (positive, pin 3) and

– (negative, pin 4)

(Channel 2) Provides a connection for an external device, such as an LC instrument.

5 Chassis

7, 8 10V Max:

+ (positive, pin 7) and

– (negative, pin 8)

Input: 0–2 Vdc (voltage clamps at 5 Vdc)

Earth ground (for pins 7 and 8)

(Channel 1) Provides a connection for an external device, such as an LC instrument.

Input: 0–10 Vdc (voltage clamps at 15 Vdc)

Orbitrap Fusion Series Getting Connected Guide

31

6

External Devices

Communication Connectors

Table 8. Pin-out descriptions for the communication connectors (Sheet 3 of 3)

Pin Name

Other connectors

– USB (2 ports)

Description

– Ethernet 1000 Base T

Provides a connection for the syringe pump and divert/inject valve.

Provides a connection for the Ethernet switch.

Figure 18. Communication connectors (left side of the MS)

Reset button

Peripheral Control connector

Analog Input connector

USB ports

Ethernet port

32

Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

G

Glossary

A

B

C D E

F

G

H

I J K L

M N

O P Q

R S

T U V W X Y Z

A

API source The sample interface between the liquid chromatograph (LC) and the mass spectrometer

(MS).

atmospheric pressure chemical ionization (APCI) A soft ionization technique done in an ion source operating at atmospheric pressure. Electrons from a corona discharge initiate the process by ionizing the mobile phase vapor molecules, forming a reagent gas.

atmospheric pressure ionization (API) Ionization performed at atmospheric pressure by using atmospheric pressure chemical ionization (APCI), heated-electrospray (H-ESI), or nanospray ionization

(NSI).

auxiliary gas The outer-coaxial gas (nitrogen) that assists the sheath (inner-coaxial) gas in dispersing and/or evaporating sample solution as the sample solution exits the H-ESI or APCI (optional) spray insert.

C

chemical ionization gas See make-up gas .

collision energy The energy used when ions collide with the collision gas.

collision gas A neutral gas used to undergo collisions with ions.

computer data system See

data system .

contact closure connection The cable connection is from the external peripheral device to the mass spectrometer contact closure pins (Start In and

Ground). The external device sends the contact closure (start) signal to the mass spectrometer.

D

damping gas Helium gas introduced into the ion trap mass analyzer that slows the motion of ions entering the mass analyzer so that the ions can be trapped by the rf voltage fields in the mass analyzer.

data system Consists of a computer, monitor, keyboard, mouse, Ethernet switch, and optional printer.

divert/inject valve A valve on the mass spectrometer that can be plumbed as a loop injector or as a divert valve.

E

electron transfer dissociation (ETD) A method of fragmenting peptides and proteins. In ETD, singly charged reagent anions transfer an electron to multiply protonated peptides within the linear ion trap mass analyzer. This leads to a rich ladder of

Thermo Scientific Orbitrap Fusion Series Getting Connected Guide

33

Glossary: electrospray (ESI) sequence ions derived from cleavage at the amide groups along the peptide backbone. Amino acid side chains and important modifications such as phosphorylation are left intact.

electrospray (ESI) A type of atmospheric pressure ionization that is currently the softest ionization technique available to transform ions in solution into ions in the gas phase.

electrospray ionization (ESI) See electrospray (ESI)

.

F

forepump The pump that evacuates the foreline. A rotary-vane pump is a type of forepump. It might also be referred to as a backing, mechanical, rotaryvane, roughing, or vacuum pump.

H

heated-electrospray (H-ESI) A type of atmospheric pressure ionization that converts ions in solution into ions in the gas phase by using electrospray (ESI) in combination with heated auxiliary gas.

heated-electrospray ionization (H-ESI) See

heatedelectrospray (H-ESI)

.

higher energy collision-induced dissociation

(HCD) Collision-induced dissociation that occurs in the ion routing multipole (IRM) of the Orbitrap™ mass analyzer. The IRM consists of a straight multipole mounted inside a collision gas-filled tube.

A voltage offset between the C-trap and IRM accelerates parent ions into the collision gas inside the IRM, which causes the ions to fragment into product ions. The product ions are then returned to the Orbitrap mass analyzer for mass analysis. HCD produces triple quadrupole-like product ion mass spectra.

M

make-up gas The gas associated with the optional

EASY-IC or EASY-ETD ion source assembly that flows from the mass flow controller to the reagent distribution assembly.

N

nanoelectrospray ionization (nanoESI or NSI) A type of electrospray (ESI) that accommodates very low flow rates of sample and solvent at 1–20 nL/min

(for static nanoelectrospray

) or 100–1000 nL/min

(for dynamic nanoelectrospray, which is also called

nanoESI nanoLC gradient separation ).

nanoESI nanoLC gradient separation Employs microscale capillary columns to separate the analytes in complex mixtures. The sample is loaded onto a column using an injection valve or a gas pressure vessel. The mixture components are then eluted by a solvent gradient and pumped through the emitter.

R

reagent carrier gas A gas used to produce positive and negative ions of the analyte through a complex series of chemical reactions.

S

sheath gas The inner coaxial gas (nitrogen), which is used in the API source to help nebulize the sample solution into a fine mist as the sample solution exits the H-ESI or APCI nozzle.

source See API source

.

static nanoelectrospray A device that performs continuous analysis of small analyte solution volumes over an extended period of time.

sweep gas Nitrogen gas that flows out from behind the sweep cone in the API source. Sweep gas aids in solvent declustering and adduct reduction.

syringe pump A device that delivers a solution from a syringe at a specified rate.

34

Orbitrap Fusion Series Getting Connected Guide Thermo Scientific

I

Index

A

API source cautions

23

ionization modes

19

spray insert, installing

20

C

communication connectors

32

compliance

EMC

15

FCC

iv

regulatory

iii

contact closure cable connecting

30

connecting with MS application control

31

signal from start instrument

29

contacting us

xix

D

data acquisition

29

data system computer, connecting

16

directive, WEEE

v

divert/inject valve, installing

25 –

26

documentation accessing

xii

additional

xii

downloading

xii

drain/waste port

22

E

electromagnetic compatibility

iii

electronics service switch

17

EMC compliance

iii ,

15

Ethernet network card, data system computer

16

switch, connecting

16

Thermo Scientific exhaust hose, connecting

5 –

6

external devices earth ground caution

29

start (trigger) signal

30

F

FCC compliance

iv

figures, list of

ix

forepump connections fume exhaust system cautions

5 ,

23

connecting

6

line power

6

relay control cable

6

vacuum hose

2

forepumps gas ballast valve, opening

5

maintenance instructions

1

G

gases connecting

12 –

13

internal schematic drawing

10

purities, pressures, and consumptions

11

H

helium gas, connecting

12

K

kits

Dual Mechanical Pumps

xv

MS Setup

xvi

Single Mechanical Pump

xiii

Orbitrap Fusion Series Getting Connected Guide 35

Index: L

L

lab exhaust system, connecting

5

LC solvents

13

line power, connecting to data system components

16

divert/inject valve

28

forepumps

6

mass spectrometer

17

syringe pump

28

M

main power switch

17

mass spectrometers

AC Output receptacle, do not use

7

installation note

1

line power, connecting

17

location of communication connectors

16

drain/waste port

22

gas inlet ports

12

power entry module

7 ,

17

mass spectrometry applications

29

N

nitrogen gases, connecting

13

P

power

See line power, connecting to

power supply cords

xviii

power switch, main

7

R

regulatory compliance

iii

relay switch circuit

31

S

safety standards

iii

solvent waste system, connecting

22

spray insert, installing

20

start signal

See contact closure, signal from start instrument

switches, MS electronics service

17

main power

7

syringe pump, installing

25

36

Orbitrap Fusion Series Getting Connected Guide

T

tools

25

troubleshooting, Ethernet switch

16

U

USB cables, connecting

28

USB ports, MS

32

V

vacuum hose, connecting

2

vacuum system

1

W

WEEE directive

v

workbench wheels, locking

18

Thermo Scientific

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