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SCIEX 3200 QTRAP, System User'S Manual

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Table A-3 Masses for Q1 and Q3 PPG Scans

System

Masses

Positive Mode

API 3200 LC-MS/MS system

59.05

175.13

616.46

906.67

1,254.93

1,545.13

3200 QTRAP LC-MS/MS system

59.05

175.13

616.46

906.67

1,254.93

1,545.13

Negative Mode

API 3200 LC-MS/MS system

45.00

585.39

933.64

1,223.85

1,572.10

1,863.31

3200 QTRAP LC-MS/MS system

45.00

585.39

933.64

1,223.85

1,572.10

N/A

Table A-4 Masses and Polarity for LIT Scans (PPG 3000)

Instrument/ Polarity

Masses

Positive

115.1

500.4

1080.8

1661.2

Negative

121.1

585.4

991.8

1630.1

Calibration Ions and Solutions

System User Guide

RUO-IDV-05-6475-C

SCIEX 3200 Systems

83/114

Summary of Contents for 3200 QTRAP

Page 1: ...SCIEX 3200 Systems System User Guide RUO IDV 05 6475 C February 2022...

Page 2: ...to use such manufacturers and or their product names as trademarks SCIEX warranties are limited to those express warranties provided at the time of sale or license of its products and are the sole and...

Page 3: ...tions 14 Environmental Precautions 14 Electromagnetic Environment 14 Decommissioning and Disposal 16 Qualified Personnel 16 Laboratory Conditions 17 Safe Environmental Conditions 17 Performance Specif...

Page 4: ...Position 48 Diverter Valve 48 Plumb the Diverter Valve in Injector Mode 49 Plumb the Diverter Valve in Diverter Mode 50 Shut Down and Vent the System 52 6 Operating Instructions User Workflows 53 7 Se...

Page 5: ...egion 88 C Ion Source Optimization 90 TurboIonSpray Probe Optimization 90 Set Up the System 91 Prepare the System 91 APCI Probe Optimization 91 Set Up the System 92 Prepare the System 92 Set the Start...

Page 6: ...s 104 F Glossary of Warnings 110 Contact Us 113 Customer Training 113 Online Learning Center 113 SCIEX Support 113 CyberSecurity 113 Documentation 113 Contents SCIEX 3200 Systems 6 114 System User Gui...

Page 7: ...in this document the manufacturer chemical safety data sheets SDSs and product label information Labels are shown with internationally recognized symbols Failure to heed these warnings could result i...

Page 8: ...of Conformity included with the system and the individual system components Applicable labels have been affixed to the system Australia and New Zealand Electromagnetic Compatibility EMC Radio Communic...

Page 9: ...nd Packaging Waste Directive 94 62 EC RoHS Restriction of Hazardous Substances RoHS Directive 2011 65 EU United States Radio Emissions Interference Regulations 47 CFR 15 as implemented in FCC Part 15...

Page 10: ...or the installation of all of the electrical supplies and fixtures and make sure that all of the installations adhere to local regulations and safety standards WARNING Electrical Shock Hazard Make sur...

Page 11: ...Connect the drain tubing to the mass spectrometer and the source exhaust drain bottle properly to prevent leaks Determine which chemicals have been used in the system prior to service and regular mai...

Page 12: ...on Required Materials CAUTION Potential System Damage Do not use any other fluid until confirmation is received from SCIEX that it does not present a hazard This is not an exhaustive list Note Use onl...

Page 13: ...ard Do not operate the mass spectrometer if the source exhaust drain and roughing pump exhaust hoses are not properly connected to the laboratory ventilation system Examine the exhaust tubing regularl...

Page 14: ...ontaining explosive gases The system is not designed for operation in an explosive environment WARNING Biohazard For biohazardous material use always comply with local regulations for hazard assessmen...

Page 15: ...Equipment Equipment which is suitable for use in all establishments other than domestic and those directly connected to a low voltage power supply network which supplies buildings used for domestic p...

Page 16: ...unicipal waste ordinances for proper disposal provisions to reduce the environmental impact of waste electrical and electronic equipment WEEE To safely dispose of this equipment contact a local Custom...

Page 17: ...re must remain within a range of 4 C 7 2 F with the rate of the change in temperature not exceeding 2 C 3 6 F per hour Ambient temperature fluctuations exceeding the limits might result in mass shifts...

Page 18: ...Crushing Hazard Wear protective footwear when moving heavy objects Use the system indoors in a laboratory that complies with the environmental conditions recommended in the mass spectrometer document...

Page 19: ...Operator Guide For information on the computer and software refer to the document Software Installation Guide for the software System Overview The 3200 series of instruments includes the following com...

Page 20: ...rails bronze bearings 2 Integrated Switching Valve Stainless steel plastic tubing fittings valve body PEEK tubing fittings 3 Ion Source Stainless steel tubing fittings heat shield micrometer bronze l...

Page 21: ...PVC cable 3 Roughing Pump Connection Aluminum hose fitting Zn plated steel hose clamps 4 I O Panel N A 5 Gas Panel Stainless steel tubing fittings 6 Ion Source Stainless steel tubing fittings heat sh...

Page 22: ...nce Switch 2 AC Mains Supply Inlet Sample Introduction Features and Status Indicators This section describes the features and controls on the front left of the mass spectrometer beside the ion source...

Page 23: ...optimization using FIA or for diverting LC flow when any precipitate or salts initially come off the LC column Below that an integrated syringe pump is available for infusing standards when the syste...

Page 24: ...m Serial port Ion source port AUX I O outlet IEEE 488 GPIB port provides a connection to the acquisition computer Figure 2 5 I O Panel Gas Panel The gas panel contains the gas supply connections and t...

Page 25: ...tain Gas Supply Max 60 PSIG 2 Sheath Gas Max 105 PSIG 3 Exhaust Supply 55 60 PSIG 4 Exhaust Waste Out 5 Valve Waste Out 6 CAD Gas Max 60 PSIG 7 Gas 1 Gas 2 Max 105 PSIG Principles of Operation System...

Page 26: ...roduces singly and multiply charged ions in a relatively mild condition so that it is suitable for a wide range of compounds including small molecules such as drugs or pesticides and larger molecules...

Page 27: ...ated by the ion source without significant contamination and the flash vaporization of the sprayed effluent allows up to 100 water to be used The probe can accept the entire effluent without splitting...

Page 28: ...temperature to 750 C depending on liquid flow Liquid flow inlet 5 L min to 3 000 L min 200 L min to 3 000 L min Ion source gas 1 ion source gas 2 Refer to the mass spectrometer document Site Planning...

Page 29: ...inlet area of the ion source APCI Probe The APCI probe consists of 100 m inner diameter i d 0 004 inch stainless steel tubing surrounded by a flow of nebulizer gas Gas 1 The liquid sample stream is p...

Page 30: ...e inlet area of the ion source Gas and Electrical Connections Gas and low and high voltage electrical connections are provided on the front plate of the vacuum interface and they connect internally th...

Page 31: ...C system until functionality of the source exhaust system has been restored WARNING Fire Hazard Do not direct more than 3 mL min of flammable solvent in the ion source Exceeding the maximum flow rate...

Page 32: ...e the source exhaust system periodically to make sure that the exhaust tubing is intact and that exhaust is not leaking in the room Theory of Operation Mass spectrometry measures the mass to charge ra...

Page 33: ...xit lens to which a DC barrier voltage is applied After the fill time elapses a time defined by the user or determined by the Dynamic Fill Time feature a DC barrier voltage is applied to the Q3 entran...

Page 34: ...es the ion source and shows the ion source identification Required Materials Ion source TurboIonSpray probe Optional APCI probe Red PEEK tubing 0 005 inch bore Prepare for Installation WARNING Punctur...

Page 35: ...nstalled in the ion source then the high voltage power for the mass spectrometer and source exhaust system is turned off 1 Make sure that the corona discharge needle tip is pointed away from the curta...

Page 36: ...s finger tight 3 Connect the other end of the tubing to the grounding union on the ion source Install the Ion Source on the Mass Spectrometer WARNING Electrical Shock Hazard Install the probe in the i...

Page 37: ...interface making sure that the guide pins on the ion source are aligned with the sockets in the vacuum interface 3 Push the ion source gently against the vacuum interface and then rotate the ion sourc...

Page 38: ...al protective equipment including a laboratory coat gloves and safety glasses to avoid skin or eye exposure Inspect fittings and tubing to make sure that there are no leaks Ion Source Installation SCI...

Page 39: ...om the room Dispose of sharps following established laboratory safety procedures Optimize the ion source whenever the analyte flow rate or mobile phase composition changes When optimizing ion source d...

Page 40: ...e than 3 mL min of flammable solvent in the ion source Exceeding the maximum flow rate can cause solvent to accumulate in the ion source Do not use the ion source if the source exhaust system is not e...

Page 41: ...Source Parameters and Voltages Set Up the System 1 Configure the LC pump to deliver the mobile phase at the required flow rate Refer to the section Source Parameters and Voltages 2 Connect the groundi...

Page 42: ...apors from escaping from the source The electrode must not be recessed within the probe WARNING Puncture Hazard Be careful when handling the electrode The tip of the electrode is extremely sharp After...

Page 43: ...At lower flow rates the probe should be closer to the aperture At higher flow rates the probe should be farther from the aperture 6 Adjust the black electrode adjustment nut on the probe to move the...

Page 44: ...o achieve the best signal or signal to noise ratio 2 Increase the flow rate of the gas for the Curtain Gas interface until the signal begins to decrease Note To prevent contamination use the highest p...

Page 45: ...ure that the electrode protrudes beyond the tip of the probe to prevent hazardous vapors from escaping from the source The electrode must not be recessed within the probe CAUTION Potential System Dama...

Page 46: ...horizontal micrometer setting to direct the liquid spray from the probe away from the aperture to Prevent contamination of the aperture Prevent piercing of the flow of gas for the Curtain Gas interfac...

Page 47: ...ct SCIEX for a copy of the Site Planning Guide if required For contact information go to sciex com contact us The source exhaust gas compressed air and nitrogen gases are connected to the mass spectro...

Page 48: ...Figure 2 1 1 Press the Release button on the right side of the syringe pump to lower the base and then insert the syringe 2 Make sure that the end of the syringe is flush with the base and that the sh...

Page 49: ...verter Valve in Injector Mode When the valve is in Position A the sample flows through the external loop When the valve switches to Position B the sample is injected Plumb the valve for Injector mode...

Page 50: ...to the mass spectrometer if a column is not installed Plumb the Diverter Valve in Diverter Mode When the valve is in Position A the sample flow goes to the mass spectrometer When the valve switches to...

Page 51: ...Figure 5 3 Diverter Valve Diverter Mode Position A Figure 5 4 Diverter Valve Diverter Mode Position B Operating Instructions System User Guide RUO IDV 05 6475 C SCIEX 3200 Systems 51 114...

Page 52: ...before shutting down the system 2 Turn off the sample flow to the system 3 Close the software 4 Follow these steps to vent the system a Press and hold the Vent button for three seconds The Vacuum LED...

Page 53: ...ftware User Guide or Help System Create projects and data folders Software User Guide or Help System Configure the LC devices Software User Guide or Help System Tune the mass spectrometer Software Use...

Page 54: ...ults Software User Guide or Help System Explore data Software User Guide or Help System Review logs Software User Guide or Help System Operating Instructions User Workflows SCIEX 3200 Systems 54 114 S...

Page 55: ...dule for cleaning and maintaining the system Tip Perform maintenance tasks regularly to make sure that the system is performing optimally Perform periodic gas leakage tests and general maintenance ins...

Page 56: ...Level Contact the local QMP or FSE to add oil if required Card cage air filter Every 6 months Replace Contact the local QMP or FSE Roughing pump oil Every 6 months or as needed Replace Contact the lo...

Page 57: ...skimmer and Q0 region if system sensitivity degrades Tip Clean the Q0 region regularly to minimize the impact of charging a significant loss of sensitivity of the ions of interest over a short period...

Page 58: ...ncluding the front of the orifice plate If routine cleaning does not resolve issues with sensitivity then a full cleaning might be necessary This section provides instructions for performing routine c...

Page 59: ...Manufacturer Optional Polyester poly swabs Tools and Supplies Available from the Manufacturer Table 7 3 Description Part Number Small poly swab thermally bonded Also available in the Cleaning kit 1017...

Page 60: ...ng Prepare and store all of the organic solutions and organic containing solutions in very clean glassware only Never use plastic bottles Contaminants can leach from these bottles and further contamin...

Page 61: ...become hot during operation CAUTION Potential System Damage Do not drop anything in the source drain when the ion source is removed Figure 7 2 Source Drain on the Vacuum Interface 1 Deactivate the har...

Page 62: ...hree retaining ball catches mounted on the orifice plate Tip If the curtain plate does not immediately separate from the orifice plate then turn the curtain plate slightly less than 90 degrees to rele...

Page 63: ...until the orifice plate is dry 4 Inspect the orifice plate for solvent stains or lint removing any residue with a clean slightly damp lint free wipe Note Persistent spotting or filming is an indicato...

Page 64: ...t the laboratory has appropriate air exchange for the work performed Note Make sure that there are no kinks sags or twists in the source waste line Inspect the source exhaust drain bottle regularly an...

Page 65: ...n 1 Connection to vent 2 Source exhaust drain tubing 2 5 cm 1 0 inch inner diameter i d 3 Roughing pump exhaust hose 3 2 cm 1 25 inch i d Service and Maintenance Information Mass Spectrometer System U...

Page 66: ...om the cap 5 Remove the cap from the drain bottle 6 Empty the drain bottle and then dispose of the waste according to laboratory procedures and local waste regulations 7 Install the cap on the bottle...

Page 67: ...ioning information To disconnect power from the mass spectrometer remove the mains supply connector from the AC mains supply Note The ion source and mass spectrometer must be transported and stored at...

Page 68: ...ce Use appropriate personal protective equipment and absorbent wipes to contain the spill and dispose of it following local regulations WARNING Electrical Shock Hazard Avoid contact with the high volt...

Page 69: ...n source components regularly to keep the ion source in good working condition CAUTION Potential System Damage Use only the recommended cleaning methods and materials to avoid damaging the equipment R...

Page 70: ...leave the system on The ion source can be removed quickly and easily without tools Always remove the ion source from the mass spectrometer before performing any maintenance on the ion source or exchan...

Page 71: ...ly regardless of the type of compounds sampled Do this by setting up a method in the control software specifically for performing a flushing operation 1 Change to a mobile phase that is 1 1 water acet...

Page 72: ...ample tubing nut and then disconnect the sample tubing from the probe 2 Loosen the retaining ring that secures the probe on the ion source housing 3 Gently pull the probe straight up out of the tower...

Page 73: ...cription 1 Electrode adjustment nut 2 1 4 inch retaining nut 3 Spring 4 Retaining ring 5 Sprayer tube 6 Electrode tip 7 Electrode tube 8 PEEK union 3 Pull the PEEK union and the attached electrode tub...

Page 74: ...section Ion Source Installation 14 Connect the sample tubing Refer to the section Connect the Ion Source Tubing 15 Adjust the electrode tip extension Refer to the section Optimize the TurboIonSpray P...

Page 75: ...ponents 3 Gently pull the corona discharge needle down through the exhaust chimney to remove it 4 Insert the new needle through the exhaust chimney in the ceramic sleeve as far as possible 5 Holding a...

Page 76: ...Replace the sample tubing with an appropriate length of tubing cut with a proper tubing cutter Refer to the section Connect the Ion Source Tubing 3 Install the ion source Refer to the section Ion Sour...

Page 77: ...applicable A system fault has occurred because the vacuum pressure is too high 1 The oil level is too low 2 There is a leak 3 The wrong orifice plate is installed 1 Inspect the oil level in the rough...

Page 78: ...cked Contact the local QMP or FSE The control software indicates that the APCI probe is in use but the TurboIonSpray probe is installed The F3 fuse is blown Contact an FSE The spray is not uniform The...

Page 79: ...lace the fittings if leaks continue 4 Install and optimize an alternate ion source 5 Contact an FSE if the issue persists Arcing or sparks occur The position of the corona discharge needle is incorrec...

Page 80: ...olve the issue then install and optimize an alternate ion source There is an issue with the LC system or connections Troubleshoot the LC system The electrode is dirty or blocked Replace the electrode...

Page 81: ...ource and front end 1 Analyst software Make sure that the interface heater is on 2 Infuse or inject 50 50 methanol water with a pump flow rate of 1 mL min 3 In the control software set the temperature...

Page 82: ...libration Resolution Optimization Scan Type Frequency Frequency Q1 and Q3 3 months to 6 months 3 months to 6 months LIT 3 months to 6 months 3 months to 6 months Table A 2 Suggested Tuning Solutions f...

Page 83: ...545 13 Negative Mode API 3200 LC MS MS system 45 00 585 39 933 64 1 223 85 1 572 10 1 863 31 3200 QTRAP LC MS MS system 45 00 585 39 933 64 1 223 85 1 572 10 N A Table A 4 Masses and Polarity for LIT...

Page 84: ...s in the droplet dispersion Ions of a single polarity are preferentially drawn in the droplets by the high voltage as they are separated from the liquid stream However this separation is incomplete an...

Page 85: ...sitivities of any given organic ion to ion evaporation are difficult to predict The importance of solvation energy is evident because surfactants that concentrate at the surface of a liquid can be det...

Page 86: ...electrons on the major neutral components of air Although NO is normally not a major constituent of clean air the concentration of this species in the ion source is enhanced due to neutral reactions i...

Page 87: ...6 Interface x solvent molecules M sample molecules The sample molecules are ionized through a process of proton transfer in Positive polarity and by either electron transfer or proton transfer in Neg...

Page 88: ...ry ions for example N2 and O2 are created by the loss of electrons that originate in the plasma in the immediate vicinity of the discharge needle tip The energy of these electrons is moderated by a nu...

Page 89: ...ny subsequent collisions occur The formation of both product ions and reactant ions is governed by equilibrium conditions at 760 torr atmospheric operating pressure The APCI probe functions as a wall...

Page 90: ...that the electrode protrudes beyond the tip of the probe to prevent hazardous vapors from escaping from the source The electrode must not be recessed within the probe CAUTION Potential System Damage I...

Page 91: ...m up for 30 minutes The 30 minute warm up stage prevents solvent vapors from condensing in the cold probe 5 Start the solvent flow and sample injection APCI Probe Optimization WARNING Ionizing Radiati...

Page 92: ...ions Note When using the APCI probe make sure that the corona discharge needle is pointing toward the aperture Set Up the System 1 Configure the LC pump to deliver the mobile phase at the required flo...

Page 93: ...s 1 in increments of five to achieve the best signal or signal to noise ratio 2 Increase the flow rate of the gas for the Curtain Gas interface until the signal starts to decrease Note To prevent cont...

Page 94: ...g Radiation Hazard Biohazard or Toxic Chemical Hazard Make sure that the electrode protrudes beyond the tip of the probe to prevent hazardous vapors from escaping from the source The electrode must no...

Page 95: ...software monitor the signal or signal to noise of the analytes 3 Use the horizontal micrometer to adjust the probe in small increments to achieve the best signal or signal to noise ratio 4 Use the ve...

Page 96: ...sition method regardless of the ion source selection position Start with a nebulizer current value of 3 and then increase or decrease it to achieve the best signal or signal to noise ratio The nebuliz...

Page 97: ...djust the ion source temperature in increments of 50 C to 100 C to achieve the best signal or signal to noise ratio Ion Source Optimization System User Guide RUO IDV 05 6475 C SCIEX 3200 Systems 97 11...

Page 98: ...ium High LC flow rate 5 L min to 50 L min 200 L min 1 000 L min 5 L min to 3 000 L min Ion source gas 1 nebulizer gas 20 psi to 40 psi 40 psi to 60 psi 40 psi to 60 psi 0 psi to 90 psi Ion source gas...

Page 99: ...min Ion source gas 1 nebulizer gas 30 psi 0 psi to 90 psi Gas for the Curtain Gas interface 20 psi 20 psi to 50 psi Ion source temperature3 400 C 100 C to 750 C Nebulizer current Positive 3 A Negativ...

Page 100: ...tain gas Controls the flow rate of the gas for the Curtain Gas interface The Curtain Gas interface is located between the curtain plate and the orifice It prevents ambient air and solvent droplets fro...

Page 101: ...ets are expelled into the ion source housing If the ion source temperature is set too high then solvent might vaporize prematurely at the probe tip especially if the probe is set too low 5 to 13 Ion s...

Page 102: ...bility of the spray and the sensitivity In the Analyst software this is the IonSpray Voltage field Interface heater This parameter is always on for 3200 series systems Turns the interface heater on an...

Page 103: ...used because they complicate the spectrum with their ion mixtures and cluster combinations They might also suppress the strength of the target compound ion signal Triethyl amine TEA Sodium phosphate...

Page 104: ...omplies with Australian Communications Media Authority ACMA EMC Requirements Alternating current A Amperes current Asphyxiation Hazard Authorized representative in the European community Biohazard CE...

Page 105: ...be immediately recycled The circling arrows indicate the product is recyclable The date code on the label or product indicates the date of manufacture China RoHS logo The device does not contain toxic...

Page 106: ...y symbol Caution risk of electric shock ISO 3864 also known as High Voltage symbol If the main cover must be removed then contact a SCIEX representative to prevent electric shock Hot Surface Hazard In...

Page 107: ...eed 99 Keep upright Lacerate Sever Hazard Laser Radiation Hazard Lifting Hazard Magnetic Hazard Manufacturer Moving Parts Hazard Pacemaker Hazard No access to people with pacemakers Pinching Hazard Gl...

Page 108: ...66 kPa to 103 kPa Transport and store the system within 75 kPa to 101 kPa Transport and store the system within the specified minimum min and maximum max levels of relative humidity noncondensing Tran...

Page 109: ...d United Kingdom Conformity Assessment Mark VA Volt Ampere power V Volts voltage WEEE Do not dispose of equipment as unsorted municipal waste Environmental Hazard W Watts yyyy mm dd Date of manufactur...

Page 110: ...nce This device complies with Part 15 of the FCC Rules Operation is subject to the following conditions 1 this device may not cause harmful interference and 2 this device must accept any interference...

Page 111: ...RED TO SAFELY LIFT THIS EQUIPMENT MINIMUM OF SIX PERSONS REQUIRED TO SAFELY LIFT THIS EQUIPMENT TIP TELL Tilt Indicator Note Indicates whether the container was tipped or mishandled Write on the Bill...

Page 112: ...ABLE PARTS INSIDE REFER SERVICING TO QUALIFIED PERSONNEL WARNING NO USER SERVICEABLE PARTS INSIDE REFER SERVICING TO QUALIFIED PERSONNEL Note Consult instructions for use Glossary of Warnings SCIEX 32...

Page 113: ...s about the system or any technical issues that might arise For more information visit the SCIEX website at sciex com or contact us in one of the following ways sciex com contact us sciex com request...

Page 114: ...umentation refer to the Customer Reference DVD that comes with the system or component The latest versions of the documentation are available on the SCIEX website at sciex com customer documents Note...

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