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System Overview

UHPLC System
Operating Manual

Page 31

3.1.1

Solvent Rack

The solvent rack provides a secure location for placing solvent
reservoirs. It can store, for example, 6 x 1 L of solvent and 2 x 0.25 L of
wash liquid as shown in the figure. The maximum volume for an
individual reservoir should not exceed 5 L.

Figure 1: Solvent rack (front view)

The front side of the solvent rack is magnetic. Here, you can attach a
magnetic label holder, for example, to show a user-specific system
name. Labels are included in the system ship kit.

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Summary of Contents for thermoscientific Vanquish UHPLC System

Page 1: ...thermoscientific Vanquish UHPLC System Operating Manual 4820 3601 EN Revision 4 0 December 2019 ...

Page 2: ... manual are subject to being changed without notice in future revisions Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free Thermo Fisher Scientific Inc assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is followed pr...

Page 3: ...mo Fisher Scientific sales organization For contact information go to Contact Us on http www thermofisher com Technical Assistance For technical support for HPLC products contact your local Thermo Fisher Scientific support organization For contact information go to Contact Us on http www thermofisher com Contacting Us UHPLC System Operating Manual Page 3 ...

Page 4: ...Contacting Us Page 4 UHPLC System Operating Manual ...

Page 5: ...3 Safety Symbols on the System 17 2 2 Intended Use 18 2 3 Safety Precautions 19 2 3 1 General Safety Information 19 2 3 2 Qualification of the Personnel 19 2 3 3 Personal Protective Equipment 21 2 3 4 General Residual Hazards 22 2 3 5 In Case of Emergency 24 2 4 Solvent and Additive Information 25 2 4 1 General Compatibility 25 2 4 2 Allowed pH Ranges 26 2 4 3 Allowed Concentrations 26 2 4 4 Furth...

Page 6: ...2 Flow Connections Overview 65 5 5 3 Guiding Capillaries and Tubing Through the System 66 5 5 4 Connecting Fittings Capillaries and Tubing 68 5 5 5 Connecting the Waste Lines 70 5 6 Turning On the System 78 5 7 Setting Up the System in the Software 79 5 8 Flushing the System 81 6 Operation 83 6 1 Introduction to this Chapter 84 6 2 Safety Guidelines for Operation 85 6 3 Power On Off Control 86 6 4...

Page 7: ...ting 115 8 2 1 Peak Shape 115 8 2 2 Ghost Peaks Negative Peaks and Spikes 116 8 2 3 Peak Area Precision 117 8 2 4 Flow 119 8 2 5 Pressure 120 8 2 6 Retention Time Variation 121 8 2 7 Baseline 121 8 2 8 Temperature Control 123 8 2 9 Power and Communication 124 8 2 10 System Diagnostics 125 9 Specifications 129 9 1 System Specifications 130 9 2 Solvent Rack and System Base Specifications 131 10 Acce...

Page 8: ... 8 UHPLC System Operating Manual 11 Appendix 141 11 1 Compliance Information 142 11 1 1 Declarations of Conformity 142 11 1 2 WEEE Compliance 143 11 1 3 FCC Compliance 143 11 1 4 Manual Release History 143 Index 145 ...

Page 9: ...LC System Operating Manual Page 9 1 Using this Manual This chapter provides information about this manual the conventions used throughout the manual and the reference documentation that is available in addition to this manual ...

Page 10: ...ghly This manual also contains safety messages precautionary statements and special notices that can prevent personal injury damage to the system or loss of data when followed properly Note the following The descriptions in this manual refer to a standard one stack VanquishTM system configuration Not all descriptions necessarily apply to your particular system Illustrations in this manual are prov...

Page 11: ...r procedure appear in the section or procedure to which they apply They appear different from the main flow of text Safety messages are often preceded by an alert symbol and or alert word The alert word appears in uppercase letters and in bold type Make sure that you understand and follow all safety messages presented in this manual 1 2 2 Special Notices and Informational Notes Special notices and...

Page 12: ...omeleon 7 Services Manager Start Instrument Controller References and Messages References to additional documentation appear italicized Messages that appear on the screen are identified by quotation marks Viewpoint If not otherwise stated the expressions left and right in this manual always refer to the viewpoint of a person that is facing the system from the front Particularly Important Words Par...

Page 13: ...on Help and documents The Chromeleon Help provides extensive information and comprehensive reference material for all aspects of the software In addition the following documentation is available availability depends on the software version Installation Guide For basic information about device installation and configuration refer to the Installation Guide Instrument Configuration Manager Help For s...

Page 14: ... Manual Page 14 UHPLC System Operating Manual Third Party Documentation Refer also to the user documentation provided by the manufacturers of third party components and materials for example Safety Data Sheets SDSs ...

Page 15: ...2 Safety UHPLC System Operating Manual Page 15 2 Safety This chapter provides general and specific safety information and informs about the intended use of the system ...

Page 16: ...es a hazardous situation that if not avoided could result in minor or moderate injury WARNING Indicates a hazardous situation that if not avoided could result in serious injury 2 1 2 Observing this Manual Observe the following Before installing or operating the device read this manual carefully to be familiar with the system and this manual The manual contains important information with regard to ...

Page 17: ...o the Operating Manual of the module Follow the safety notices in these manuals to prevent the risk of operator injury or damage to the system Safety Symbols on the System Base Symbol Description Indicates a potential hazard Refer to this manual to avoid the risk of personal injury and or to prevent damage to the device Indicates a power button that switches the system between on and off states ...

Page 18: ...al Laboratory Equipment GLE They are not intended for use in diagnostic procedures Laboratory Practice Thermo Fisher Scientific recommends that the laboratory in which the Vanquish system is used follow best practices for LC analyses This includes among others Using appropriate standards Regularly running calibration Establishing shelf life limits and following them for all consumables used with t...

Page 19: ...ditional components options and peripherals specifically authorized and qualified for the system by Thermo Fisher Scientific Perform only the procedures that are described in this operating manual and in supporting documents for the system Follow all instructions step by step and use the tools recommended for the procedure Open the enclosure of the system and other components only if specifically ...

Page 20: ... than a Thermo Fisher Scientific service engineer installs and sets up the system the installer is responsible for ensuring the safety of the system System configuration with Charger Installation by Service Engineer only Service personnel certified by Thermo Fisher Scientific must perform the installation for brevity referred to as Thermo Fisher Scientific service engineer Operation General Operat...

Page 21: ...ity and a sink should be available nearby If any substance contacts your skin or eyes wash the affected area and seek medical attention Protective Clothing To protect you from chemical splashes harmful liquids or other contamination put on appropriate protective clothing such as a lab coat Protective Eyewear To prevent liquids from striking your eyes put on appropriate protective eyewear such as s...

Page 22: ...of substances to the minimum volume required for sample analysis Do not operate the system in a potentially flammable environment Avoid accumulation of harmful substances Make sure that the installation site is well ventilated Dispose of hazardous waste in an environmentally safe manner that is consistent with local regulations Follow a regulated approved waste disposal program WARNING Biohazard B...

Page 23: ...r fumes CAUTION Escape of Hazardous Substances from PEEK Capillaries In the Vanquish system capillaries made of PEEK may be used Swelling or attack by acids can cause PEEK capillaries to start leaking or to burst Certain chemicals for example trichlormethane CHCl3 dimethyl sulfoxide DMSO or tetrahydrofuran THF can cause PEEK to swell Concentrated acids such as sulfuric acid and nitric acid or a mi...

Page 24: ...cularly present with insulating capillaries and non conductive solvents for example pure acetonitrile Discharge of electrostatic energy might lead to sparking which could constitute a fire hazard Prevent the generation of static electricity near the chromatography system 2 3 5 In Case of Emergency WARNING Safety Hazard In case of emergency disconnect the system from the power line ...

Page 25: ...and additives that are compatible with all parts in the flow path TIP In a Vanquish Core system normal phase NP compatible solvents and additives may be used if the VC pumps and the VC autosamplers are modified with the components from the Normal Phase NP kit Refer to the Operating Manuals for the pumps and autosamplers NOTICE If the system flow path includes a Vanquish charged aerosol detector ob...

Page 26: ...disconnect the detector from the system Mobile phases containing ammonium hydroxide In rare cases a shortened lifetime of reversed phase UHMW PE piston seals has been observed with high pH ammonium hydroxide containing mobile phases and prolonged exposure Vanquish Horizon Vanquish Flex 2 12 2 4 3 Allowed Concentrations Allowed concentrations standard system configuration System Standard Configurat...

Page 27: ...ations page 130 Follow any specific recommendations presented in other sections of this manual Refer also to the operating manuals for all modules in the Vanquish system They may provide additional guidelines and information Observe the general guidelines and recommendations on the use of solvents and additives in the chromatography system see Use of Solvents and Additives page 89 ...

Page 28: ...2 Safety Page 28 UHPLC System Operating Manual ...

Page 29: ...3 System Overview UHPLC System Operating Manual Page 29 3 System Overview This chapter introduces you to the system and the main components ...

Page 30: ...p VC P20 Quaternary VF P20 Binary VF P10 VH P10 System base Vanquish system base 1 The appropriate flow cell has to be ordered separately 2 In the standard configuration the Vanquish system includes one column compartment installed to the right side of the system For other configurations see System Stack Setup page 46 For a description of the solvent rack and system base see further down in this c...

Page 31: ...or example 6 x 1 L of solvent and 2 x 0 25 L of wash liquid as shown in the figure The maximum volume for an individual reservoir should not exceed 5 L Figure 1 Solvent rack front view The front side of the solvent rack is magnetic Here you can attach a magnetic label holder for example to show a user specific system name Labels are included in the system ship kit ...

Page 32: ...ontroller is installed the power button allows power on off control of the system controller 2 System power button Allows power on off control for all modules of the system that are connected to the system base via the System Interlink port 3 Drawer for tools Allows storing any tools that are necessary to install or maintain the Vanquish system Push the drawer front to open or close the drawer 4 D...

Page 33: ...ent control and automated sample analysis with the Chromeleon software see Operating the System from the Software page 92 TIP The system can be operated also with other data systems such as Thermo ScientificTM XcaliburTM In this case installation of additional software is required in addition to the data system software For details contact the Thermo Fisher Scientific sales organization Keypads ar...

Page 34: ...3 System Overview Page 34 UHPLC System Operating Manual ...

Page 35: ...4 Unpacking UHPLC System Operating Manual Page 35 4 Unpacking This chapter provides information for unpacking the system and informs you about the scope of delivery ...

Page 36: ...lvent Rack and System Base To unpack the solvent rack and system base follow these steps 1 Place the shipping container on the floor and open it 2 Remove the ship kit 3 Carefully remove the solvent rack and liquid reservoirs from the shipping container 4 Place the solvent rack on a stable surface 5 Carefully remove the system base from the shipping container 6 If applicable Remove any additional p...

Page 37: ...ting Manual Page 37 4 2 Scope of Delivery The following items are included in the delivery System base Solvent rack Solvent reservoirs Ship Kit For details about the kit content see Ship Kit page 135 Printed system operating manual ...

Page 38: ...4 Unpacking Page 38 UHPLC System Operating Manual ...

Page 39: ...5 Installation UHPLC System Operating Manual Page 39 5 Installation This chapter specifies the requirements for the installation site and describes how to set up install and configure the system ...

Page 40: ...ollowing safety guidelines Observe all warning messages and precautionary statements presented in Safety Precautions page 19 Observe all warning messages and precautionary statements presented in the Safety Guidelines for Installation section in the Operating Manual for the individual modules of the Vanquish system ...

Page 41: ...details If personnel other than a Thermo Fisher Scientific service engineer installs the system follow the steps below 1 Pay attention to the safety guidelines and observe all site requirements For the safety guidelines when installing the system see Safety Guidelines for Installation page 40 For the site requirements see Site Requirements page 43 2 Set up the system hardware See Setting Up the Ha...

Page 42: ...n Operating Instructions The manual provides information about the required materials and detailed instructions NOTICE If the system is operated with another data system refer to the documentation for the software that you are using and or perform the qualification manually The Instruments Installation Qualification Operating Instructions provide information about the parameters to be adapted and ...

Page 43: ...lvents For dimensions and weight see System Specifications page 130 Workbench Requirements Part Requirements Workbench Sturdy A height that ensures convenient access to the interior of each device in the system The bench top must be dry clean and resistant to chemicals Site for the workbench The workbench must stand in a secure and level position that is free of vibrations System Clearance Require...

Page 44: ...vice Never use a power cord other than the power cords provided by Thermo Fisher Scientific for the device Only use a power cord that is designed for the country in which you use the device Do not use extension cords Never plug the power cord to a power socket that is shared with other equipment for example multiple sockets Operate the device only from a power outlet that has a protective ground c...

Page 45: ...nce of the system Avoid locations with significant changes in temperature and strong air drafts For example do not place the system in the direct sunlight near heating or cooling sources or under an air duct Humidity The relative humidity of the operating environment is important for the performance of the system Operate the system in the specified humidity range with no condensation When the humi...

Page 46: ...handling of the modules including lifting or moving requires a team effort of two persons A team effort is in particular required when lifting the modules into the system stack or when removing them Modules with carrying handles Use the carrying handles that were shipped with the modules to move or transport the modules Never move or lift the modules by the front doors This will damage the doors o...

Page 47: ...Installation UHPLC System Operating Manual Page 47 Figure 3 Vanquish system standard configuration example No Description 1 Solvent Rack 2 Detector 3 Autosampler 4 Pump 5 System Base 6 Column Compartment ...

Page 48: ... personal injury If your system configuration includes more than 4 stacked modules but no Charger you need to stabilize the stack with one of the following safety measures IonBench with stack mounting kit Stack stabilizer kit Build up the system in two separate stacks 1 Place the system base on the workbench 2 If necessary unlock the system base see Unlocking the System Base page 61 to be able to ...

Page 49: ...ard the rear Figure 6 Sliding off the carrying handle from the left rail 7 Repeat the previous three steps for the autosampler and detector by placing the autosampler on the pump and the detector on the autosampler 8 Place the solvent rack on the detector approximately 5 cm before the end of the rails Push the solvent rack towards the rear until it clicks into place TIP System modules on the syste...

Page 50: ... configuration of the column compartment is also available Observe the following notes The extended configuration on the right side can include up to three column compartments For the extended configuration of the column compartment up to two conversion kits are required The column compartment can also be installed to the left side of the Vanquish system stack For the left side installation one co...

Page 51: ...ces 4 screws 4 spacers Tools required Screwdriver Torx T20 Follow these steps 1 Align the screw holes of the two T slot nuts the spacers and the crosspiece Figure 7 Mounting bar No Description 1 Spacer 2 Groove 3 Screw 4 T slot nut 5 Crosspiece 2 With the screws fix the T slot nuts and the spacers onto the crosspiece The T slot nuts must face each other as shown above ...

Page 52: ...on the system housing and push until stop The grooves on the mounting bars must face upwards Make sure that the orientation of the crosspiece is as indicated on the picture 4 Tighten the screws on the mounting bars Figure 8 Installing the mounting bars on the system housing No Description 1 Rail 2 Mounting bar ...

Page 53: ...e Vanquish system stack even over short distances on the workbench can damage and impair the functionality of the system base Observe the following Configuration with one column compartment Before moving the system stack unlock the system base using the locking tools For details see Unlocking the System Base page 61 Configuration with two or three column compartments or a Charger Before moving the...

Page 54: ...em base and device communication For details on system interlink connections see System Interlink Connections page 57 2 Digital I O ports not available in all modules Allow exchange of digital signals with external instruments For information on connection and pin assignment see the Operating Manual for the related module 3 USB Universal Serial Bus hub A type connector Allows connection to other m...

Page 55: ...The flat rectangular end of the cable is the A connector The smaller hexagonal end is the B connector TIP The USB standard limits the USB cable length to 5 meters Each USB device can be separated from the computer or next USB hub by no more than 5 meters After connecting the USB cables and before turning on the power to a device for the first time verify that the chromatography software is install...

Page 56: ...ting Manual Connecting the USB Cables USB Cable Overview Figure 12 USB cable connections example No Description USB connection 1 From pump to detector 2 From autosampler to pump 3 From column compartment to detector 4 From detector to computer ...

Page 57: ...o the USB port on the UV VIS detector and connect the A connector of the USB cable to a USB port 2 0 or higher on the computer In order to control the modules that use a USB hub on another module the module that provides the hub must be turned on NOTICE Never use defective communication cables If you suspect that a cable is defective replace the cable To ensure trouble free operation use only the ...

Page 58: ... Interlink Cables System Interlink Cable Overview Figure 14 USB and system interlink cable connections example No Description System interlink connection 1 From system base to pump 2 From pump to autosampler 3 From autosampler to detector 4 From detector to column compartment ...

Page 59: ...ctions After setting up the Vanquish system as required by the system configuration you can connect the modules to the power source Follow the steps below Do not turn on the system or modules yet 1 Verify that the power switch on each device is set to OFF 2 Connect the power cord to the power inlet connector on each device NOTICE Condensation in a device can damage the electronics Before connectin...

Page 60: ...cable clip on each side and the autosampler has two cable clips on each side The location of the cable clips cutouts for the cable clips is shown below Figure 15 Cable clips cable clip cutouts in the autosampler and detector If not already done install the cable clips in the cutouts of the housing as shown below Figure 16 Inserting a cable clip To insert the cables into the clip open the flap ...

Page 61: ...cludes two or three column compartments or a Charger a Thermo Fisher Scientific service engineer must dismount the mentioned modules before you can un lock the system base with the locking tools 5 4 5 1 Unlocking the System Base 1 Have all but one column compartment and the Charger dismounted by a Thermo Fisher Scientific service engineer 2 Insert one locking tool into another Figure 18 Extended l...

Page 62: ...nlock the system base by turning the locking tools as shown below In the unlocked position the locking tools cannot be removed from the system base Figure 20 Unlocking the system base 6 Move the system to the final position 7 Lock the system base according to Locking the System Base page 63 8 Have the additional column compartments and the Charger mounted by a Thermo Fisher Scientific service engi...

Page 63: ...e The following instructions and images assume that the column compartment is installed on the right side of the system 1 Lock the system base by turning the locking tools as shown below Figure 21 Locking the system base 2 Remove the locking tools and store them in a safe place for example in the system base drawer 3 Have the column compartment s and charger re installed by a Thermo Fisher Scienti...

Page 64: ...ous substances Observe the warning messages and precautionary statements presented in Safety Precautions page 19 Dirty components can contaminate the chromatography system Contamination leads to poor performance of the modules and entire system or can even cause damage to the modules and system Therefore Always wear appropriate gloves Place the components only on a clean lint free surface Keep you...

Page 65: ...en designed for optimized and simple leak liquid and waste handling Leak liquid from the solvent rack detector autosampler and pump flows through pipes from the modules to the system base drain port Seal wash and needle wash liquids from the pump and autosampler as well as condensate from the autosampler are also guided to the system base drain port Leak liquid from the column compartment flows to...

Page 66: ... applicable or the detector inlet capillary depending on system configuration and column switching valve if applicable and route it to waste Do not install a flow cell yet 6 Turn on the system see Turning On the System page 78 7 Set up the system in Chromeleon see Setting Up the System in the Software page 79 8 Flush the system without column see Flushing the System page 81 9 Install a column For ...

Page 67: ...ubing guides Each guide can hold up to three tubes or lines In each module push the tube or line into the appropriate guide Figure 23 Tubing chase with tubing guides left view from inside right view from top No Use for 1 Solvent tubing up to three solvent lines 2 Solvent tubing up to three solvent lines 3 Wash liquid tubing seal wash autosampler needle wash 4 Detector waste line Tubing brackets ar...

Page 68: ...so in the manual 5 5 4 Connecting Fittings Capillaries and Tubing This section provides information about how to connect and handle capillaries fittings and tubing 5 5 4 1 General Guidelines When connecting capillaries and tubing follow these general recommendations Use only the capillaries and tubing for example solvent lines or waste tubing that are shipped with the product or additional or spar...

Page 69: ... the Viper capillaries only when the system pressure is down to zero Figure 25 Viper fitting with knurl No Description 1 Knurl 2 Capillary 3 Slot 1 Insert the Viper capillary into the connection port 2 Tighten the connection by the knurl TIP Note the slot in the knurl For narrow connections you can easily remove the knurls from neighboring capillaries through this slot and attach them again later ...

Page 70: ...Lines 5 5 5 1 Waste Connections Overview WARNING Escape of Hazardous Substances Hazardous substances can escape from waste lines and waste containers if connections and waste containers are not properly installed Exposure to these substances can pose health and safety risks Verify the correct installation of connections and containers by testing the drain system see Testing the Drain System page 7...

Page 71: ...tion 1 Drainage from the modules in the stack to the system base 1a System drain port 1b Waste line for system drainage 2 Module waste lines 2a Detector waste line 2b Pump waste line here in VH P10 pump 3 Drainage from the column compartment 3a Column compartment drain port 3b Waste line for column compartment drainage ...

Page 72: ...e 75 TIP Make sure that you guide the detector waste line through the separate outlet in the system base which is located next to the drain port in the system base Figure 27 Funnel and waste outlets on the system base No Description 1 Funnel for system drainage 2 Detector waste outlet 2a Detector waste line 3 System drain port hidden behind the elbow connection 3a System waste line Connect a waste...

Page 73: ...e drain tubing into a waste container 4 Only if guiding the drain tubing toward the system s rear Insert the drain tubing into the clips and make sure that the drain tubing does not form a siphon Figure 28 Inserting the drain tubing into clips TIP If routing the drain tubing of the column compartment also toward the system s rear you can insert the drain tubing of the column compartment into the c...

Page 74: ...must not be submerged in waste liquid see figure below Shorten the tubing if required Observe the liquid level in the waste container Empty the waste container as necessary Figure 29 Free end of waste line in waste container 5 5 5 3 Testing the Drain System Check the drain system for proper drainage of waste 1 Pour water or isopropanol into the drain in the solvent rack 2 Verify that the liquid le...

Page 75: ... connect the waste line through the detector waste outlet to the waste follow the steps below For instructions on how to connect the waste line from the flow cell outlet refer to the Operating Manual for your Vanquish detector Suitable waste container Follow these steps 1 Locate the outlet for the detector waste line in the system base see figure below 2 Route the waste line through the detector w...

Page 76: ... the free end of the waste line into a waste container Figure 31 Guiding the waste line to the waste container 4 Ensure proper drainage of the waste from the detector You may need to cut the waste line to length 5 Ensure proper drainage of waste see next section ...

Page 77: ... nor pinched 3 To prevent liquid from flowing back into the system the entire drain tubing must remain below the drain port Avoid the formation of siphons TIP To allow the waste liquid flowing off properly and avoid liquid accumulation in the system base the end of the waste line must not be submerged in waste liquid see figure below Shorten the tubing if required Observe the liquid level in the w...

Page 78: ...red USB drivers are automatically found and the Windows operating system can detect the device To turn on the power to the system follow these steps 1 Check that the power button on the front left of the Vanquish system base system power button is pressed in If the power button stands out press the power button to turn on the power on the system base 2 Turn on each module with its main power switc...

Page 79: ... and launches a wizard instead this indicates that you connected the devices to the computer and turned on the power for the first time before you installed the Chromeleon software In this case cancel the wizard install the software and then repeat the steps Starting the Instrument Controller and Instrument Configuration Manager 1 Start the Chromeleon Instrument Controller Right click the Chromele...

Page 80: ...quish Binary Pump Repeat this step for each module of the system 4 On the General configuration page for each module make sure that simulation mode is deactivated and click Browse to select the module address The Chromeleon software connects to the module and transfers the settings from the device firmware to the software Check and change the settings on the other configuration pages if necessary ...

Page 81: ...r a short time Flushing the System with Column Installed Flush the system again for a short time after connecting the column with a solvent suitable for your application Follow these steps 1 Verify that the detector is not connected to the flow path 2 Have the pump deliver the solvent for a short time Observe the pressure limit and other properties of the column Flushing the System with Column and...

Page 82: ...5 Installation Page 82 UHPLC System Operating Manual ...

Page 83: ...6 Operation UHPLC System Operating Manual Page 83 6 Operation This chapter provides information for routine operation and for shutdown ...

Page 84: ...mation in this chapter assumes that the initial setup of the system has already been completed If this is not the case refer to the instructions in Installation page 39 Software descriptions in this manual refer to Chromeleon 7 Terminology may be slightly different with other software versions ...

Page 85: ...When operating the chromatography system always set the lower pressure limit for the pump This prevents damage resulting from leakage or from running the pump dry If there is evidence of leakage in the device turn off the pump flow and remedy the situation immediately If the pump flow is interrupted act appropriately to protect the components in the detector For details refer to the Operating Manu...

Page 86: ...m interlink cables are turned on or off simultaneously when the system power button is pressed When the power is on the system power button is pressed in When the power is off the system power button stands out If the main power switch on a device is off you cannot turn on the device with the system power button To turn off a device completely you have to turn it off with the main power switch on ...

Page 87: ... System page 81 Some components of the system are filled with isopropanol when the system is shipped from the manufacturing site When operating the system for the first time use solvents that are miscible with isopropanol If they are not use an appropriate intermediate solvent Verify that any air bubbles are completely flushed out of the system flow path Refer to the Operating Manual for each syst...

Page 88: ... in the autosampler Flow cell in a fluorescence detector Evaporation tube in a charged aerosol detector Turning on the lamp or lamps in the UV VIS detector Monitoring the pump pressure and pressure ripple and checking that the pressure is stable and the ripple within reasonable limits for the application Monitoring the detector signal and checking whether the detector signal is stable so that the ...

Page 89: ...se membrane filtration 0 2 µm to remove any particulate matter and to reduce microbial growth When using water use high quality water for example UHPLC grade or LC MS grade 0 2 µm filtered When you use water from water purification systems keep in mind that polymeric contamination may occur if the purification system is not maintained properly Before filling a solvent reservoir always rinse the re...

Page 90: ...r regularly at short intervals VF pumps The pumps are shipped with UHMW PE piston seals Using tetrahydrofuran ketones or ammonium hydroxide as solvents can damage the seals Under harsh conditions consider replacing the UHMW PE piston seals with carbon fiber filled PTFE piston seals part no 6040 0306 In this case also install new pistons Exchanging the piston seals but keeping the pistons that were...

Page 91: ...ion If a charged aerosol detector is connected in the system flow path Observe the specific mobile phase guidelines for the detector in the Vanquish Charged Aerosol Detector Operating Manual TIP In a Vanquish Core system normal phase NP compatible solvents and additives may be used if the VC pumps and the VC autosamplers are modified with the components from the Normal Phase NP kit Refer to the Op...

Page 92: ...on tray icon on the Windows taskbar the icon is crossed out in red and Click Start Chromeleon Instrument Controller The icon changes to gold indicating that the Instrument Controller Service is starting The icon changes to gray when the Instrument Controller Service is running idle If the Chromeleon tray icon is not available on the Windows taskbar click Start All Programs or Programs depending on...

Page 93: ...n and perform commands To access the ePanel Set 1 On the Console click the Instruments Category Bar 2 In the Navigation Pane click the instrument that you want to control The Chromeleon software connects to the instrument and displays the ePanel Set The ePanel Set opens to the Home panel which shows basic status information about each module in the system and provides access to the instrument Audi...

Page 94: ...oring the Baseline When an instrument is idle you can monitor the baseline signals without starting a sequence During baseline monitoring the monitored signals are displayed on the real time signal plot on the ePanel for the module You may have to add the signal to the plot in the Plot Properties for details refer to the Help To monitor the baseline signals 1 Open the ePanel Set 2 On the toolbar a...

Page 95: ...hod eWorkflows provide a set of predefined templates and rules for creating a new sequence Sequence Wizard Creating a Sequence via eWorkflows 1 On the Console click the eWorkflows Category Bar 2 In the Navigation Pane click the eWorkflow name 3 In the Work Area click the instrument name and then click Launch 4 The eWorkflow Wizard guides you through the process Complete the steps in the wizard For...

Page 96: ...Starting the new sequence 1 On the Sequence Control Bar click Start 2 The sequence is appended to the queue and a Ready Check is performed If the Ready Check passes and if the instrument is not currently running another sequence the sequence is started ...

Page 97: ...ode array detector only The shutter can be moved to a closed position for protection of the flow cell Fluorescence detector Turn off temperature control for the flow cell Apply a flow of 0 05 mL min and have the pump deliver an appropriate solvent Check the lower pressure limit for the pump and adapt the value if necessary If the pressure falls below the lower limit the pump stops the flow Set the...

Page 98: ... pump Situation after Shutdown If no additive is used If an additive is used System remains in the laboratory after shutdown Flush the system for example with methanol 100 acetonitrile should not be used Flush the system with several volumes of methanol and water 50 50 for example 1 0 mL min for 10 minutes with the standard system to prevent salt buildup in the fluidics If the solvents in the devi...

Page 99: ...dules shall be removed from the system stack turn off all system modules with their main power switch Pressing the system power button will not be sufficient to turn off the power to the devices completely If the system shall be transported or shipped after shutdown follow the instructions in Transporting or Shipping the System page 109 ...

Page 100: ...6 Operation Page 100 UHPLC System Operating Manual ...

Page 101: ...7 Maintenance and Service UHPLC System Operating Manual Page 101 7 Maintenance and Service This chapter gives general guidelines on maintenance and transport of the system ...

Page 102: ... and Service This chapter describes the routine maintenance that the user may perform for the system Additional maintenance or service procedures must be performed only by service personnel certified by Thermo Fisher Scientific for brevity referred to as Thermo Fisher Scientific service personnel ...

Page 103: ... health risks Solvent can spray when capillaries burst slip out of their fittings or are not properly tightened or when capillary connections are otherwise open Wear appropriate protective equipment and follow good laboratory practice Before starting maintenance or repair procedures flush out harmful substances with an appropriate solvent WARNING Tilting Liquid Reservoirs Liquids in the reservoirs...

Page 104: ...wait until the system pressure is down to zero Unscrew the caps of the solvent reservoirs and remove the solvent lines together with the caps from the reservoirs Empty the solvent lines Refer to the Operating Manual for the pump Retighten the reservoir caps CAUTION Electric Shock or Damage to the Device After the power to the device is turned off the device is still energized as long as the power ...

Page 105: ...e pump flow and wait until the system pressure is down to zero Dirty components can contaminate the chromatography system Contamination leads to poor performance of the modules and entire system or can even cause damage to the modules and system Therefore Always wear appropriate gloves Place the components only on a clean lint free surface Keep your tools clean Use only lint free cloth for cleanin...

Page 106: ...egular intervals This is especially important when using aqueous solvents Aqueous solvents may contaminate the filters with algae and other microorganisms that deposit on the filter frits Therefore also replace the solvents at regular intervals Rinse the reservoirs thoroughly before refilling them Empty the waste container or containers Inspect the flow connections for damage such as cracks nicks ...

Page 107: ...ing cleaning detergents may form flammable and explosive gas mixtures when exposed to air Use such cleaning detergents only when required and only in adequately ventilated rooms Avoid open flames or exposure to excessive heat during the cleaning process Wipe the cleaned components thoroughly dry after cleaning Do not operate the device before it is completely dry NOTICE Observe the following Only ...

Page 108: ... with a clean dry soft lint free cloth or wipe If necessary slightly dampen the cloth or wipe with a solution of lukewarm water and a suitable cleaning detergent 2 Allow the cleaning detergent to react as recommended by the manufacturer 3 Wipe the cleaned surfaces with purified water to ensure that all cleaning detergent residues have been removed 4 Wipe the surfaces dry using a soft lint free clo...

Page 109: ...e system stack dismount the system stack for instructions see below Dismounting the system stack Preparations 1 Turn off all modules with their main power switch 2 Remove the solvent reservoirs and solvent lines from the solvent rack 3 Remove all flow connections between the modules within the Vanquish system and all waste lines 4 Remove all signal cables and power cords 5 Grasp the system by its ...

Page 110: ...ng handles attached No Description 1 Carrying handles 2 Attachment screw one on each carrying handle CAUTION Risk of Injury and Device Damage Handles can slide off the device if the attachment screws are not fixed properly Also the slide in module can fall out if not fixed properly This could cause personal injury and damage to the device Verify the following before lifting a device The handles ar...

Page 111: ...to Thermo Fisher Scientific contact your local Thermo Fisher Scientific support organization for the appropriate procedure CAUTION Possible Contamination Hazardous substances may have contaminated the device during operation and may cause personal injury to service personnel Decontaminate all parts of the device that you want to return for repair Fill in and sign the Health and Safety Form Thermo ...

Page 112: ...7 Maintenance and Service Page 112 UHPLC System Operating Manual ...

Page 113: ...8 Troubleshooting UHPLC System Operating Manual Page 113 8 Troubleshooting This chapter is a guide to troubleshooting issues that may arise during operation of the system ...

Page 114: ...e quick visual feedback on the operational status of the module If the firmware detects a problem the status indicators are red Chromeleon Audit Trail Messages If the device firmware detects a problem the problem is reported to the Chromeleon software The Chromeleon software logs information about all events related to instrument operation for the current day in an Audit Trail The Audit Trail is n...

Page 115: ...tailing Possible Cause Remedial Action Extra column volume too large Use short capillary connections with a suitable inner diameter Use appropriate Viper capillaries Improper capillary connections Check fittings for correct placement Loosen and retighten Viper fittings refer to the Viper Installation and Operation Guide Use only the appropriate fittings see Connecting Fittings Capillaries and Tubi...

Page 116: ...elength The sample must not absorb in the range of the reference wavelength Consider using a method without reference wavelength Wrong polarization of analog output If you are using analog output check the analog output polarization Spikes Possible Cause Remedial Action Air trapped in flow cell Check all fluid connections for tightness in particular in the intake path Degas the mobile phase Instal...

Page 117: ...mpartment Operating Manual 8 2 3 Peak Area Precision Contamination or carry over Possible Cause Remedial Action Contamination in the system Flush the system using an appropriate solvent Autosampler carry over The needle may be contaminated Wash the needle in the wash port If carry over persists replace the needle seat refer to Split Sampler Operating Manual Environmental conditions Possible Cause ...

Page 118: ...rated any more Select a shorter response time Injection volume variation Possible Cause Remedial Action Autosampler draws air from vial There is not enough amount of sample in the vial the needle height setting is incorrect or there are too many replicates Air trapped in autosampler flow path Perform a wash cycle Check that the injection valve is in Inject position and the flow components of the a...

Page 119: ...mperature refer to Column Compartment Operating Manual Flow fluctuations Possible Cause Remedial Action Pump inlet path clogged Check the solvent inlet lines solvent line filters and solvent selectors proportioning valve for example for signs of clogging Air trapped in pump inlet path Purge the pump Inspect the degasser for indications for leakage Check in the Chromeleon software whether the degas...

Page 120: ... Sampler Operating Manual High backpressure Possible Cause Remedial Action One or more capillaries in the system clogged or damaged by bending Check the capillaries in the system systematically from the detector to the pump Replace the capillaries as needed Pump inline filter or static mixer clogged Check the permeability of the inline filter or static mixer Replace the inline filter or static mix...

Page 121: ... Clean the inlet check valve or outlet check valve and replace the check valve if necessary refer to Pump Operating Manual A solvent selector proportioning valve may be defective Contact Technical Support Pressure fluctuations from pump Purge the pump Check the compression values and take remedial action refer to Pump Operating Manual Check the pump for piston seal leakage refer to Pump Operating ...

Page 122: ...time Improper wavelength or optical bandwidth Select an appropriate wavelength Select a higher bandwidth In particular with critical conditions low absorption few light Flow cell not properly installed Check that the flow cell is installed properly refer to Detector Operating Manual Detector defective Contact Technical Support Optical transmission of the flow cell too low Vanquish system with VH D...

Page 123: ...eon software TempCtrl On turns temperature control on Ventilation grid obstructed Make sure that the ventilation grids of the column compartment are not obstructed in any way Ambient air enters column chamber Improper sealing of the column chamber may impair the heating and cooling performance of the column compartment and lead to a considerable amount of condensed water When guiding capillaries t...

Page 124: ...tus bars unlit Possible Cause Remedial Action System power button turned off Turn on the system with the power button on the front left of the system base Single module has no power LED status bar unlit Possible Cause Remedial Action Module power turned off Turn on the module with its main power switch Module not connected to the mains Connect the power cord Fuse has blown Replace the fuses refer ...

Page 125: ...s from Chromeleon Test Remarks Basic Tightness Test Depending on the Vanquish system configuration the available tests may vary If a test is grayed out in the Chromeleon software the test is currently not available When a test is running the LED bar on the module shows a blue running light Grating Motor Test Intensity Test Shutter Motor Test Automatic Testing You can set up a schedule in Chromeleo...

Page 126: ... For remedial actions refer to the Troubleshooting section in the Operating Manual for the module for which the test failed 8 2 10 2 Grating Motor Test The Grating Motor Test checks the mechanical stability of the grating drive The test is available for the variable wavelength detector Follow these steps 1 Install the diagnostics cell in the detector 2 Run the test from the Chromeleon software Ref...

Page 127: ...tics cell for indications of contamination that prevent the light to pass the cell unhindered Repeat the test with a clean cell If the test fails again replace the lamp 2 Replace the lamp Refer to the Operating Manual for the detector 3 If the test fails with the new lamp the optics may be defective Contact Thermo Fisher Technical Support 8 2 10 4 Shutter Motor Test The Shutting Motor Test checks ...

Page 128: ...8 Troubleshooting Page 128 UHPLC System Operating Manual ...

Page 129: ...9 Specifications UHPLC System Operating Manual Page 129 9 Specifications This chapter provides important system specifications ...

Page 130: ...e functions for scheduling maintenance procedures based on the actual operating and usage conditions of the system All system parameters logged in the Chromeleon Audit Trail Safety features Leak detection and safe leak handling Range of use Indoor use only Ambient operating temperature 5 C 35 C Ambient storage temperature 20 C 45 C Ambient operating humidity 20 80 relative humidity non condensing ...

Page 131: ... system refer to the Specifications section in the Operating Manual for each module Type Specification System Interlink 2 System Interlink ports RJ45 8 connectors Max volume of an individual solvent reservoir 5 L Solvent rack dimensions height x width x depth 12 cm x 42 cm x 60 cm Solvent rack weight 4 kg System base dimensions height x width x depth 6 cm x 42 cm x 42 cm System base weight 5 kg Sy...

Page 132: ...9 Specifications Page 132 UHPLC System Operating Manual ...

Page 133: ... Page 133 10 Accessories Consumables and Replacement Parts This chapter describes the standard accessories that are shipped with the system and the accessories that are available as an option This chapter also provides information for reordering consumables and replacement parts ...

Page 134: ...acement parts and additional components options and peripherals specifically authorized and qualified by Thermo Fisher Scientific Accessories consumables and replacement parts are always maintained at the latest technical standard Therefore part numbers are subject to change If not otherwise stated updated parts will be compatible with the parts they replace ...

Page 135: ... for Vanquish Core system Item Quantity in shipment Fuses kit Vanquish system The kit includes the appropriate fuses for the Vanquish system modules 1 Viper union 1 Tubing connector straight for tubing I D 1 0 2 0 mm set of 5 1 Tubing connector tapered I D 1 16 5 Viper capillary kit Vanquish Core system including Capillary pump autosampler SST I D x length 0 18 x 350 mm length Passive pre heater S...

Page 136: ...tubing I D 1 0 2 0 mm set of 5 1 Tubing connector tapered I D 1 16 5 Viper capillary kit Vanquish Horizon and Flex system including Capillary pump autosampler MP35N I D x length 0 1 x 350 mm length Active pre heater MP35N I D x length 0 1 x 380 mm Passive pre heater MP35N I D x length 0 1 x 530 mm 1 Drainage kit Vanquish system including L piece elbow pack of 4 different sizes Drain tubing 6 25 m ...

Page 137: ...ased on real physical measurement Solvent monitor 4 channel version 6230 1320 Solvent monitor 8 channel version 6230 1310 Stack stabilizer kit 6036 1710 USB isolator The USB Isolator improves the reliability of the USB connection between the USB port of an HPLC system module and the data system computer 6287 0540 Vanquish User Interface Can be used to display and monitor the vital parameters of th...

Page 138: ...izon and Flex systems 6042 2340 Active pre heater MP35N I D x length 0 1 x 380 mm 6732 0110 Passive pre heater SST I D x length 0 18 x 530 mm for Core systems 6732 0170 Passive pre heater MP35N I D x length 0 1 x 530 mm for Horizon and Flex systems 6732 0174 Vanquish system drainage L pieces set of 4 different sizes 6036 0003 Viper inline filter 6036 1045 Viper union 6040 2304 Drainage Kit Descrip...

Page 139: ...ive pre heater MP35N I D x length 0 1 x 530 mm 6036 2303A 10 4 2 Solvents and Wash Systems Reservoirs for solvents and wash liquids Description Part No Reservoir 1 L including cap 2270 0012 Reservoir 0 25 L including cap 2270 0026 Cap for reservoirs screw cap pack of 4 6270 0013 Plugs and retaining guides for reservoir caps kit including Cap plug to close open holes in the reservoir cap pack of 10...

Page 140: ...for the Vanquish system modules 6036 0002 System interlink cable 6036 0004 USB cable type A to type B high speed USB 2 0 Cable length 1 m 6035 9035 USB cable type A to type B high speed USB 2 0 Cable length 5 m 6911 0002 10 4 4 Other Parts Description Part No Base module system base all Vanquish systems 6036 1100 Packing material 6036 7005 Solvent rack 6036 1350 System base locking tool 6036 1160 ...

Page 141: ...11 Appendix UHPLC System Operating Manual Page 141 11 Appendix This chapter provides additional information about compliance ...

Page 142: ...ion of the use of certain hazardous substances in electrical and electronic equipment The CE mark on the device indicates that the product is compliant with the directive China RoHS regulations Measures for Administration of the Pollution Control of Electronic Information Products One of the following logos may be present on the device if applicable Logo Description The green logo marks items that...

Page 143: ...ate radio frequency energy and if not installed and used in accordance with the instructions may cause harmful interference to radio communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his expense 11 1 4 Manual Release History Revision Covering 4 0 Vanquish Core system with s...

Page 144: ...11 Appendix Page 144 UHPLC System Operating Manual ...

Page 145: ...utomated module control 95 client 92 ePanel Set 93 eWorkflow 95 Instrument Configuration Manager 79 Instrument Controller 79 92 module control 93 monitor baseline 94 Sequence Wizard 95 cleaning 106 condensation 45 59 connectors 54 consumables 133 138 D decontamination 106 107 delivery 37 Diagnostics 125 digital I O 54 drainage 70 E ePanel Set 93 equilibration 88 eWorkflow 95 F FCC 143 flow connect...

Page 146: ...pt 97 power on off 86 preparation 87 safety guidelines 85 overview functional 29 P peak shape 115 pH range 26 power connections 59 power considerations 44 power cord 44 power on off 86 power up the system 78 protective clothing 21 R regulatory compliance 142 reordering 133 replacement parts 133 138 RoHS mark 142 S safety glasses 21 safety guidelines case of emergency 24 general 19 general hazards ...

Page 147: ...nstallation 48 locking 63 preparing for operation 87 troubleshooting 115 unlocking 61 system arrangement 46 system base 32 installation 48 safety symbols 17 ship 109 system base lock 61 system equilibration 88 System Interlink 32 54 T transport 109 troubleshooting 113 baseline 121 communication 124 flow 119 general information 114 ghost peaks 116 negative peaks 116 peak area precision 117 power 12...

Page 148: ...Thermo Fisher Scientific Inc 168 Third Avenue Waltham Massachusetts 02451 USA www thermofisher com ...

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