Orbitrap Fusion Series Getting Connected Guide Revision B

Orbitrap Fusion Series
Getting Connected Guide
80011-97002 Revision B
May 2016
© 2016 Thermo Fisher Scientific Inc. All rights reserved.
EASY-Max NG, Fusion, Lumos, and Orbitrap Fusion Lumos are trademarks, and 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; Rev B, May 2016
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 MS
• Orbitrap Fusion MS
Orbitrap Fusion Lumos MS
Low Voltage Directive 2006/95/EC
This device complies with Low Voltage Directive 2006/95/EC and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.
EMC Directive 2004/108/EC
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: 20103
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 MS
Low Voltage Directive 2006/95/EC
This device complies with Low Voltage Directive 2006/95/EC and the harmonized safety standard IEC/EN/CSA/
UL 61010-1, 3rd Edition.
EMC Directive 2004/108/EC
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 weee.recycle@thermofisher.com 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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Special Notices, Symbols, and Cautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Chapter 1
Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Connecting the Forepumps to the Mass Spectrometer. . . . . . . . . . . . . . . . . . . . . 1
Connecting the Forepumps to the Lab Exhaust System . . . . . . . . . . . . . . . . . . . . 3
Chapter 2
Gas Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Chapter 3
API Source and Waste Container Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Installing the API Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Connecting the Solvent Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 4
Syringe Pump and Modular Valve Assembly. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Chapter 5
Electrical Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Chapter 6
External Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Contact Closure Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Communication Connectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Appendix A Installation Kits and Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Syringe Pump and Modular Valve Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Single Mechanical Pump Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Dual Mechanical Pumps Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
MS Setup Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25
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P
Preface
The Orbitrap Fusion Series Getting Connected Guide describes how to install the Thermo
Scientific Orbitrap Fusion™ Series Tribrid™ 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 mass spectrometry applications, such as the
Thermo Xcalibur™ data system.
This guide is intended for the following Thermo Scientific mass spectrometers (MSs):
• Orbitrap Fusion (also known as Fusion™) (requires one forepump)
• Orbitrap Fusion Lumos™ (also known as Lumos™) (requires two forepumps)
IMPORTANT Service engineers access internal components by opening the top cover.
Ensure that the instrument location allows for a minimum vertical clearance distance of
92 cm (36 in.) above the instrument. For additional clearance guidelines, refer to the
Orbitrap Fusion Series Preinstallation Requirements Guide.
Contents
• Accessing Documentation
• Special Notices, Symbols, and Cautions
• 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.
Thermo Scientific
Orbitrap Fusion Series Getting Connected Guide
ix
Preface
Accessing Documentation
The Orbitrap Fusion Series MS includes complete documentation. For system requirements,
refer to the release notes on the software DVD.
 To view the product manuals
From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo
Instruments > model x.x, and then open the applicable PDF file.
 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.
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 (Sheet 1 of 2)
x
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.
Orbitrap Fusion Series Getting Connected Guide
Thermo Scientific
Preface
Table 1. Notices, symbols, labels, and their meanings (Sheet 2 of 2)
Notice, symbol, or label
Meaning
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 Fusion 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 Fusion Series Getting Connected Guide
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Preface
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
us.customer-support.analyze
@thermofisher.com
us.techsupport.analyze
@thermofisher.com
 To find global contact information or customize your request
1. Go to thermofisher.com.
2. Click Contact Us 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:
• Send an email message to Technical Publications (techpubs-lcms@thermofisher.com).
• Complete a survey at surveymonkey.com/s/PQM6P62.
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Orbitrap Fusion Series Getting Connected Guide
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1
Vacuum System
Follow the procedures in this chapter to connect the forepumps to the Orbitrap Fusion Series
MS and the lab exhaust system.
Contents
• Connecting the Forepumps to the Mass Spectrometer
• Connecting the Forepumps to the Lab Exhaust System
CAUTION In addition to reading the forepump’s operating and maintenance instructions,
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.
Connecting the Forepumps to the Mass Spectrometer
Before you begin, lift up and remove the workbench’s front panel.
CAUTION Possible pinch points. Be aware where you place your hands when you
remove or attach the workbench’s front panel.
IMPORTANT For optimal performance of the forepumps, place them as follows:
• For the Orbitrap Fusion Lumos MS, place the forepumps under the workbench.
• For the Orbitrap Fusion MS, place the forepump under the workbench or within
2.4 m (8 ft) of the instrument.
Thermo Scientific
Orbitrap Fusion Series Getting Connected Guide
1
1
Vacuum System
Connecting the Forepumps to the Mass Spectrometer
 To attach the vacuum hose assembly
Orbitrap Fusion Lumos MS – or – Orbitrap Fusion MS
1
Using a centering ring and a swing
clamp, connect a 90-degree
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.
1
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).
2
Orbitrap Fusion Series Getting Connected Guide
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, and then
move them under the mass spectrometer.
Thermo Scientific
1 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. 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.
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.
CAUTION Possible pinch points. Be aware where you place your hands when you
remove or attach the workbench’s front panel.
 To connect the forepumps to the exhaust system
(Orbitrap Fusion Lumos MS)
2
If you removed the workbench’s front
panel (as shown), reattach it.
1
Connect one end of the exhaust tubing to the forepump
exhaust ports, and then secure the other end to the lab
exhaust system.
Thermo Scientific
Orbitrap Fusion Series Getting Connected Guide
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1
Vacuum System
Connecting the Forepumps to the Lab Exhaust System
4
Orbitrap Fusion Series Getting Connected Guide
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2
Gas Connections
Follow the procedure in this chapter to connect the gas lines to the back of the
Orbitrap Fusion Series MS. 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.
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.
Table 2. Summary of the required gases for the Orbitrap Fusion Series MS
a
Required gas
pressure
Typical daily
consumptiona
Function
UHP (99.999%)—Has less than
1.0 ppm each of water, oxygen,
and total hydrocarbons.
275 ±70 kPa
(40 ±10 psi)
9.22 L
(0.325 ft3)
Linear ion trap damping gas
and collision gas
UHP (99.999%)—Has less than
3.0 ppm each of water, oxygen,
and total hydrocarbons.
345 ±70 kPa
(50 ±10 psi)
46 L (1.62 ft3)
Venting gas, ion routing
multipole (IRM) collision
gas, and make-up gas and
reagent carrier gas for the IC
and ETD configurations
HP (99%)
690 ±140 kPa
(100 ±20 psi)
11 500–26 700 L API source auxiliary gas,
(406–943 ft3)
sheath gas, and sweep gas
Type
Recommended purity
Helium
Nitrogen
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.
CAUTION After completing these connections, route the tubing so that they are not a trip
hazard.
Thermo Scientific
Orbitrap Fusion Series Getting Connected Guide
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2
Gas Connections
 To connect the gas lines to the back of the mass spectrometer
(Orbitrap Fusion Lumos MS)
1
2
For the UHP nitrogen gas, cut a length of the copper
tubing, attach the 1/8 in. ID Swagelok™-type nut and
ferrule set, and then connect it to the UHP Nitrogen
inlet. On the other end, connect an appropriate fitting
that connects to your UHP nitrogen gas supply.
For the 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.
3
For the UHP helium gas, repeat Step 2 with another
length of copper tubing, except connect it between
the Helium In inlet and your UHP helium gas supply.
Swagelok fittings, 1/8 in. ID
IMPORTANT
• After you start using the mass spectrometer, 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 mass spectrometer.
• If you intend to use helium for sparging your LC solvents, you must have a second tank and regulator.
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Orbitrap Fusion Series Getting Connected Guide
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3
API Source and Waste Container Connections
Follow the procedures in this chapter to install the Thermo Scientific EASY-Max NG™ API
source and the solvent waste container to the Orbitrap Fusion Series MS.
Contents
• Installing the API Source
• 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 Ion Max NG and
EASY-Max NG Ion Sources User Guide.
 To install the API source onto the MS
Unlock the source
locking levers.
Install the ion sweep
cone on the MS.
1
2
3
Align the source mounting holes with the MS pins and carefully
attach the source. Then, lock the source levers.
1
Thermo Scientific
APCI and APPI modes require that you purchase and install the applicable kits.
Orbitrap Fusion Series Getting Connected Guide
7
3
API Source and Waste Container Connections
Connecting the Solvent Waste Container
Connecting the Solvent Waste Container
The mass spectrometer internally routes the solvent waste from the bottom of the API source
to the back drain/waste port. 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
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 ft3/h).
 To connect the solvent waste container to the MS
2
(Orbitrap Fusion Lumos MS)
Connect the filling/venting cap to the solvent
waste container, and then connect the Tygon
waste tubing (1 in. ID) to the cap openings.
Connect the tubing to the
MS’s Drain/Waste port and
the external vent system.
1
CAUTION After completing these connections, route the tubing so that they are not a trip
hazard.
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Orbitrap Fusion Series Getting Connected Guide
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4
Syringe Pump and Modular Valve Assembly
To attach 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 Orbitrap Fusion Series Getting Started Guide.
 To assemble the syringe pump and modular valve
1
Using the screwdriver and two of the provided
screws, attach the bottom shelf to the holder.
3
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.
2
4
Place the valve on the shelf and attach the top shelf
above it by using the screwdriver and two screws.
Thermo Scientific
(Not shown) Place the assembly on the top, left
surface of the mass spectrometer and adjust its
position, as needed.
Orbitrap Fusion Series Getting Connected Guide
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4
10
Syringe Pump and Modular Valve Assembly
Orbitrap Fusion Series Getting Connected Guide
Thermo Scientific
5
Electrical Connections
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.”
After you complete the installation, follow the procedure To lock the workbench wheels.
CAUTION Avoid an electric shock and equipment damage.
• Mass spectrometer—Before you begin, placed the Main Power Switch in the Off
(down) position and the Electronics service switch in the Service Mode (down)
position. The AC Output receptacle is not used at this time—do not plug the
forepump power cord into this receptacle.
• 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.
• 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
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5
Electrical Connections
 To connect the MS and data system cables and power cords
5
Connect the Ethernet cables from
the Ethernet switch to the computer’s
LC/MS Ethernet network card and
the MS.
(Not shown) Connect both ends of the power cords
(for the computer, Ethernet switch, modular valve,
syringe pump, MS, and forepumps).
IMPORTANT For the MS and the forepumps, plug
their power cords into separate, dedicated 230 Vac
electrical outlets—that is, circuits A, B, and C for a
dual-forepump system.
Note If the modular valve’s LED remains off, press its
front Remote button to exit local mode.
1
(Not shown) Connect the contact
closure cable and the Ready Out
cable (not provided) between the
MS and the external device. See
Chapter 6, “External Devices.”
4
2
Connect the relay control
cable between the MS
(SV65 Pump Enable) and the
one or two forepumps.
3
Connect the USB cables from the
MS to the syringe pump and the
modular valve.
IMPORTANT Do not turn on the mass spectrometer until after you 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.
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5
Electrical Connections
 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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14
Electrical Connections
Orbitrap Fusion 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 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.
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 Fusion Series Getting Connected Guide
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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 3). If it
does not meet this requirement, you cannot use it with the mass spectrometer.
• To help prevent sample waste if the mass spectrometer 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.
 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 1).
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 mass spectrometer 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.
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
16
1
Ground
Earth ground.
2
5V
Provides a 5 Vdc, 500 mA output (with pin 1).
Orbitrap Fusion 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 mass
spectrometer rate.
Thermo Scientific
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
Earth ground (for pins 7 and 8).
7, 8
10V Max:
+ (positive, pin 7) and
– (negative, pin 8)
(Channel 1) Provides a connection for an external
device, such as an LC instrument.
Input: 0–2 Vdc (voltage clamps at 5 Vdc)
Input: 0–10 Vdc (voltage clamps at 15 Vdc)
Orbitrap Fusion Series Getting Connected Guide
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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
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Orbitrap Fusion Series Getting Connected Guide
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A
Installation Kits and Power Cords
The Orbitrap Fusion 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 Orbitrap Fusion Series Hardware Manual.
Contents
• Syringe Pump and Modular Valve Assembly
• Single Mechanical Pump Kit (one-forepump system)
• Dual Mechanical Pumps Kit (two-forepump system)
• MS Setup Kit
• Power Cords
Syringe Pump and Modular Valve Assembly
Table 4. Syringe pump and modular valve assembly
Image
Thermo Scientific
Item
Quantity
Part number
Holder, L-shaped, syringe pump and modular valve
1
80000-60363
Chemyx™ Fusion 100T syringe pump with a power 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 cord,
USB interface cable, and high-pressure fitting sets
1
00109-99-00046
Orbitrap Fusion Series Getting Connected Guide
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A
Installation Kits and Power Cords
Single Mechanical Pump Kit
Single Mechanical Pump Kit
Table 5. Single Mechanical Pump Kit (P/N 80100-62004)
Image
Item
Quantity
Part number
Forepump, Oerlikon Leybold Vacuum™ Sogevac™
SV65BI (rated single-phase 230 Vac, 50/60 Hz)
1
00108-01-00032
Forepump oil tray, stainless steel, caster wheels
1
00201-99-00549
Relay control cable, single pump, 2.4 m (8 ft) long
(preassembled)
1
80000-63139
Single pump vacuum hose assembly, KF40
(preassembled; exploded view shown)
1
80000-60229
Elbow, aluminum, NW40, 90 degree
2a
00108-02-00010
Centering ring with O-ring, nitrile and aluminum,
NW40
2a
00108-02-00005
Swing clamp, aluminum, NW32/40
2a
00108-02-00004
Tubing, Tygon, 3/4 in. (19.1 mm) OD, 0.5 in.
(12.7 mm) ID, 3 m (10 ft) long
1
00301-22920
Elbow connection
Exhaust waste connection
a
Only one piece is required
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Orbitrap Fusion Series Getting Connected Guide
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A
Installation Kits and Power Cords
Dual Mechanical Pumps Kit
Dual Mechanical Pumps Kit
Table 6. Dual Mechanical Pumps Kit (P/N 80011-62006)
Image
Item
Quantity
Part number
Forepump, Oerlikon Leybold Vacuum Sogevac SV65BI
(rated single-phase 230 Vac, 50/60 Hz)
2
00108-01-00032
Forepump oil tray, stainless steel, caster wheels
2
00201-99-00549
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
Fitting Tee, barbed, nylon, for 0.5 in. (12.7 mm) ID
tubing
1
00103-01-00012
Tubing, Tygon, 3/4 in. (19.1 mm) OD, 0.5 in.
(12.7 mm) ID, 6 m (20 ft) long
1
00301-22920
Exhaust waste connection
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A
Installation Kits and Power Cords
MS Setup Kit
MS Setup Kit
Table 7. MS Setup Kit (P/N 80100-62003) (Sheet 1 of 2)
Image
Item
Quantity
Part number
Communications connection
Connector plug, MINI-COMBICON™, 8-pin,
26.67 mm (1.05 in.) long, rated 160 V, 8 A (contact
closure)
2
00004-21512
–
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,
0.6/0.3 A input; 18 W, 12 Vdc, 1.5 A output)
1
00012-01-00039
Ethernet switch, 5-port Gigabit
1
00825-01-00111
–
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,
4.6 m (15 ft) long (for the UHP helium and UHP
nitrogen gases)
1a
00301-22701
–
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 HP
nitrogen gas)
1
00101-50100
–
Fittings to connect the copper and PFA tubings to the
gas supplies (customer provided)
–
–
Container, Nalgene™, 4 L heavy-duty; filling/venting cap
1
80100-20265
Gas connections
Solvent waste connection
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Installation Kits and Power Cords
Power Cords
Table 7. MS Setup Kit (P/N 80100-62003) (Sheet 2 of 2)
Image
a
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
Your order ships with a second length of copper tubing outside of this kit.
Power Cords
Table 8. Power cord specifications
Device
Cord length
Country or territorya
Plug configuration
Plug rating
Mass spectrometer
2.5 m (8 ft)
North America
(P/N 96000-98035)
NEMA 6-15
250 Vac, 15 A
Internationalb
(P/N 80000-63188)
CEE (3-pole)
250 Vac, 16 A
North America
(no separate part number)
NEMA 6-15
250 Vac, 15 A
International
(P/N 80000-63186)
CEE (3-pole)
250 Vac, 16 A
–c
–
–
Forepump
Peripheral components
2.5 m (8 ft)
1.8 m (6 ft)
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 Fusion Series Getting Connected Guide
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A
Installation Kits and Power Cords
Power Cords
24
Orbitrap Fusion Series Getting Connected Guide
Thermo Scientific
I
Index
C
K
communication connectors 18
compliance
EMC 11
regulatory iii
contact closure, start instrument signal 15
contacting us xii
kits, installation 19
D
directives
regulatory iii
WEEE v
documentation, accessing x
E
electromagnetic compatibility iii
EMC compliance 11
exhaust hose, connecting 3
external devices
earth ground caution 15
important notes 16
F
forepump connections
fume exhaust system cautions 3
vacuum hose 2
forepumps
fume exhaust system cautions 8
gas ballast valve, opening 3
maintenance instructions 1
required placement 1
G
gases, specifications and consumptions 5
Thermo Scientific
P
power cords 23
procedures
API source, installing 7
contact closure cable, connecting 16
forepumps, connecting 1
gases, connecting 6
modular valve and syringe pump, installing 9
MS and data system, connecting the cables 12
solvent waste container, connecting 8
workbench wheels, locking 13
R
regulatory compliance iii
relay switch circuit, external device 17
Reset pin 16
S
safety standards iii
solvent waste system, connecting 8
start signal
See contact closure, start instrument signal
symbols, meaning x
T
Thermo Fisher Scientific website, user documents x
tools 9
troubleshooting, Ethernet switch 12
V
viewing documents x
Orbitrap Fusion Series Getting Connected Guide
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