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 [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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 Thermo Scientific Orbitrap Fusion Series Getting Connected Guide vii Contents viii Orbitrap Fusion Series Getting Connected Guide Thermo Scientific 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 xi 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 ([email protected]). • Complete a survey at surveymonkey.com/s/PQM6P62. xii Orbitrap Fusion Series Getting Connected Guide Thermo Scientific 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 3 1 Vacuum System Connecting the Forepumps to the Lab Exhaust System 4 Orbitrap Fusion Series Getting Connected Guide Thermo Scientific 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 5 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. 6 Orbitrap Fusion Series Getting Connected Guide Thermo Scientific 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. 8 Orbitrap Fusion Series Getting Connected Guide Thermo Scientific 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 9 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 Orbitrap Fusion Series Getting Connected Guide 11 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. 12 Orbitrap Fusion Series Getting Connected Guide Thermo Scientific 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. Thermo Scientific Orbitrap Fusion Series Getting Connected Guide 13 5 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 15 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 17 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 18 Orbitrap Fusion Series Getting Connected Guide Thermo Scientific 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 19 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 20 Orbitrap Fusion Series Getting Connected Guide Thermo Scientific 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 Thermo Scientific Orbitrap Fusion Series Getting Connected Guide 21 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 22 Orbitrap Fusion Series Getting Connected Guide Thermo Scientific A 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 23 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 25
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