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Thermo Scientific ISQ EC, Operating Manual

The Thermo Scientific ISQ EC Preinstallation Manual is a comprehensive guide that provides step-by-step instructions for setting up the ISQ EC instrument. Easily downloadable for free from our website, this essential manual ensures a smooth installation process, helping you get the most out of your product.

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8   

   Troubleshooting 

ISQ EC and ISQ EM Mass Spectrometer Operating Manual 

Page 207 

Operating Issues 

Leaks are a potential safety issue. Therefore, if a leak sensor detects 
leakage, beeping starts to alert you beeping starts to alert you in addition to 
the warning code and a message on the display. Follow the instructions in 
this manual to find and eliminate the source for the leakage. 

For information on all operating issues that may occur and affect detector 
performance, see

 Chapter 6

, “Operation.” 

TIP The Diagnostics screen provides helpful information for troubleshooting 
if a problem occurs in the mass spectrometer. 
If other values are subject to fluctuations or outside of a range, contact 
Technical Support. 

 

 

 

 

Summary of Contents for ISQ EC

Page 1: ...ISQ EC and ISQ EM Mass Spectrometer Operating Manual 1R120591 0002 Revision E February 2019 ...

Page 2: ... part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc This manual is provided as is The contents of this 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...

Page 3: ...fic 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 Legal Manufacturer Address Thermo Finnigan LLC a part of Thermo Fisher Scientific 355 River Oaks Parkway San Jo...

Page 4: ...Page 4 ISQ EC and ISQ EM Mass Spectrometer Operating Manual ...

Page 5: ...ement utilisés dans ce manuel 17 2 1 2 Observing this Manual 19 2 1 3 Safety Symbols on the Instrument 19 2 2 Intended Use 22 2 3 Safety Precautions 23 2 3 1 General Safety Information Consignes Générales de Sécurité 23 2 3 2 Qualification of the Personnel 24 2 3 3 Personal Protective Equipment 26 2 3 4 Electrical Safety Precautions 28 2 3 5 General Residual Hazards 29 2 4 Solvent and Additive Inf...

Page 6: ...Pump 92 5 5 4 Installing the Solvent Trap 96 5 5 5 Installing the Source Housing Drain Insert and Sweep cone 98 5 5 6 Switching Between HESI and APCI Modes on the ISQ EM Source Housing 103 5 5 7 Installing the Internal Calibration Solution 104 5 5 8 Connecting the IC or LC to the MS Inlet 106 5 5 9 Flushing the Calibration Solution 108 5 5 10 Connecting the System to the PC 110 5 6 Summary of Hard...

Page 7: ... 3 AS AP Autosampler 165 6 8 4 Integrion Autosampler no AS AP 165 7 Maintenance and Service 167 7 1 Introduction to Maintenance and Service 168 7 2 Safety Guidelines for Maintenance and Service 169 7 3 General Rules for Maintenance and Service 172 7 4 Routine and Preventive Maintenance 173 7 4 1 Maintenance Plan 173 7 4 2 Preventive Maintenance Schedule 174 7 4 3 Cleaning or Decontaminating the In...

Page 8: ...217 11 Appendix 221 11 1 Compliance Information 222 11 1 1 Declarations of Conformity 222 11 1 2 WEEE Compliance 223 11 1 3 FCC Compliance 224 11 1 4 Regulatory Compliance 225 11 1 5 Low Voltage Safety Compliance 225 11 1 6 Notice on Lifting and Handling of Thermo Scientific Instruments 225 11 1 7 Notice on the Proper Use of Thermo Scientific Instruments 225 11 1 8 Notice on the Susceptibility to ...

Page 9: ...EM Mass Spectrometer 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: ...r detector read this manual thoroughly This manual also contains safety messages precautionary statements and special notices that can prevent personal injury damage to the detector or loss of data when followed properly Note the following The detector configuration may vary therefore not all descriptions necessarily apply to your particular detector If some detail applies to only one model or var...

Page 11: ...to which they apply Safety messages that apply to only a particular section or 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 ...

Page 12: ...ights information of general interest or helpful information that can make a task easier or optimize the performance of the detector TIP Veuillez noter Signale des informations d intérêt général ou utiles qui peuvent simplifier l exécution d une tâche ou optimiser le fonctionnement du détecteur 1 2 3 Typographical Conventions These typographical conventions apply to the descriptions in this manual...

Page 13: ...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 detector from the front Particularly Important Words Particularly important words in the main flow of text appear italicized Electronic Manual Version PDF The electronic version PDF of the manual contains numerous links that you ...

Page 14: ...ation includes the following Chromeleon 7 Help and documents The Chromeleon 7 Help provides extensive information and comprehensive reference material for all aspects of the software For basic information about device installation and configuration refer to the Installation Guide for specific information about a certain device refer to the Instrument Configuration Manager Help In Chromeleon 7 devi...

Page 15: ...d in the software shipment 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 Third party documentation includes the user documentation for the gas supply as applicable User documentation for the nitrogen generator ...

Page 16: ...2 Safety Page 16 ISQ EC and ISQ EM Mass Spectrometer Operating Manual 2 Safety This chapter provides general and specific safety information and informs about the intended use of the detector ...

Page 17: ...nsequences of what you are doing CAUTION Indicates 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 Ce manuel contient des messages de sécurité visant à prévenir les blessures chez les utilisateurs du détecteur Les symboles de sécurité et les mentions d avertissement utilisé...

Page 18: ...2 Safety Page 18 ISQ EC and ISQ EM Mass Spectrometer Operating Manual AVERTISSEMENT Indique une situation dangereuse qui si elle n est pas évitée peut entraîner de graves blessures ...

Page 19: ...al near the instrument for quick reference Save this manual and pass it on to any subsequent user Read understand and comply with all safety messages and precautionary statements presented in this manual Il est important de lire de comprendre et de respecter tous les messages et consignes de sécurité présentés dans ce manuel 2 1 3 Safety Symbols on the Instrument The table lists the safety symbols...

Page 20: ...tive grounding Indicates that an electrical shock could or might occur Alerts you to the presence of a hot surface that could or might cause burn injuries Indicates that eye damage could or might occur Alerts you to carefully read your instrument s documentation to ensure your safety and the instrument s operation ability Failing to carefully read the documentation could or might put you at risk f...

Page 21: ...e de mise à la terre Indique un risque de choc électrique Vous avertit de la présence d une surface chaude présentant un risque de blessure par brûlure Indique un risque de lésion oculaire Vous avertit qu il est important de lire attentivement la documentation de l instrument afin de garantir votre sécurité et la capacité opérationnelle de l instrument Si vous ne lisez pas attentivement la documen...

Page 22: ...for laboratory research use only It is not intended for use in diagnostic procedures Laboratory Practice Thermo Fisher Scientific recommends that the laboratory in which the MS system is used follow best practices for LC MS and IC MS analyses This includes among others Using appropriate standards Regularly running calibration Establishing shelf life limits and following them for all consumables us...

Page 23: ... If the instrument is used in a manner not specified by Thermo Fisher Scientific the protection provided by the detector could be impaired Observe the following Operate the instrument only within its technical specifications Use only the replacement parts and additional components options and peripherals specifically authorized and qualified for the detector by Thermo Fisher Scientific Perform onl...

Page 24: ...es du détecteur Ouvrez le boîtier du détecteur et les autres composants uniquement si cela est spécifiquement indiqué dans ce manuel Thermo Fisher Scientific ne peut être tenu pour responsable des dommages matériels ou autres résultant de l utilisation inappropriée ou incorrecte du détecteur En cas de questions concernant l usage approprié contactez Thermo Fisher Scientific avant de poursuivre Saf...

Page 25: ...e regulations Thermo Fisher Scientific recommends always having service personnel certified by Thermo Fisher Scientific perform the installation for brevity referred to as Thermo Fisher Scientific service engineer If a person other than a Thermo Fisher Scientific service engineer installs and sets up the module the installer is responsible for ensuring the safety of the module and system General O...

Page 26: ... qualifié Tous les utilisateurs doivent connaître les risques inhérents au détecteur et aux substances utilisées Ils doivent également respecter les fiches techniques santé sécurité FTSS 2 3 3 Personal Protective Equipment Wear personal protective equipment and follow good laboratory practice to protect you from hazardous substances The appropriate equipment depends on the hazard For advice on the...

Page 27: ...S for the substance you are using Vêtements de protection Pour vous protéger des projections chimiques des liquides dangereux ou d autres contaminants lors d une intervention sur le système LC MS ou IC MS ou à proximité de ce dernier portez des vêtements de protection appropriés comme une blouse de laboratoire Pour obtenir des renseignements sur la manipulation correcte d une substance particulièr...

Page 28: ...h voltages are present inside the device that could cause an electric shock or damage to the device Do not make any changes to the electrical or grounding connections If you suspect any kind of electrical damage disconnect the power cord and contact Thermo Fisher Scientific Technical Support for assistance Do not open the housing or remove protective panels unless specifically instructed to do so ...

Page 29: ...don d alimentation et contactez l assistance technique de Thermo Fisher Scientific Sauf instruction contraire dans ce manuel n ouvrez pas le boîtier et ne retirez pas les panneaux de protection Ne placez pas de réservoir de liquide directement sur l appareil En cas de fuite le liquide peut pénétrer dans l appareil entrer en contact avec les composants électriques et provoquer un court circuit Plac...

Page 30: ...cturer Observe the guidelines of Good Laboratory Practice GLP Be sure that you know the properties of all substances that you are using Avoid exposure to harmful substances If you have any doubt about a substance handle the substance as if it is potentially harmful Wear personal protective equipment as required by the hazard and follow good laboratory practice Reduce the volume of substances to th...

Page 31: ...iche technique santé sécurité FTSS du fabricant Veillez à bien connaître les propriétés de toutes les substances utilisées Évitez toute exposition à des substances nocives En cas de doute sur une substance manipulez la comme si elle était potentiellement dangereuse Portez l équipement de protection individuelle requis en fonction du risque et respectez les bonnes pratiques de laboratoire Réduisez ...

Page 32: ...ollow a regulated approved waste disposal program AVERTISSEMENT Risque biologique Les matières dangereuses par exemple les microorganismes les cultures cellulaires les tissus les fluides corporels et autres agents biologiques peuvent transmettre des maladies infectieuses Pour éviter toute infection avec ces agents Considérez toute substance biologique comme étant au moins potentiellement infectieu...

Page 33: ...ystème de chromatographie Évitez d utiliser ces solvants WARNING Hazardous Vapors Install the LC MS or IC MS system in a well ventilated laboratory If the mobile phase or sample includes volatile or flammable solvents do not allow them to enter the workspace If the mobile phase or sample includes volatile or flammable solvents avoid open flames and sparks The exhaust gas may contain hazardous fume...

Page 34: ...tif de ventilation Assurez une ventilation adéquate dans le laboratoire N évacuez pas directement dans le laboratoire Évitez les flammes nues et les sources d étincelles à proximité N utilisez pas le détecteur en présence de gaz ou de fumées inflammables CAUTION Escape of Hazardous Substances from PEEK Capillaries In the LC or IC system capillaries made of PEEK may be used Swelling or attack by ac...

Page 35: ... ou un mélange hexane acétate d éthyle et méthanol peuvent attaquer le PEEK L exposition brève dans le cadre de procédures de nettoyage n entraîne pas le gonflement ni l attaque du matériel en PEEK Pour obtenir plus d informations consultez la documentation technique sur la résistance chimique du PEEK CAUTION Fused silica is used in flow cells and capillaries To avoid personal injury always wear s...

Page 36: ...ough capillaries can generate static electricity This effect is particularly 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 ATTENTION Étincelles dues aux décharges électrostatiques Le...

Page 37: ...additives that are compatible with all parts in the flow path Follow any specific recommendations presented in other sections of this manual Refer also to the operating manuals for all modules in the LC or IC system They may provide additional guidelines and information Some of the cleaning procedures in this manual call for the use of methanol If methanol is unavailable or prohibited for use in c...

Page 38: ...etails see section 11 1 page 222 Changes that you make to the device may void compliance with one or more of these EMC and safety standards Changes to the device include replacing a part or adding components options or peripherals not specifically authorized and qualified for the product by Thermo Fisher Scientific To ensure continued compliance with EMC and safety standards replacement parts and ...

Page 39: ...3 Instrument Overview ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 39 3 Instrument Overview This chapter introduces you to the mass spectrometer and the main components ...

Page 40: ...erful analytical technique used in a number of fields including Identification of unknown compounds Quantitation of known compounds Determination of chemical structure The basic function of an MS detector is to measure the mass to charge ratio of ions The unit of mass used is the Dalton Da One Dalton is equal to 1 12 of the mass of a single atom of carbon 12 This follows the accepted convention th...

Page 41: ...ample into the mass spectrometer as described in Table 1 Method Description Direct infusion Connect a syringe pump directly to the atmospheric pressure ionization API source of the mass spectrometer High flow infusion Use a union tee to combine the flow from a syringe pump with the flow from an LC or IC pump Manual loop injection Connect a sample loop a needle port fitting and an LC IC pump to an ...

Page 42: ... single run See Figure 1 for an overview of the ISQ EC and ISQ EM systems Figure 1 Diagram of ISQ EC and ISQ EM systems The ISQ EC and ISQ EM Single Quadrupole Mass Spectrometers each operate as a conventional mass spectrometer with one stage of mass analysis The ion source ionizes the sample ion optics transfer the created ions through the vacuum system mass analysis of the ion products occurs in...

Page 43: ...ion and ion polarity modes but the scan mode and scan type provides greater flexibility in the instrumentation for solving complex analytical problems The method editor in Chromeleon allows the user to set up scans in a variety of ways combining both full scans and SIM scans The user can also call for scans of either or both polarities Simplified ion source controls and a simplified method editor ...

Page 44: ...4 Unpacking Page 44 ISQ EC and ISQ EM Mass Spectrometer Operating Manual 4 Unpacking This chapter provides information for unpacking the system and informs you about the scope of delivery ...

Page 45: ... if reported immediately Unpacking the Instrument CAUTION Heavy Load Bulky Device The instrument is too heavy or bulky for one person alone to handle safely A minimum of two people are required to lift the instrument from the shipping crate to the lab bench To avoid personal injury or damage to the instrument observe the following guidelines Physical handling of the instrument including lifting or...

Page 46: ...lacer Ce travail d équipe est tout particulièrement nécessaire pour soulever l instrument et l installer sur l empilage du système ou pour l en retirer Pour soulever ou déplacer l instrument saisissez le par les côtés Ne saisissez pas l instrument par le cadran frontal pour le soulever ou le déplacer Vous risqueriez d endommager le cadran ou l instrument Tools required Screwdriver Torx T20 Follow ...

Page 47: ...ift the detector out of the shipping container and place it on a stable surface 5 Transport the mass spectrometer to the installation site if it is not already there and place it in the system stack TIP Keep the shipping container and all packing material These items will be needed if the detector is transported to a new location or shipped Inner Tray Accessory Kit ...

Page 48: ...ss top of the quadrupole manifold assembly in place must be removed prior to turning on the instrument ATTENTION Risque d endommagement de l instrument La pièce en mousse qui maintient en place la partie supérieure en verre de l ensemble collecteur quadripolaire pendant le transport doit être retirée avant la mise sous tension de l instrument ...

Page 49: ...items are included in the delivery Mass spectrometer Accessory Kit For details about the kit content see section 10 2 Ship Kit page 215 Foreline pump Operating manual NOTICE The delivery scope is limited to the ISC EC or ISQ EM system Refer to the HPLC IC or other accessory manuals for their delivery inventory ...

Page 50: ...n Page 50 ISQ EC and ISQ EM Mass Spectrometer Operating Manual 5 Installation This chapter specifies the requirements for the installation site and describes how to set up install and configure the mass spectrometer ...

Page 51: ...he instrument is too heavy or bulky for one person alone to handle safely A minimum of two people are required to lift the instrument from the shipping crate to the lab bench To avoid personal injury or damage to the instrument observe the following guidelines Physical handling of the instrument including lifting or moving requires a team effort of two persons A team effort is in particular requir...

Page 52: ...r soulever l instrument et l installer sur l empilage du système ou pour l en retirer Pour soulever ou déplacer l instrument saisissez le par les côtés Ne saisissez pas l instrument par le cadran frontal pour le soulever ou le déplacer Vous risqueriez d endommager le cadran ou l instrument CAUTION INSTRUMENT DAMAGE Clean tubing cutters with methanol prior to use Otherwise tubing may be contaminate...

Page 53: ... See section 5 5 page 68 3 Set up the flow connections See section 5 6 page 113 4 Turn on the system See section 5 7 page 115 Adjust the display brightness and date and time as required 5 Installation in the Chromeleon software optional When the display shows the Main Menu after the self test set up the detector in the software See section 6 4 page 123 TIP Before turning on the power to the instru...

Page 54: ... the Instruments Installation Qualification Operating Instructions The manual provides information about the required materials and detailed instructions 7 Recommended Perform Operational Qualification The qualification kit includes all materials required for the qualification and detailed instructions ...

Page 55: ...ifications page 211 Provide a sturdy workbench of a height that ensures convenient access to the interior of each device in the system The workbench must stand in a secure and level position that is free of vibrations The bench top must be dry clean and resistant to chemicals Allow sufficient free space on the sides for gas connections and for proper air circulation Allow at least 5 cm of clearanc...

Page 56: ...onnect the device to a power socket that is shared with other equipment for example multiple sockets Do not use defective multiple socket or extensions cords as they could result in personal injury or damage to the device After the power to the device is turned off the device is still energized as long as the power cord is connected Repair work on the device while the device is connected to power ...

Page 57: ...ce dernier est toujours raccordé au secteur pourraient blesser le personnel Par conséquent débranchez toujours le cordon d alimentation avant de procéder à des réparations à l intérieur de l appareil Si vous avez reçu pour consigne de retirer des couvercles ou panneaux ne branchez pas le cordon d alimentation tant que les couvercles ou panneaux ne sont pas remis en place 5 3 3 Power Cord The power...

Page 58: ... Spectrometer Operating Manual Region Thermo Scientific Part Number C13 for PC monitors and autosamplers Thermo Scientific Part Number C19 for LC IC and MS North America 120V North America 250V Japan 125V Switzerland 250V Australia 250V China 250V ...

Page 59: ...trometer Operating Manual Page 59 Region Thermo Scientific Part Number C13 for PC monitors and autosamplers Thermo Scientific Part Number C19 for LC IC and MS Europe Schuko 250V United Kingdom 250V Denmark 250V Italy 250V Israel 250V India 250V ...

Page 60: ...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 defective multiple socket or extensions cords as they could result in personal injury or damage to the device 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 ...

Page 61: ...trique mise à la terre En cas d urgence le cordon d alimentation doit être facilement accessible à tout moment pour pouvoir débrancher l appareil WARNING Electric Shock or Damage to a Product Misuse of the power cords could cause personal injury or damage the instrument Use the power cords provided by Thermo Fisher Scientific only for the purpose for which they are intended Do not use them for any...

Page 62: ... operating conditions Temperature Temperature fluctuations can affect the performance of the detector Avoid locations with significant changes in temperature and strong air drafts For example do not place the detector 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 detect...

Page 63: ...ENTION Fumées dangereuses Les gaz d échappement de l instrument peuvent contenir des fumées dangereuses qui représentent un risque pour la santé et la sécurité Évitez toute accumulation de gaz Les gaz d échappement doivent toujours être évacués par une ventilation appropriée Assurez vous que le site d installation est bien ventilé N évacuez pas directement dans le laboratoire Make sure that the lo...

Page 64: ...with particles size 0 1 µm water vapor or other non volatile substances it can impair the performance or even damage the instrument Observe all requirements and specifications for the supply gas in this manual to avoid damage to the detector Make sure that the location fulfils the following requirements Make sure that the gas supply is regulated to a stable gas pressure that is within the specifie...

Page 65: ...n generator These are available in larger units that may be remotely located or as point of use systems Work with the specific vendor in order to determine output purity via an oxygen sensor Point of use systems require compressor maintenance every 3 000 hrs Facility size Dewar These are large globes located outside a facility They are filled as needed Portable Dewar These are roll around Dewars B...

Page 66: ...5 Installation Page 66 ISQ EC and ISQ EM Mass Spectrometer Operating Manual ...

Page 67: ...In order to remove the shipping foam please follow the instructions below 1 Be sure the instrument is unplugged 2 Using the provided tool kit remove the top panel and right hand side panel of the instrument 3 Unscrew the power supply 4 Lift up the power supply module as shown in Figure 3 5 Remove the black foam insert 6 Swing the power supply module back in place and secure it with the screw 7 Rep...

Page 68: ... quiet at only 48 dB A The pump size is 470 mm length x 158 mm width x 229 mm height and weighs 28 kg It should be placed on the floor or located somewhere where its vibration will not adversely affect instrument performance Figure 4 Foreline Pump Check the foreline pump voltage setting as indicated in Figure 5 It shows a pump configured for 110 V operation The voltage must match that of the suppl...

Page 69: ...voltage may result in pump and or instrument damage AVERTISSEMENT Risque de choc électrique ou d endommagement d un produit La tension de la pompe doit correspondre à celle fournie au spectromètre de masse Dans le cas contraire la pompe ou l instrument risque d être endommagé Figure 5 Foreline Edwards pump voltage setting Then check that the pump is set to high vacuum mode The mode selector knob o...

Page 70: ...tion reservoir located at the base of the housing The oil is then returned to the pump through the oil return kit Follow the steps below to install the oil return kit 1 The gas ballast adapter has two parts a metal adapter and a plastic adapter First assemble the metal gas ballast adapter by following the steps below All the necessary parts are shipped with the Edwards pump a Add the smaller O rin...

Page 71: ...to the small O ring on the metal gas ballast adapter c Add the large O ring to the base of the metal adapter See Figure 8 Figure 8 Attaching the large O ring to the metal gas ballast adapter 2 Attach the metal O ring to the black plastic adapter and the black O ring on the metal adapter See Figure 9 ...

Page 72: ...ure 9 Installing the metal O ring on the plastic gas ballast adapter 3 Screw the black adapter into the metal adapter See Figure 10 Figure 10 Screwing the adapters together 4 Remove the gas ballast knob from the top of the foreline pump by pushing down and turning it See Figure 11 ...

Page 73: ...ballast knob NOTICE Be sure the spring inside the inlet port stays in the inlet If it comes out when you remove the cover put it back in the inlet before adding the gas ballast adapter 5 Locate the pins on the gas ballast adapter and the mating notches on the inlet port on the foreline pump See Figure 12 ...

Page 74: ...gure 12 Finding the mating pins and notches 6 Insert the adapter assembly into the inlet port using the matching notches See Figure 13 Figure 13 Installing the adapter into the inlet 7 Push down on the adapter and turn it to the right to secure it to the inlet port See Figure 14 ...

Page 75: ...al Page 75 Figure 14 Securing the adapter 8 Turn the adapter so the flats are positioned as shown One of the flats should face towards the number II on the pump It should now be properly installed in the inlet port See Figure 15 Figure 15 Correctly installed adapter ...

Page 76: ... Install the brass restrictor bushing into the small black hose for the oil mist filter See Figure 16 Figure 16 Installing the brass restrictor bushing into the oil mist filter hose 10 Push the bushing all the way into the hose See Figure 17 Figure 17 Correctly installed bushing ...

Page 77: ...l Page 77 11 Attach the hose from the oil mist filter to the adapter using the included clamp Push the hose all the way down on the adapter This will push the restrictor bushing up into the hose See Figure 18 Figure 18 Attaching the oil mist filter hose to the adapter ...

Page 78: ...e 78 ISQ EC and ISQ EM Mass Spectrometer Operating Manual 12 Tighten the clamp using a tool if necessary Be sure the clamp is flush against the top of the adapter See Figure 19 Figure 19 Tightening the clamp with a tool ...

Page 79: ...SQ EM Mass Spectrometer Operating Manual Page 79 13 Install the foreline hose from the back of the mass spectrometer to the inlet port on the foreline pump See Figure 20 Figure 20 Installing the foreline hose to the foreline pump ...

Page 80: ...n place See Figure 21 Figure 21 Installing the clamp for the exhaust hose NOTICE Be sure to attach the foreline hose from the rear of the MS instrument to the inlet port of the foreline pump as shown on in Figure 41 TIP The instrument can be pushed completely against the back wall of the laboratory counter The hose can bend to either side ...

Page 81: ...rique ou d endommagement d un produit La tension de la pompe doit correspondre à celle fournie au spectromètre de masse Dans le cas contraire la pompe ou l instrument risque d être endommagé WARNING Instrument Damage The foreline hose length cannot be extended because it will adversely affect the pressure in the vacuum manifold AVERTISSEMENT Risque d endommagement de l instrument Le tuyau foreline...

Page 82: ... 5 2 Installing the Oil Mist Filter To install the oil mist filter 1 Remove the plug rom the oil mist filter Leave the metal O ring in place See Figure 22 Figure 22 Removing the plug from the oil mist filter 2 Install the skinny hose adapter Ensure it is hand tight See Figure 23 ...

Page 83: ...r Operating Manual Page 83 Figure 23 Installing the skinny hose adapter 3 Install the oil mist filter adapter on the gray exhaust port adapter on the pump See Figure 24 Figure 24 Installing the oil mist filter adapter on the gray exhaust port adapter ...

Page 84: ...le wrench It is important that this is tight to prevent oil from leaking See Figure 25 Figure 25 Tightening the gray exhaust port adapter NOTICE Install the oil mist filter into the installed gray adapter Do NOT replace the gray adapter with the black one that ships with the Edwards pump 5 Place the oil mist filter onto the adapter See Figure 26 ...

Page 85: ...nto the adapter NOTICE The oil mist filter must be installed in the same direction as the exhaust flow as indicated by the arrow on the lower housing 6 Use the included clamp to attach secure the oil mist filter to the adapter Do not loosen the gray exhaust port adapter when installing the oil mist filter See Figure 27 ...

Page 86: ...r with a clamp 7 Trim the hose to remove extra length The hose should not be so short that it kinks It should not be so long that it extends above the fitting on the oil mist filter The orientation should be approximately horizontal so that oil does not collect in the hose See Figure 28 Figure 28 Trimming the hose ...

Page 87: ...he oil mist filter to connect it to the pump exhaust First slide a clamp over the hose then attach it to the oil mist filter See Figure 29 Figure 29 Attaching the pump exhaust hose to the oil mist filter assembly 9 Tighten the clamp with a tool See Figure 30 Figure 30 Tightening the oil mist filter assembly small hose clamp ...

Page 88: ...rt adapter when installing the oil mist filter 10 Now install the top exhaust adapter to the oil mist filter First unscrew the cap at the top of the oil mist filter and discard 11 Add the oil mist filter top O ring See Figure 31 Figure 31 Installing the oil mist filter top O ring 12 Add the top adapter See Figure 32 ...

Page 89: ...er Operating Manual Page 89 Figure 32 Installing the oil mist filter top adapter 13 Install and secure the clamp that attaches the top adapter and O ring to the oil mist filter See Figure 33 Figure 33 Securing the top adapter and O ring with a clamp ...

Page 90: ...Manual 14 Install the exhaust hose clamp and hose on the adapter See Figure 34 Figure 34 Installing the hose clamp and hose to the top adapter 15 Secure the clamp with a nut driver or flat handled screwdriver See Figure 35 Figure 35 Tightening the clamp with a nut driver ...

Page 91: ...st port adapter Figure 36 shows a close up picture of a correctly installed oil mist filter with the clear white bottom housing connected directly to the pump exhaust manifold Be sure to attach the included gas ballast oil drain kit tubing from the bottom of the housing back to the pump ballast manifold Figure 36 Foreline pump oil mist filter assembly and oil return kit ...

Page 92: ...r Operating Manual 5 5 3 Adding Oil to the Foreline Pump This section contains instructions for adding oil to your foreline pump 1 Use only the same type of Edwards pump oil that ships with the foreline pump See Figure 37 Figure 37 Edwards s foreline pump oil ...

Page 93: ...5 Installation ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 93 2 Unscrew the cap on the oil reservoir and set aside See Figure 38 Figure 38 Unscrewing the oil reservoir cap ...

Page 94: ...the pump a little over the halfway mark on the sight glass See Figure 39 Figure 39 Adding oil to the foreline pump 4 Close and tighten the reservoir cap See Figure 40 NOTICE After tuning on the pump the oil level might drop If the oil level goes below halfway on the sight glass vent the mass spectrometer and add oil ...

Page 95: ...pectrometer Operating Manual Page 95 Figure 40 Closing and tightening the oil reservoir cap 5 The power cord from the pump should be plugged directly into the back of the MS instrument as shown in Figure 41 Figure 41 Rear side of instrument ...

Page 96: ... the exhaust Two 90 elbows are included to make bends around the edge of the table if desired This tubing can be cut to any length required See Figure 42 The outlet of the solvent trap bottle must be connected to a suitable exhaust WARNING Hazardous Vapors The solvent gas may contain hazardous fumes Maintain a well ventilated laboratory AVERTISSEMENT Vapeurs dangereuses Les gaz miscibles peuvent c...

Page 97: ...5 Installation ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 97 Figure 42 Instrument solvent trap 90 elbow connector Tubing Solvent trap bottle ...

Page 98: ...NING Instrument Damage Wear gloves and eye protection to avoid contamination of sensitive parts AVERTISSEMENT Risque d endommagement de l instrument Portez des gants et des lunettes de protection pour éviter de contaminer les parties sensibles 1 Open the front bezel by grasping the door on the left edge 2 Lift up the top hatch of the instrument to provide sufficient space to remove the source hous...

Page 99: ...m levers located on the lower right and left hand side of the source housing As the cams rotate the source housing will come away from the bulkhead and will slide off the two metal guide rods as shown in Figure 46 Figure 45 Removal of source housing 5 Slowly remove the source housing as shown in Figure 46 taking care to avoid damage to the ESI probe and capillary connection ...

Page 100: ... a safe location and install the sweep cone as shown in Figure 47 Figure 47 Installation of sweep cone 7 The cone should snap in place and make a snug seal against the Teflon collar 8 Re install the source housing in the reverse order as shown in Figure 48 with special care taken to be sure to slide the source housing onto the metal guide rods ...

Page 101: ...ISQ EM Mass Spectrometer Operating Manual Page 101 Figure 48 Reinstalling the Source Housing 9 Re attach the PEEK capillary tubing to the grounding union See Figure 49 Figure 49 Reattaching the PEEK tubing to the grounding union ...

Page 102: ...nections Damage to LC or IC might occur if the system is not properly grounded AVERTISSEMENT Risque d endommagement de l instrument Pour assurer un fonctionnement sûr la jonction de mise à la terre métallique doit toujours être solidement fixée au raccord de mise à la terre qui est attaché au boîtier métallique de la source d ions Vérifiez que les vis à oreilles sont serrées lors de la réinstallat...

Page 103: ...ting your analysis 1 If you want to use the HESI probe on your ISQ EM ensure that the probe switch on the side of the source housing is turned to the side The HESI label will show clearly Ensure the probe switch on the left side of the source housing faces up so that the needle is positioned correctly for analyzing samples See Figure 50 Figure 50 Ensuring the ISQ EM Source Housing is in HESI mode ...

Page 104: ...e APCI switch so that it is horizontal This moves the APCI needle to a more secure position in at the top of source housing for transport 5 5 7 Installing the Internal Calibration Solution Your instrument ships with an empty bottle in place of the internal calibration solution It will be necessary to remove this shipping bottle and replace it with the labeled version as shown in Figure 52 ...

Page 105: ...NG Instrument Damage Wear protective clothing eyewear and gloves during the calibrant bottle installation procedure AVERTISSEMENT Risque d endommagement de l instrument Portez des vêtements des lunettes et des gants de protection lors de la procédure d installation de la bouteille d étalonnage 1 Remove the cap from the empty bottle at the front of the instrument taking care not to damage the capil...

Page 106: ...bottle prior to performing any autotune experiment TIP If any liquid spills unto the drain area located directly below the bottle be sure to clean and dry the liquid leak sensor as shown in Figure 16 5 5 8 Connecting the IC or LC to the MS Inlet This section provides instructions for connecting the LC or IC to the ISQ EC inlet Figure 54 shows the various fluidic connections for the MS instrument S...

Page 107: ... B Inlet to valve C Valve to grounding union D Grounding union to source probe E Reference calibrant to valve Table 3 MS Instrument Fluidics The LC to MS inlet or instrument inlet connection can be rotated 90 to face upwards in the event that the user wishes to connect to the MS instrument from the top hatch Using the tool kit provided with the instrument remove ...

Page 108: ...can be freely moved to the other set of two holes The inlet has a tapped hole and a pin to position it and can be conveniently positioned as required for the application as shown in Figure 55 Figure 55 LC to MS inlet assembly 5 5 9 Flushing the Calibration Solution This section provides instructions for flushing the calibration solution The instrument must be completely connected and running befor...

Page 109: ...56 Flushing the calibrant 2 Check the Calibration Valve Pressurization box See Figure 57 Figure 57 Checking the calibration valve pressurization box 3 Watch for liquid entering the clear drain line behind the bulkhead union 4 Let the calibration solution flush for approximately 30 sec ...

Page 110: ... of the LC MS or IC MS system to the PC 5 5 10 1 Connecting the ISQ EC and EM Mass Spectrometer to the PC The mass spectrometer requires a local LAN connection 10Base T connection The cabling has been provided to connect directly to the PC The PC has two LAN connections located on the rear of the PC Plug the 10Base T cable into the PC card as shown in Figure 59 by the red cable For Internet and lo...

Page 111: ...e follow the manufacturer s recommended guidelines on how to connect the PC to the front end chromatograph instrument Refer to the Unpacking chapter for more information regarding the pre installed software 5 5 10 3 Configuring the LAN If you purchased a PC with the mass spectrometer the network settings will be configured for you If you purchased a PC independently please follow ...

Page 112: ... appropriate LAN 5 5 10 4 Connecting the Fluidics System to the Mass Spectrometer The instrument ships with various PEEK capillaries to assist in the connection to front end chromatograph Do not bypass or alter PEEK capillaries that are internal to the MS instrument These connect the internal reference inlet system and valve to the ion source ...

Page 113: ...y glasses and gloves 5 Attach the nitrogen supply line CAUTION Gas Supply Safety The nitrogen supply line should not be delivering gas or set to the on position for a generator or source valve and set to open Failure may result in personal injury Wait until the supply line is firmly attached to the instrument prior to turning on the gas ATTENTION Sécurité de l alimentation en gaz La conduite d ali...

Page 114: ...rrect voltage on foreline pump matches lab building power supply 13 Connect foreline pump power cord to pump and MS instrument 14 Verify MS instrument power switch is set to the off position 15 Connect MS instrument power cord to wall outlet 16 Switch on the MS instrument 17 The MS instrument will automatically turn on the foreline pump and the system will begin to achieve nominal vacuum TIP The m...

Page 115: ...n the switch is in the up right position as shown The MS instrument will automatically switch between 110V and 230V There is no manual adjustment required Figure 60 Location of power switch Check the foreline pump voltage setting as indicated in Figure 61 The voltage must match that of the supplied voltage to the MS instrument For example if the MS instrument is using 110V it is important that the...

Page 116: ...5 Installation Page 116 ISQ EC and ISQ EM Mass Spectrometer Operating Manual Figure 61 Foreline Edwards pump voltage setting ...

Page 117: ... Operation ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 117 6 Operation This chapter describes the elements for instrument control provides information for routine operation and for shutdown ...

Page 118: ...al setup of the system has already been completed If this is not the case refer to the instructions in chapter 5 Installation before proceeding see page 50 For a basic description of instrument control and automated sample analysis with the Chromeleon software see section 6 4 Details on control and operation of the detector are available in the Chromeleon Help ...

Page 119: ...etrahydrofuran or other highly combustible solvents ATTENTION Risque d explosion ou d endommagement du détecteur Lors de l utilisation de tétrahydrofurane THF il y a un risque d explosion si le gaz d alimentation est l air Cela peut représenter un risque pour la sécurité et la santé et endommager le détecteur Utilisez toujours de l azote avec le tétrahydrofurane ou d autres solvants hautement infl...

Page 120: ... detector gas flow first wait at least 5 minutes and only then turn on the pump flow When turning off pump flow and detector gas flow Turn off the pump flow first wait at least 5 minutes and only then turn off the detector gas flow During the waiting period the drain pump drains any remaining mobile phase to waste before it automatically turns off Observe the requirements for gas supply and ventil...

Page 121: ...This section provides an overview of the MS instrument Figure 62 shows the various fluidic connections for the MS instrument See Table 4 for descriptions of the MS fluidics Figure 62 ISQ EC and ISQ EM MS fluidics overview Letter Description A Instrument inlet B Inlet to valve C Valve to grounding union ...

Page 122: ...6 Operation Page 122 ISQ EC and ISQ EM Mass Spectrometer Operating Manual Letter Description D Grounding union to source probe E Reference calibrant to valve Table 4 MS Instrument Fluidics ...

Page 123: ... configure the MS within Chromeleon 7 2 2 The MS instrument should be powered On under vacuum and supplied with nitrogen gas 3 Open Chromeleon Service Manager and select the Configure Instruments option Follow documented Chromeleon procedures to create a new instrument within Chromeleon 7 to add either an IC or LC system 4 Once the front end LC or IC is configured select Add module to instrument a...

Page 124: ...ISQ EM Mass Spectrometer Operating Manual Figure 63 Location of ISQ EC or ISQ EM instrument module 6 If you purchased a PC with your mass spectrometer the instrument will configure automatically and display an IP address See Figure 64 ...

Page 125: ...endently please follow the instructions below to configure the IPv4 settings on the appropriate LAN 8 Turn on the computer and allow it to complete its boot processes 9 Select Start Control Panel Network and Internet Network and Sharing Center to open the Network Connections window 10 Configure the network card that will connect to the mass spectrometer ...

Page 126: ... except the Internet Protocol TCP IP Version 4 by unchecking the boxes 11 Under Communication Settings click the Edit button next to the IP address The Local Area Connection Status window opens See Figure 65 Figure 65 Local area connection status window 12 Click Properties to open the local area network properties 13 Under the Networking tab lot the Local Area Connection Properties window double c...

Page 127: ...EC and ISQ EM Mass Spectrometer Operating Manual Page 127 Figure 66 Selecting the network connection 14 Configure the IP Address and Subnet as shown in Figure 67 6 8 Figure 67 Configuring the IP address and subnet mask ...

Page 128: ...ect the instrument transferring large data files using the USB hub that the adapter is installed in while simultaneously collecting data on the instrument can cause occasional communication issues 15 Click OK and return to the General tab on the Chromeleon configuration pane See Figure 68 Figure 68 ISQ Family Configuration General Tab ...

Page 129: ...n should not be used See 164 for additional information about remote start cables 19 If Hardware Inject Synchronization is checked set Remote Start to Active Low or Active High The selection should be the same as the setting on the autosampler 20 To set the split flow multiplier check Split Flow The split flow multiplier can be set from 1 100 21 If you would like to perform mass directed fraction ...

Page 130: ...lect the Maintenance tab and verify that all entries are enabled as shown in Figure 69 Figure 69 ISQ EC or ISQ EM MS configuration Maintenance tab Use the Maintenance tab to set maintenance intervals for the foreline pump oil turbo pump oil and bearing and the electron multiplier To view usage times for these items open the Chromeleon Console and go to ISQ EC ISQ EM Wellness See ...

Page 131: ...erating Manual Page 131 Figure 70 Viewing maintenance intervals In the Chromeleon Console 25 Click OK when you have finished setting the maintenance intervals 26 Select the Associate Pump Info tab to associate a pump or change pump types See Figure 71 ...

Page 132: ...he Associate a Pump box If this box is not checked you must set the pump flow in the instrument method editor for each method The software will also prompt you to check the pump flow before tuning the instrument if you have not associated a pump 28 Use the drop down menus for Manufacturer and Model to choose the proper settings for the pump installed on the system See Figure 72 ...

Page 133: ...SQ EC and ISQ EM Mass Spectrometer Operating Manual Page 133 Figure 72 MS configuration Adding pump information 29 Enter the Main Device and Pump Device names The names must match the ones for the pump See Figure 73 ...

Page 134: ...n Entering the device names 30 Select the OK button and Chromeleon will attempt initial communication with the MS instrument A successful attempt will provide several entries in the instrument configuration audit trail window as shown in Figure 74 below Figure 74 MS instrument audit trail information ...

Page 135: ...6 Operation ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 135 ...

Page 136: ...rmation and values with a default ePanel may be displayed once Chromeleon 7 2 is launched and connects with the configured system This ePanel is termed ISQ EC or ISQ EM If the ePanel is missing please follow the instructions under Adding the MS instrument ePanel below 6 5 1 1 Chromeleon ePanel You should see a user interface similar to what is shown in Figure 75 and Figure 76 depending on whether ...

Page 137: ...tus Displays the main nitrogen gas pressure used for desolvation nebulization Sweep gas pressure status Counter flow gas pressure coming out of sweep cone Used for dirtier sample matrices and more complex mobile phase compositions Aux gas pressure status Gas flow around the outside of the spray needle This gas can be heated to aid in desolvation Vaporizer temp status Heat applied to aux gas to aid...

Page 138: ...ased on the internal reference solution calibrant and provide a result in the Chromeleon audit trail similar to what is shown in Table 6 Parameter Enables direct software control over the MS instrument This can be toggled on or off with the slide bar Tune status Indicates the overall status of the tune experiment Current tune task name Indicates the sub task name currently being performed Current ...

Page 139: ...ure is designed to work based on injection or direct infusion of the analyte s into the MS instrument In order to enter into acquisition mode select the Play button at the top left hand corner of the real time scanning window Once the Play button is pressed the system will allow the user to modify the instrument settings in real time See Table 7 for a list of real time scanning features TIP Ensure...

Page 140: ... Ion transfer tube temp Select the heat applied to transfer tube after the exit cone Vaporizer temp Select the heat applied to the ESI probe out of the manifold for aiding in desolvation Source voltage Select the voltage applied to the ESI capillary for ionization Source CID voltage Voltage applied within the source to induce collisional dissociation Tube lens voltage Select the voltage applied to...

Page 141: ... chromatographic effluent or the reference solution Figure 78 Reference Inlet System To deliver the reference solution to the ion source a 500 µL calibrant loop is first filled by setting the 6 port valve to load and pressurizing a bottle of reference solution Then the 6 port valve is switched back to inject so the flow from the chromatograph pushes the reference solution into the ion source IMPOR...

Page 142: ... µL min 5 From the ISQ EC instrument ePanel select Real Time Scanning 6 Check the Use Calibrant box and press the Play button to initiate infusion of the internal reference solution 7 Flush the system with the mobile phase for 5 min 8 Turn on the calibrant TIP Liquid should be exiting from the valve into the instrument waste stream for several minutes after pressing Play 9 Press Stop The valve and...

Page 143: ... MS instrument is properly connected and controlled by Chromeleon the user may create an instrument method Select create a new method in Chromeleon 7 2 and follow the automated prompts The method editor is divided into two sections source settings top and scan settings bottom Each section has different modes based upon user preference and workflows 6 6 1 Getting Started The ISQ EC and ISQ EM instr...

Page 144: ...s calculate new iterative values from the default setting See Table 8 Parameter Description Use This Detector Select the check box to enable the currently installed detector Installed Probe Type Indicates the installed probe type For an ISQ EC MS the only choice is HESI for an ISQ EM MS the choices are HESI and APCI Method Source Type Set this to the source type for the method you are developing T...

Page 145: ...ss Volatile Mobile Phase Highly Volatile Mobile Phase Slider is used to select whether the mobile phase is volatile or nonvolatile Thermally Stabile Analyte Thermally Labile Analyte Slider is used to select whether analyte is stable or labile unstable Ionic Analyte in Mobile Phase Non Ionic Analyte in Mobile Phase Slider is used to indicate if analytes are ionized in the mobile phase Total Pump Fl...

Page 146: ...nts for the best optimization of the source parameters the user can select the advanced view This will carry over the set values from the easy mode Using the easy mode default settings allows for a convenient starting point for optimization in the advanced mode See Figure 81 TIP Once adjustments are made in the advanced view if the user switches back to the easy settings the closest slider values ...

Page 147: ... C 550 C Ion transfer tube temperature Heat applied to the transfer tube at the source to aid in desolvation and transmission 150 C 400 C Sheath gas pressure Primary gas flow for liquid nebulization 0 psig 80 psig Aux gas pressure Auxiliary heated gas that aids in desolvation 0 psig 15 psig Sweep gas pressure Counter current gas flow at the sweep cone to improve robustness 0 psig 2 psig Source vol...

Page 148: ...s until the desired rate is selected The sampling rate is applied to each scan line item entered in the scan table See Figure 82 Parameter Description Vaporizer temperature Heat applied the auxiliary gas for desolvation 0 C 550 C Ion transfer tube temperature Heat applied to the transfer tube at the source to aid in desolvation and transmission 150 C 400 C Sheath gas pressure Primary gas flow for ...

Page 149: ... Individual masses or multiple values separated by a comma Ion Polarity Indicates whether positive or negative ions are generated Source CID voltage Accelerates ions into the background gas to aid in desolvation Can increase sensitivity or reduce noise for some analytes Range 0 100 V default 0 V no source CID Transfer scans Select button to transfer scan information typed in Basic Mode to Scan Mod...

Page 150: ...s Based on the start and end times the instrument will optimize the dwell time for each SIM entry to maximize ion detection On the right pane there are advanced options Acquisition rates are still determined by the peak width and desired scan per peak entries however this value is now calculated into the corresponding scan dwell times for the table A single full scan is added to the method if the ...

Page 151: ...ge Accelerates ions into the background gas to aid in desolvation Can increase sensitivity or reduce noise for some analytes Range 0 100 V default 0 V no source CID Tube lens voltage Voltage applied to tube lens after the ion transfer tube 0 V 300 V Higher values can aid in desolvation Lower values can reduce fragmentation Can increase sensitivity or reduce noise for some analytes Note Use 0 to 30...

Page 152: ...ease sensitivity or reduce noise for some analytes Range 0 100 V default 0 V no source CID Use last tune tube lens voltage Voltage applied to tube lens after the ion transfer tube 0 V 300 V Higher values can aid in desolvation Lower values can reduce fragmentation Can increase sensitivity or reduce noise for some analytes Note Use 0 to 300 V for positive ions Use 0 to 300 V for negative ions Use h...

Page 153: ...ettings Parameter Description Time min The time the system begins scanning Scan name Description of the scan perhaps the name of the compound being scanned Mass list or range amu The masses the system will scan Full scan mode Start and end mass are separated by a dash SIM mode Individual masses or multiple values separated by a comma Dwell or scan times sec SIM mode the amount of time in seconds t...

Page 154: ... sensitivity or reduce noise for some analytes Range 0 100 V default 0 V no source CID Tube lens voltage Voltage applied to tube lens after the ion transfer tube 0 V 300 V Higher values can aid in desolvation Lower values can reduce fragmentation Can increase sensitivity or reduce noise for some analytes Note Use 0 to 300 V for positive ions Use 0 to 300 V for negative ions Use higher values for h...

Page 155: ...ng to a higher baseline It can be more informative to have narrower mass ranges to start with rather than a scan over the entire mass range of the instrument Some methods require optimal sensitivity There are many factors that can be optimized and will improve instrument sensitivity Selected Ion Monitoring or SIM will give the best performance by increasing the number of analyte ions detected comp...

Page 156: ...n the Chromeleon ISQ EC ePanel 6 6 9 Custom Variables The ISQ EC and ISQ EM support custom variables The variables must match in the sequence and the method See the Chromeleon Help for instructions on setting up custom variables in the instrument method 6 6 10 Chromeleon Audit Trail The Chromeleon audit trail will log numerous informational events for all of the modules in your instrument configur...

Page 157: ...nstrument for a short period short term shutdown for example overnight observe these guidelines for the detector Keep the instrument connected to the system flow path Turn off the pump flow If you operate the instrument from a chromatography data system keep the detector connected to the data system When resuming operation let the flow equilibrate and verify that the operating parameters for the o...

Page 158: ... affects the operation of the system When shutting down the MS also observe the shutdown instructions for the other system modules and take appropriate action refer to the Operating Manuals for the modules To power off follow the instructions below 1 Flush the system with an appropriate pure solvent minimum LC MS grade that does not contain any salts Make sure that residual sample components impur...

Page 159: ...o zero before you continue d Turn off the gas supply to the system 4 Turn off the system with its main power switch Setting Smart Shutdown Parameters To set Smart Shutdown parameters go to the Chromatography Studio and select Smart shutdown Set the shutdown parameters for the MS using the check boxes See Figure 86 Figure 86 Smart Shutdown Parameters Restarting the Mass Spectrometer To restart the ...

Page 160: ...m equilibrate and be sure that it is ready for operation Setting Smart Start Up Parameters To set Smart Start Up parameters go to the Chromatography Studio and select Smart Start Up Set the start up parameters for the MS using the check boxes See Figure 87 Figure 87 Smart Start Up Parameters Using the Chromeleon Queue You can set the post run instrument state for the ISQ EC in the queue In the Chr...

Page 161: ...6 Operation ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 161 Figure 88 Setting the MS state in the Chromeleon queue ...

Page 162: ... Disconnect the data system from the instrument in Chromeleon software 2 Push the power button at the back of the instrument down to the off position to power off the mass spectrometer See Figure 89 Figure 89 Powering off the mass spectrometer 3 Wait 5 minutes 4 Loosen the vent valve knob inside the front door of the instrument next to the source housing See Figure 90 ...

Page 163: ...6 Operation ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 163 Figure 90 Venting the mass spectrometer ...

Page 164: ...tart Port on the MS The Start Port consists of a 6 pin mini DIN connector The pins are used as described in Table 18 Table 18 Correct use of connection pins The MS default polarity is to start on an active low signal pulled to ground to indicate start of run In instrument configuration this can be changed to active high You must configure the autosampler or other modules to output the start signal...

Page 165: ...mber 1R76396 1062 grey pigtail cable Attach remote start cable to a 12 port phoenix connector PN 923686 part of IC ship kit Wiring MS AS AP Pin 6 Pin 10 RLY 4 Port NO Pin 5 Pin 11 RLY 4 Port COM Connect to MS LC IC Start port AS AP RLY port 6 8 4 Integrion Autosampler no AS AP Remote start cable part number 1R76396 1062 grey pigtail cable Attach remote start cable to a 12 port phoenix connector PN...

Page 166: ...6 Operation Page 166 ISQ EC and ISQ EM Mass Spectrometer Operating Manual MS LC IC Start port Integrion RLY port ...

Page 167: ...tenance and Service ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 167 7 Maintenance and Service This chapter describes the routine maintenance and the service procedures that the user may perform ...

Page 168: ...rm 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 The instrument is designed for easy maintenance and service The user serviceable parts can be accessed from the front If not stated otherwise the maintenance procedures do not require that you remove ...

Page 169: ...strument is unplugged AVERTISSEMENT Haute tension Les hautes tensions présentes à l intérieur de l instrument peuvent provoquer un choc électrique N ouvrez le boîtier et ne retirez les panneaux de protection que si l instrument est débranché WARNING Escape of Hazardous Substances from Flow Connections Flow and capillary connections can be filled with substances that can pose health risks Solvent c...

Page 170: ...t ouvertes Portez un équipement de protection approprié et respectez les bonnes pratiques de laboratoire Avant de démarrer les procédures d entretien ou de réparation éliminez les substances dangereuses avec un solvant approprié CAUTION Spraying Solvent Solvents can spray when under high pressure Stop the pump flow prior to opening the flow path Wait until the system pressure is down to zero Wear ...

Page 171: ...age 171 NOTICE Detector Gas Flow and Pump flow Improper handling of detector gas flow and pump flow start and stop can damage the detector When turning on detector gas flow and pump flow turn on the detector gas flow first wait at least 5 minutes and only then turn on the pump flow ...

Page 172: ...rmation see Section 10 3 page 217 Follow all instructions systematically and use the tools recommended for the procedure Before opening the flow path to replace capillaries in the system turn off the pump flow and wait until the system pressure is down to zero Dirty components can contaminate the system Contamination leads to poor performance of the modules and entire system or can even cause dama...

Page 173: ...ct the connections for signs of leakage or blockage Regularly Inspect the connections for damage such as cracks nicks cuts or blockage Check that all warning labels are still present on the detector and clearly legible If they are not contact Thermo Fisher Scientific for replacement Check the drain tubes Check that the drain tubes properly connect to the drain ports on the bottom right side of the...

Page 174: ... preventive maintenance features of the detector provide information about internal parameters and service intervals If a date is expired it appears in red 7 4 3 Cleaning or Decontaminating the Instrument Cleaning and decontamination must be performed by qualified personnel wearing suitable personal protective equipment Always observe national and local regulations NOTICE Wipe up all liquids spill...

Page 175: ... during the cleaning process Wipe the cleaned components thoroughly dry after cleaning Do not operate the detector before it is completely dry ATTENTION Mélanges gazeux explosifs provenant des détergents de nettoyage à base d alcool Les détergents de nettoyage à base d alcool peuvent former des mélanges gazeux explosifs et inflammables lorsqu ils sont exposés à l air N utilisez ce type de détergen...

Page 176: ...ith the electronic components Preparations Turn off the power to the mass spectrometer and disconnect the power cord from the power source Follow these steps 1 Wipe the surfaces clean 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 ...

Page 177: ...to capillary replacement and allow at least 5 minutes for cool down prior to capillary removal Failure to do so may result in physical injury ATTENTION Chaleur excessive Avant de retirer le capillaire pour le remplacer désactivez le chauffage de la sonde puis laissez la refroidir au moins 5 minutes Le non respect de cette consigne peut entraîner des blessures corporelles NOTICE Be sure to wear glo...

Page 178: ...robe temperature on Chromeleon ePanel 6 Stop liquid flow of the front end chromatograph 7 Open the front door and top hatch of the MS instrument 8 Disconnect the PEEK capillary going from the probe to the grounding union as shown in Figure 100 9 Locate the black plastic knob of the ESI probe assembly and slowly turn counter clockwise to remove from the source spray chamber housing as shown in Figu...

Page 179: ...d fitting counter clockwise as shown in Figure 100 Figure 93 Removing the capillary from the ESI probe assembly TIP The old probe is made out of stainless steel and will be discolored from previous use under high temperature conditions This is normal 11 Place the old probe aside and replace with a new probe that ships in the instrument accessory kit 12 During replacement it is important to careful...

Page 180: ... assembly alignment marks on source housing 15 Once the length is correctly adjusted lock the needle in place by turning the top of the probe so it lines up with the square in the spring on the spray probe See Figure 95 Figure 95 Correct needle adjustment 16 Align the pin on the capillary assembly with the slot in the source housing and screw the needle in place See Figure 96 ...

Page 181: ...nd spray probes A turn in or out from the pictured penetration could be correct depending on the tolerances of the probe itself If the beam is unstable try both directions 7 4 5 Replacing the APCI Probe Capillaries for the ISQ EM Follow the instructions in this section to replace the APCI probe capillaries CAUTION Eye Damage Please be sure to wear protective eyewear during the probe replacement pr...

Page 182: ...e la sonde puis laissez la refroidir au moins 5 minutes Le non respect de cette consigne peut entraîner des blessures corporelles NOTICE Be sure to wear gloves during the probe replacement procedure in order to avoid contamination of the capillary and ESI probe assembly Please follow the following procedure in the event that the probe must be replaced 1 Follow all safety precautions as outlined ab...

Page 183: ...ct the PEEK capillary going from the probe to the grounding union as shown in Figure 97 Figure 97 Disconnecting PEEK capillary connection of source at grounding union 9 Locate the black plastic knob of the APCI probe assembly and slowly turn counter clockwise to remove from the source spray chamber ...

Page 184: ...igure 98 Removal of APCI probe assembly TIP The source chamber housing does not need to be removed in order to replace the probe assembly IMPORTANT As the APCI probe assembly is removed from the source chamber housing there will be an audible sound along with a physical change as nitrogen gas escapes into the atmosphere ...

Page 185: ...ng Manual Page 185 10 To remove the capillary from the APCI probe assembly loosen the top of the APCI probe with a 3 8 wrench See Figure 99 Figure 99 Loosening the nut on the APCI probe 11 Use 3 16 wrench to loosen the nut and then unscrew the PEEK fitting See Figure 101 ...

Page 186: ... Spectrometer Operating Manual Figure 100 Removing the capillary from the APCI probe assembly 12 Remove the PEEK fitting See Figure 101 Figure 101 Removing the PEEK fitting 13 Remove the capillary and clear ferrule from the stainless steel nut See Figure 102 ...

Page 187: ... new silica tubing cut to the length of the probe 15 Add the clear ferrule and reinsert the PEEK capillary until it bottom into the stainless steel nut 16 Use the 3 16 wrench to tighten the PEEK fitting 17 Reinsert the capillary into the APCI probe and tighten it with the 3 8 wrench 18 During replacement it is important to carefully thread the capillary back into the APCI assembly body See ...

Page 188: ...ding capillary assembly into APCI probe 19 Align the pin on the APCI probe assembly with the slot in the source housing and screw the probe in place See Figure 104 Figure 104 Aligning the pin on the APCI probe with the source housing 20 Screw the probe into the source housing and reconnect the liquid line ...

Page 189: ...he steps below to replace the APCI needle 1 Follow the instructions for removing the APCI probe in Section 7 4 5 2 Ensure the APCI needle is down so that it can be accessed See Figure 105 Figure 105 Locating the APCI Needle 3 With gloved hands pull the APCI needle out of the source housing and install a new needle See Figure 106 ...

Page 190: ...ction 7 4 6985 5 5 7 4 7 Cleaning the Front Optics Follow the procedure below to remove and clean the front optics of the ISQ EC and ISQ EM mass spectrometers 1 Turn the power off on the mass spectrometer See Section 6 7 2 2 Vent the mass spectrometer See Section 6 7 3 3 Allow the ion transfer tube to cool to a safe temperature 4 Remove the six source housing screws as shown in Figure 107 ...

Page 191: ...ntly screw in the three set screws as shown in Figure 108 Screwing in the set screws The set screws will push the cone assembly out of the instrument Figure 108 Screwing in the set screws 6 The cone should move out enough to break the internal seal Once that occurs remove the cone and front optics by hand See Figure 109 View of front optics with seal broken ...

Page 192: ...ctrometer Operating Manual Figure 109 View of front optics with seal broken 7 Set in on a piece of aluminum foil or other sterile surface See Figure 110 Figure 110 View of removed optics 8 Remove the ion transfer tube See Figure 111 Removing the ion transfer tube ...

Page 193: ... transfer tube 9 Remove the three screws that hold the Q00 L0 assembly to the PEEK piece Then remove the Q00 L0 assembly See Figure 112 Figure 112 Removing the Q00 L0 assembly 10 Insert the pegs on the L0 removal tool included in the accessory kit into the two holes on L0 See Figure 113 L0 with removal tool in place ...

Page 194: ...r Operating Manual Figure 113 L0 with removal tool in place 11 Turn L0 using the tool until the rectangular slots line up with the beryllium copper fingers Turn the Q00 L0 assembly upside down and L0 should come off the assembly See Figure 114 L0 separated from assembly ...

Page 195: ...meter Operating Manual Page 195 Figure 114 L0 separated from assembly 12 Using your thumb push on the tapered side of Q00 to remove it from the cage holding it See Figure 115 Removing Q00 from cage assembly This step takes a fair bit of force Do not drop Q00 ...

Page 196: ...eter Operating Manual Figure 115 Removing Q00 from cage assembly 13 Q00 and L0 should now be separate from the cage assembly See Figure 116 Figure 116 Q00 and L0 14 Using a small Allen key unscrew the PEEK piece between the jumper wires Remove the piece See Figure 117 ...

Page 197: ...meter Operating Manual Page 197 Figure 117 Removing the PEEK piece between the jumper wires 15 Very carefully unplug the two jumper wires that connect to the skimmer and tube lens See Figure 118 Removing the Jumper Wires Figure 118 Removing the Jumper Wires ...

Page 198: ...on so if you unplugged the wire in the previous step it should just take a little bit of force to remove it See Figure 119 Figure 119 Removing the Skimmer Cone 17 Remove the three screws holding the tube lens in place To remove the tube lens press on the electrical pin through the second hole where the jumper was unplugged using a tool like an Allen wrench See Figure 120 Figure 120 Removing Tube L...

Page 199: ...r and Liquinox for 5 to 10 minutes c Rinse the optics parts using 18 MΩ or Optima LCMS grade water d Sonicate the optics parts in 18 MΩ or Optima LCMS grade water for 5 to 10 minutes e Rinse the optics parts using Optima LCMS grade methanol f Sonicate the optics parts in Optima LCMS grade methanol g Blow the optics parts dry with nitrogen gas h Reverse the steps above to reassemble the optics and ...

Page 200: ...mage the bezel or the instrument ATTENTION Charge lourde appareil volumineux L instrument est trop lourd ou encombrant pour être soulevé ou déplacé par une personne seule Au moins deux personnes doivent le soulever pour le transférer de la caisse d expédition à la paillasse Pour éviter les blessures et les dommages à l instrument respectez les consignes suivantes Deux personnes sont nécessaires po...

Page 201: ...s that stand on top of the detector in the system stack 2 Remove the mass spectrometer from the system stack The following steps require a team effort a Take the mass spectrometer on both sides and lift it slightly b Grasp the mass spectrometer from below and lift it from the stack c Place the mass spectrometer on a clean and stable surface ...

Page 202: ...ious version Items required Firmware version Chromeleon Service Release as appropriate TIP When a new firmware version is released the new version will be included in the next available Chromeleon Service Release The new firmware will not be transferred automatically to the device when you install the Chromeleon Service Release Preparations Read the release notes provided with the firmware and or ...

Page 203: ...ware and the MS at any time during the procedure At the beginning of the update process a message appears showing the firmware version currently installed in the detector and the version that will be transferred from the Chromeleon software If the firmware installed in the detector is a later version than the version in Chromeleon cancel the download The firmware update may take several minutes Mo...

Page 204: ...7 Maintenance and Service Page 204 ISQ EC and ISQ EM Mass Spectrometer Operating Manual ...

Page 205: ...8 Troubleshooting ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 205 8 Troubleshooting This chapter is a guide to troubleshooting issues that may arise during operation of the instrument ...

Page 206: ... Scientific Status Indicator on the Instrument Display The instrument display provides an overview of the instrument status If no warnings are active the Status is Normal Troubleshooting Check If a problem occurs with the instrument performing a troubleshooting check helps identifying and isolating the cause of the problem Warning and Error Codes If a problem occurs during operation of the detecto...

Page 207: ...arning code and a message on the display Follow the instructions in this manual to find and eliminate the source for the leakage For information on all operating issues that may occur and affect detector performance see Chapter 6 Operation TIP The Diagnostics screen provides helpful information for troubleshooting if a problem occurs in the mass spectrometer If other values are subject to fluctuat...

Page 208: ...rospray needle Adjust electrospray needle Autotune runs for a while but then fails The flow rate out of the liquid pump is unstable AXP pumps in particular require high back pressures to provide a stable flow When using an AXP pump backpressure coils should be installed between the pump and the instrument to allow the pump to run at a stable flow rate Reference solution not flowing down the drain ...

Page 209: ...f the calibrant delivery system may be clogged This valve is located on the gas control module under the main power supply inside of the instrument Reference solution does not stop flowing after fill time The waste line may be inserted too far down the drain tube This will cause the liquid to be siphoned from the bottle Table 20 Autotune problems TIP If you are unable to resolve a problem followin...

Page 210: ... leaky source gases try tightening the spray chamber pins 1 Shut down and vent the instrument as described in Section 6 7 2 Remove the source housing as described in Section 5 5 5 3 Check if the spray chamber pins are tight If they are loose use a T10 screwdriver to tighten the spray chamber guide pins as shown in Figure 122 Figure 122 Tightening spray chamber pins ...

Page 211: ... EC and ISQ EM Mass Spectrometer Operating Manual Page 211 9 Specifications This chapter provides the physical and performance specifications including information about the materials used in the flow path of the detector ...

Page 212: ... use Indoor use only Ambient temperature 15 35 C Ambient humidity 20 80 relative humidity non condensing Pollution degree 2 Power requirements 230 10 or 120 6 10 V AC 50 60 Hz 15A Overvoltage category II Emission sound pressure level 70 dB A Dimensions height x width x depth 52 x 42 x 91 cm 20 5 x 16 5 x 36 in Weight Approx 71 kg 156 lbs Table 21 Physical Specifications of the ISQ EC and ISQ EM Ma...

Page 213: ...ting Manual Page 213 10 Accessories Consumables and Replacement Parts This chapter describes the standard accessories that are shipped with the detector and the accessories that are available as an option This chapter also provides information for reordering consumables and replacement parts ...

Page 214: ... with the replacement 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 215: ...ent 15 ft 1R76396 0052 1 Fuse kit 1R120458 0001 1 Grounding union 1R76256 0090 1 Cotton tipped swabs A0301 0200 1 pack PEEK tubing red 1 16 in OD 0 005 in ID 5 ft 1R76433 3006S 1 PEEK tubing green 1 16 in OD 0 030 in ID 5 ft 1R76433 3007S 1 Nut 1 4 in brass 1R4038 0004 2 Ferrule 1 4 in back brass 1R4039 0015 2 Ferrule 1 4 in front brass 1R4039 0004 2 Fitting fingertight 1 piece 1R4034 0020 4 Fitti...

Page 216: ...Spray Needle HESI II 80000 60317 1 Foreline pump tray 1R7800 0032 1 Bulkhead LC IC Input PEEK 1R4035 0600 1 Oil mist filter connects to oil return kit 1R76505 0037 1 Oil return kit connects to oil mist filter 1R76505 0022 1 Vacuum hose clamp NW25 1R76505 2002 2 O ring with centering ring NW25 1R76505 2001 2 Hose adapter NW25 to 1 in 1R76505 5004 2 Hose clamp 21 38 mm 1R4120 0003 2 Sweep cone 1R120...

Page 217: ...EK Tubing Green 1 16 in OD 0 03 in ID 5 ft PEEK Tubing Red 1 16 in OD 0 003 in ID 5 ft Replacement Rubber Slit Top Left Corner of Instrument 80000 60317 Spray Needle HESI II spare included in installation kit 80000 60321 Spray Probe HESI II 1R120590 0032 HESI Spray Chamber full assembly 1R120590 0024 HESI APCI Spray Chamber Assembly ISQ EM only 80000 60165 Spray Probe APCI ISQ EM only 1R76022 1463...

Page 218: ...utter 1 16 PEEK Tubing Cutter 1 8 Plastic Tubing Cutter Large Hose Tool Ion Transfer Tube Removal Tool Lens 0 Removal 1R120554 0010 Fan Filter for Electronics Fan Left Side 1R76475 5002 Fan Filter for Turbomolecular Pump Fan right side 1R120590 6063 Front Lower Bezel with front LED board 1R120590 6064 ISQ EC Front Door 1R120590 6085 ISQ EM Front Door 1R120590 0007 Top Hatch 1R120590 0021 Top Cover...

Page 219: ... Tubing Foreline Pump Exhaust 1R78001 0026 Source Exhaust 90 Elbow Connector 1R120590 6226 Communications Cable Kit Cable Shielded 10 Base T Crossover 15 ft Cable Remote Start for Vanquish Cable Remote Start for Ultimate 3000 Cable Remote Start for IC or other module USB 3 0 to Gigabit Ethernet Adapter Cable Internal Ethernet Patch Cable 15 in 1R120590 6040 Front Cone and Q00 Assembly 1R120590 207...

Page 220: ...ss cover 1R120590 2178 Skimmer Cone 1R76505 0022 Oil Return Kit Connects to oil mist filter 70005 98033 Corona APCI Needle ISQ EM only 1R120590 2809 APCI Needle Switch Knob ISQ EM only 1R120590 6207 APCI Kit ISQ EM only 1R120590 6208 APCI Spare Parts Kit ISQ EM only 1R76505 0037 Oil Mist Filter Connects to oil return kit A0301 15101 Vacuum Pump Oil 1R76505 3010 Foreline Pump 1R120590 6227 Foreline...

Page 221: ...11 Appendix ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 221 11 Appendix This chapter provides additional information about compliance ...

Page 222: ...t the product is compliant with the directive China RoHS regulations Measures for Administration of the Pollution Control of Electronic Information Products One of following logos may be present on the device if applicable The green logo marks items that do not contain the hazardous substances identified by the regulations The orange logo including a one digit or two digit number mark items that c...

Page 223: ...Electrical Electronic Equipment WEEE Directive 2002 96 EC It is marked with the following symbol Figure 123 WEEE symbol Thermo Fisher Scientific has contracted with one or more recycling or disposal companies in each European Union EU Member State and these companies should dispose of or recycle this product For further information contact Thermo Fisher Scientific ...

Page 224: ...reasonable protection against harmful interference when the equipment is operated in a commercial environment This equipment generates uses and can radiate 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 c...

Page 225: ...nt parts and additional components options and peripherals must be ordered from Thermo Fisher Scientific or one of its authorized representatives 11 1 5 Low Voltage Safety Compliance This device complies with Low Voltage Directive 2014 35 EU and harmonized standard EN 61010 1 2001 11 1 6 Notice on Lifting and Handling of Thermo Scientific Instruments For your safety and in compliance with internat...

Page 226: ...11 Appendix Page 226 ISQ EC and ISQ EM Mass Spectrometer Operating Manual phones in close proximity to the instrument For manufacturing location see the label on the instrument ...

Page 227: ...eter Operating Manual Page 227 11 1 9 Manual Release History Revision Released Covering A August 2017 ISQ EC MS B December 2017 ISQ EC MS C October 2018 ISQ EC MS ISQ EM MS D December 2018 ISQ EC MS ISQ EM MS E February 2019 ISQ EC MS ISQ EM MS ...

Page 228: ...12 Index Page 228 ISQ EC and ISQ EM Mass Spectrometer Operating Manual 12 Index ...

Page 229: ...12 Index ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 229 ...

Page 230: ...171 maintenance plan 171 O oil mist filter 69 77 84 90 operating principle 40 operation 43 117 interrupt 155 overview functional 39 P Power cord 28 55 56 57 60 94 114 174 preventive maintenance 172 protective clothing 27 R regulatory compliance 38 reordering 210 replacement parts 210 RoHS mark 219 S safety glasses 27 safety guidelines electrical safety 28 general 23 general hazards 29 installation...

Page 231: ...12 Index ISQ EC and ISQ EM Mass Spectrometer Operating Manual Page 231 T troubleshooting 202 U unpack 45 V ventilation 63 W WEEE 220 ...

Page 232: ...Thermo Fisher Scientific Inc 168 Third Avenue Waltham Massachusetts 02451 USA www thermofisher com ...

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