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Chapter 3: Annotated Figures of CyTOF XT Components

Main Components of the CyTOF XT Instrument

CyTOF XT User Guide

Other Components of CyTOF XT

Part

Image

Location

AC distribution box

Right side of CyTOF XT

™

system

Sampler cone

Inside the vacuum interface

Skimmer-reducer
assembly

Inside the vacuum interface

Summary of Contents for CyTOF XT

Page 1: ...FLDM 00254 Rev 03...

Page 2: ...e The purchase of this Fluidigm Instrument and or Consumable product conveys to the purchaser the limited nontransferable right to use with only Fluidigm Consumables and or Instruments respectively ex...

Page 3: ...nd Acquisition Data File Format 36 Data Acquisition and Analysis 37 Chapter 3 Annotated Figures of CyTOF XT Components 38 Main Components of the CyTOF XT Instrument 38 CyTOF XT Status Panel 39 Autosam...

Page 4: ...ter 127 Check the Autosampler Air Filter 129 Appendix A Troubleshooting 132 Appendix B Recommendations for Extended Shutdown 137 Expected Power Outages 137 CyTOF XT Shutdown Procedure 137 CyTOF XT Sta...

Page 5: ...injury to personnel and or damage to the system or to property For complete safety information see Appendix F Safety Alert Conventions Fluidigm documentation uses specific conventions for presenting i...

Page 6: ...at indicates a potentially hazardous situation that could result in serious injury or death if not avoided CAUTION Signal word that indicates a potentially hazardous situation that could result in min...

Page 7: ...ed automated sample introduction system the CyTOF XT Autosampler The new sample introduction system consists of a chilled carousel to hold both 5 mL and 15 mL tubes and a syringe driven fluidics syste...

Page 8: ...w Rate cfm L sec Anemometer m sec ft min Vented Outside Lab Power kW BTU hr Torch Box 100 4 75 15 35 7 5 917 System 3 6 12276 One dedicated electrical branch circuit single phase 30 A single phase 200...

Page 9: ...ore i7 9700K 3 6 GHz RAM GB DDR Data storage 3 6 TB 2x 2 TB RAID0 Power supply 300 W Monitor cm in LED Keyboard mouse Wired Data File Size Specifications File Type Size up to fcs 4 bytes channel event...

Page 10: ...Chapter 1 Product Overview Instrument and Computer Connections 10 CyTOF XT User Guide Instrument and Computer Connections Figure 1 Computer rear view...

Page 11: ...nt facing CyTOF XT Equipment and Consumables Standard Equipment Part Number Standard Equipment 117002 CyTOF XT instrument 108490 Monitor standard 34 inch LG 118783 CyTOF XT computer including keyboard...

Page 12: ...Holder O Ring 2 026 905055 5 each 1 pack 130355 Heated Spray Chamber O Ring Kit CyTOF XT contains Injector Holder O Ring 2 014 905499 5 each Nebulizer Port O Ring 2 010 905016 5 each Injector Holder O...

Page 13: ...712 Carousel CyTOF XT 1 118757 Autosampler Bottle Tray CyTOF XT 1 202221 1 L Empty bottle for CyTOF XT 1 118492 Autosampler Sample Loop Agitator CyTOF XT 1 118342 Autosampler Waste Bottle Cap CyTOF XT...

Page 14: ...ty Test Tubes with Cap 12 x 75 mm Round Bottom Polypropylene Sterile Falcon C352063 Carousel tubes 15 mL skirted polypropylene sample tube with cap 15 mL Screw Cap Tube 20 x 76 mm Conical Bottom Skirt...

Page 15: ...Standards IEC EN 61326 1 IEC EN 61010 1 IEC EN 61010 2 081 UL Standard Number 61010 1 2nd Edition CAN CSA C22 2 No 61010 1 04 FCC Part 15 Subpart B ICES 003 2019 EN ISO 12100 Conformity Symbols on th...

Page 16: ...16 CyTOF XT User Guide Chapter 2 Mass Cytometry and CyTOF XT CyTOF XT Instrument Overview Figure 3 CyTOF XT front view...

Page 17: ...he CyTOF XT system consists of 4 major components the carousel the probe line the pump and valve unit and the bottle station Together these components form a liquid sampling automation system where sa...

Page 18: ...kirted bottom 20 X 76 mm Conical Bottom Skirted Polypropylene Sterile Sarstedt Inc 60 732 001 The carousel is insulated and chilled to 4 8 C NOTE For instructions on turning on or off the carousel chi...

Page 19: ...Figure 6 Autosampler carousel housing Probe Line The probe line draws samples and beads from the carousel into the Autosampler fluidics lines The probe line always draws from the same position and the...

Page 20: ...ions Raised and vertical This is the default rest position for the probe line Figure 8 The Autosampler probe line raised and vertical Raised and horizontal When the probe line is raised you can move i...

Page 21: ...s lines Figure 10 The Autosampler probe line lowered and vertical Wash Tube Rinsing of the probe line takes place inside the wash tube which is specially designed with a notch fitting only in Location...

Page 22: ...ne and flushing the Autosampler fluidics lines It is also used as a sample carrier and to resuspend cell pellets Maxpar WASH is used for washing the Autosampler fluidics lines and Maxpar Water is used...

Page 23: ...Autosampler fluidics lines where samples loaded into the carousel are automatically introduced into the system allowing unattended instrument operation and sample acquisition The Autosampler fluidics...

Page 24: ...e reservoir bottle to the nebulizer Rotary Valves There are 2 rotary valves in the pump and valve unit the selector valve and the switching valve The selector valve has ports connected to the probe li...

Page 25: ...le is pushed to the nebulizer via the push pump Maxpar CAS Plus is used as a carrier to push sample to the injector and into the system An air bubble is loaded in between Maxpar CAS Plus and the sampl...

Page 26: ...Only 5 mL tubes should be used for pelleted samples Pelleted samples in 15 mL skirted conical tubes are not part of the recommended workflow Acquisition of Suspension Samples You can choose to manuall...

Page 27: ...mp and 1 on the fill pump These sensors are used to monitor pressure During sample injection the software takes readings from the push pump every 5 6 sec If the average pressure for 5 consecutive read...

Page 28: ...e exits the tip shear force exerted by the exiting nebulizer gas onto the liquid breaks it up into fine aerosol droplets IMPORTANT Ensure that the nebulizer gas line is disconnected from the nebulizer...

Page 29: ...er mount complete the gas and liquid connections to the nebulizer when it is fully assembled When not in use the nebulizer can be placed in the nebulizer rest located above the pump and valve unit on...

Page 30: ...to the injector holder which is threaded onto the heater assembly cap The injector cap is then placed over the injector and tightened in place The nebulizer tip is inserted into the nebulizer port on...

Page 31: ...sample to 200 C as it passes through the spray chamber This high flow of heated gas partially evaporates the droplets to reduce their size as it directs the aerosol to the plasma torch Figure 21 The s...

Page 32: ...ssembly The outermost chamber between the torch holder tubes contains argon plasma gas flowing at 12 L min that is ignited to form the plasma The central chamber between the inner torch holder tube an...

Page 33: ...power supplied to the load coil creates a strong electromagnetic field as the plasma gas exits the outer chamber of the torch A high voltage spark strips free electrons from the exiting argon atoms T...

Page 34: ...on and finally through the reducer cone The ions that emerge from the reducer cone are accelerated and deflected by an electrostatic field of the deflector toward the time of flight region The interfa...

Page 35: ...Analyzer The ion clouds that exit the high pass ion optics consist of a mixture of high atomic weight probes in a randomly distributed array These ions are sent to the time of flight TOF mass analyzer...

Page 36: ...These criteria include a minimum signal threshold and a range for event duration consistent with single cell events and bead event detection As a result the data acquired contains the integrated numb...

Page 37: ...d for every channel CyTOF Software plots the entire data range on a single dual signal scale the units of which are actual counts of particles that hit the detector To achieve this two things are done...

Page 38: ...38 CyTOF XT User Guide Chapter 3 Annotated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument Figure 29 Main components of the CyTOF XT instrument...

Page 39: ...e front lid of the instrument must be closed to see the status panel When the LED is illuminated red it indicates that the instrument is powered on without plasma ignited Figure 30 Instrument status p...

Page 40: ...of CyTOF XT Components Main Components of the CyTOF XT Instrument 40 CyTOF XT User Guide Autosampler Module Figure 32 Main components of the Autosampler Module Pump and Valve Unit Figure 33 Autosample...

Page 41: ...Chapter 3 Annotated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument CyTOF XT User Guide 41 Probe Line Figure 34 Autosampler Module probe line...

Page 42: ...Annotated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument 42 CyTOF XT User Guide Carousel Housing Figure 35 Autosampler Module carousel housing Figure 36 Autosampler Module...

Page 43: ...ed Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument CyTOF XT User Guide 43 Nebulizer Rest Figure 37 Autosampler Module nebulizer rest Bottle Station Figure 38 Autosampler Modu...

Page 44: ...3 Annotated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument 44 CyTOF XT User Guide Nebulizer Assembly Figure 39 The nebulizer assembly Figure 40 The nebulizer assembly expand...

Page 45: ...pter 3 Annotated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument CyTOF XT User Guide 45 Heater Assembly Figure 41 The heater assembly Figure 42 The heater assembly expanded v...

Page 46: ...Chapter 3 Annotated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument 46 CyTOF XT User Guide Torch Assembly Figure 43 Torch assembly Figure 44 Torch assembly expanded view...

Page 47: ...Annotated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument CyTOF XT User Guide 47 Interior View of CyTOF XT Interface Assembly Figure 45 Interface assembly Torch Box Figure 46...

Page 48: ...Components of the CyTOF XT Instrument 48 CyTOF XT User Guide Other Components of CyTOF XT Part Image Location AC distribution box Right side of CyTOF XT system Sampler cone Inside the vacuum interfac...

Page 49: ...F XT Components Main Components of the CyTOF XT Instrument CyTOF XT User Guide 49 Part Image Location Nebulizer Nebulizer assembly Nebulizer holder with nebulizer Nebulizer assembly Outer torch Torch...

Page 50: ...notated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument 50 CyTOF XT User Guide Part Image Location Spray chamber Heater assembly Injector holder Heater assembly Injector Heat...

Page 51: ...Chapter 3 Annotated Figures of CyTOF XT Components Main Components of the CyTOF XT Instrument CyTOF XT User Guide 51 Part Image Location Injector cap Heater assembly...

Page 52: ...ystem It is important to clean the nebulizer and sample loop probe line glassware spray chamber and cones regularly to ensure optimal instrument performance NOTE Always wear non latex powder free glov...

Page 53: ...off the CyTOF Software is closed and the nebulizer is resting in the nebulizer rest after use WARNING Ultraviolet light hazard Take special care whenever the nebulizer assembly is removed while plasm...

Page 54: ...T User Guide Remove the Nebulizer 1 Disconnect the nebulizer gas line by pulling the quick connect coupling 2 Disconnect the nebulizer line by unscrewing the fitting from the nebulizer assembly 3 Loos...

Page 55: ...d on the heater assembly CAUTION Finger cut hazard Broken glass may cause injury or cutting of fingers or hands To avoid breakage keep the nebulizer assembly straight while removing and replacing 5 En...

Page 56: ...t 105910 IMPORTANT Do not sonicate the nebulizer or put pressure on the fragile nebulizer tip Daily Cleaning Method 10 Contrad Decon NOTE Use this method first to remove any clogs that are not part of...

Page 57: ...g from the sample inlet and discard the detergent from the syringe and tubing in a liquid waste container by depressing the syringe plunger 9 Repeat Steps 7 8 for a total of 3 times 10 Soak the nebuli...

Page 58: ...arefully transfer the beaker to a lab bench 4 Connect a vacuum aspirator suitable for liquid waste disposal to the nebulizer using the appropriate tubing If the clog is near the nebulizer tip connect...

Page 59: ...from the nebulizer using a flashlight It should appear as a fine aerosol that leaves the nebulizer in an even symmetrical V pattern 9 Keep the reassembled nebulizer connected and stored in the nebuliz...

Page 60: ...and fill it with fresh DIW 3 Reconnect the tube to the nebulizer rest by turning the tube clockwise 4 If the tube tilts remove and replace the tube as many times as required until threaded correctly s...

Page 61: ...e heater assembly loosen the 2 wing nuts by turning them counterclockwise to unlock the heater assembly from the torch assembly 2 Gently slide the heater assembly away from the instrument CAUTION Fing...

Page 62: ...nce Clean the Injector and Spray Chamber 62 CyTOF XT User Guide 3 Place the heater assembly into its holder on the left side of the instrument Remove the Injector Cap and Injector 1 Unscrew and remove...

Page 63: ...for 1 hr IMPORTANT If injector tip is chipped or broken do not use Replace the injector 2 Scrub the injector with the glassware brush provided 3 Rinse thoroughly with DIW 4 Spray isopropanol inside th...

Page 64: ...XT User Guide NOTE A plastic pipette tip can be used to help remove and replace the injector cap O ring Remove the Spray Chamber and Injector Holder 1 With the heater assembly in its holder gently pus...

Page 65: ...eping it in the upright position because the spray chamber and the injector holder may not be secured tightly to the heater assembly cap 3 Remove the spray chamber and injector holder from the heater...

Page 66: ...ring removal tool to remove the damaged O rings Clean the Vacuum Interface Cones WARNING Before performing maintenance on the cones switch off the RFG power using the red circuit breaker at the right...

Page 67: ...the system may not reach XY boundaries 120 000 steps If this occurs manually rehome the system from Instrument Configuration Alignment 1 Turn RFG switch off and wait 5 min 2 Press and hold the button...

Page 68: ...you to release the sampler cone from the vacuum interface NOTE For easier removal drip isopropanol around the edges of the sampler cone to lubricate the sampler O ring 6 Inspect the sampler cone O ri...

Page 69: ...ove the skimmer reducer assembly using the cone removal tool Insert the other end of the cone removal tool with 2 magnets into the 2 holes on the skimmer reducer assembly 9 Turn the cone removal tool...

Page 70: ...NOTE Place the tip up to avoid damage to the cone orifice Clean Cones 1 Stack the cones as follows in the cone cleaning container IMPORTANT Add 10 Citranox as each part is placed in the container to e...

Page 71: ...2 Sonicate cones in 10 Citranox Do not soak for longer than 15 min 3 Pour off the Citranox and rinse the cones adapters and container with DIW Then stack cones as follows IMPORTANT Add DIW as each par...

Page 72: ...easier and smoother 3 Place the skimmer reducer assembly flush into the interface and begin to turn it clockwise 4 After a few clockwise turns turn the skimmer reducer assembly counterclockwise by a q...

Page 73: ...icate the sampler O rings with a small amount of isopropanol to make the installation of the sampler cone smoother 7 While pressing on the sampler cone with 2 fingers detach the cone removal tool 8 Pr...

Page 74: ...CyTOF XT User Guide 9 Close the instrument front door Reassemble the Injector and Spray Chamber 1 Ensure that the O ring is seated correctly in the spray chamber NOTE If this O ring is damaged or los...

Page 75: ...ber CyTOF XT User Guide 75 2 Place the spray chamber narrow end with O ring first in the heater assembly Press down gently on the spray chamber 3 Place the injector holder in the heater assembly cap E...

Page 76: ...ent Install the heater assembly cap on the heater assembly and lock the cap in place by gently pushing down and then turning clockwise 5 Make sure the injector is completely dry 6 With the injector ca...

Page 77: ...thread the nut of the injector cap clockwise to lock the injector in place Ensure that THIS SIDE OUT can be seen on the injector holder IMPORTANT The injector must be in the lowest position to avoid...

Page 78: ...Chapter 4 Maintenance Reassemble the Injector and Spray Chamber 78 CyTOF XT User Guide 10 Firmly push the 2 wing nuts while turning clockwise to lock the heater assembly in place...

Page 79: ...r Port O Ring CyTOF XT User Guide 79 Replace the Nebulizer Port O Ring 1 Using the torch removal tool provided insert the 4 pins of the torch removal tool into the holes on the nebulizer retainer for...

Page 80: ...counterclockwise to remove the retainer from the base of the heater assembly 3 Remove the damaged O ring using a 100 L plastic pipette tip and replace it with a new nebulizer port O ring 4 Use the to...

Page 81: ...User Guide 81 Check the Nebulizer Holder O Ring 1 Pull on the nebulizer release collar to remove the nebulizer holder from the nebulizer mount 2 Firmly hold the nebulizer holder with one hand With th...

Page 82: ...Ring 82 CyTOF XT User Guide 3 Unscrew the O ring retainer to remove it from the nebulizer shell 4 Inspect and replace the O ring if damaged If damaged remove the O ring with a 100 L pipette tip 5 Rec...

Page 83: ...older should be flush with the nebulizer mount when correctly installed 3 Connect the nebulizer line to the nebulizer assembly 4 Store the nebulizer assembly in the nebulizer rest or reconnect the neb...

Page 84: ...he nebulizer gas line to the nebulizer assembly IMPORTANT Ensure that the nebulizer gas line is disconnected from the nebulizer whenever the nebulizer is stored in the nebulizer rest to prevent DIW fr...

Page 85: ...Place the nebulizer in the nebulizer rest 3 Turn down the nebulizer gas flow to 0 02 L min NOTE At this flow rate liquids do not aerosolize but it prevents liquid from building up within the nebulizer...

Page 86: ...86 CyTOF XT User Guide b Under Settings set Flow Rate L min to 50 c Under Sample Settings set Sample Location to 1 d Click OK to close the Flow Rate notification e Click to save the changes 8 To load...

Page 87: ...the lines Under Sample Settings change the sample location to 2 and click the icon 11 Click Load and wait for loading to complete 12 After DIW has been loaded into the sample loop click Inject The in...

Page 88: ...ry 50 hr of sample acquisition Clean injector if buildup or discoloration is observed at tip 10 Contrad 100 Decon 90 in DIW 1 Soak in 10 Contrad Decon for 1 hr 2 Scrub with brush 3 Rinse with DIW 4 Dr...

Page 89: ...d in the heater cap assembly pointing away from the spray chamber This Side Out should be out should be visible on injector holder when installed properly The heater cap assembly is in the locked posi...

Page 90: ...ANT We recommend using only Type 1 ultrapure 18 2 M water DIW to rinse the CyTOF XT system and its parts Table 6 Frequency for periodic maintenance Component Frequency Carousel Monthly or immediately...

Page 91: ...oth of its LOOP positions on the switching valve of the pump and valve unit 2 Pull to remove the sample loop agitator connector from the pump and valve unit and then slide the sample loop agitator mot...

Page 92: ...gitator motor into the new sample loop and reinsert the sample loop agitator connector onto the pump and valve unit Replace the Probe Line 1 Turn the probe line counterclockwise to loosen the fitting...

Page 93: ...dible click 5 Insert the other end of the probe line in the PROBE gold position of the selector valve on the pump and valve unit and tighten by turning clockwise until finger tight taking care to not...

Page 94: ...uration tab Expand the Autosampler menu and click Carousel to display the Carousel tab 4 Under Carousel Tray in Sample Location enter the location number of the empty tube 5 Click Probe Calibration St...

Page 95: ...mpler Module Maintenance CyTOF XT User Guide 95 NOTE Watch the Autosampler Camera to see the probe line enter the tube An example of the probe line in a 5 mL and a 15 mL sample tube is shown below 6 E...

Page 96: ...wn arrows until the end of the probe line is approximately 1 2 mm above the bottom of the tube 8 Click Save New Lower Position after the correct probe line position is achieved NOTE Use the Autosample...

Page 97: ...and the hole on the Autosampler top plate 3 Gently remove the bottle line from the groove on the syringe guard 4 Remove the other end of the bottle line from its place on the pump and valve unit 5 Con...

Page 98: ...s are installed close and restart the software to prime the lines before proceeding Clean the Carousel NOTE Clean the carousel monthly or immediately after spillage 1 Tilt the probe line stir assembly...

Page 99: ...Guide 99 3 Remove all tubes from the carousel 4 Remove the carousel from the base by holding it at the top and pulling straight up away from the carousel tray 5 Wipe the carousel and the carousel tray...

Page 100: ...OF XT User Guide 6 Reinstall the carousel by lining up the pin on the carousel base with the notch inside the carousel 7 Replace the carousel housing over the carousel 8 Tilt the probe line stir assem...

Page 101: ...NT To prevent cross contamination do not allow lines from the bottle caps to touch any fluid in the bottle tray Let them hang in front of the system 2 Remove the bottle tray and rinse with tap water D...

Page 102: ...e glass syringe barrel Stroke the syringe barrel 10 times while applying steady and even pressure Avoid twisting movements 2 Disconnect the Autosampler CAS green and WASTE black fluidic lines from the...

Page 103: ...03 a Under Actions Push Pump click Down b Under Fill Pump click Down 6 Using a No 2 Phillips screwdriver remove the screw from the right side of the syringe guard on the pump and valve unit This allow...

Page 104: ...pler Module Maintenance 104 CyTOF XT User Guide 7 Fold the autosampler fluidic lines forward while connected to the syringe guard to gain access to the syringe pumps 8 Rotate the syringe from the luer...

Page 105: ...le Maintenance CyTOF XT User Guide 105 9 Depress the syringe halfway towards the mount Be mindful as some liquid may eject 10 While holding the syringe unscrew the thumbscrew under the mount from the...

Page 106: ...new syringe plunger to the center of the stroke 12 Insert the luer end of the new syringe into the valve and rotate it until finger tight 13 Pull the plunger down until it reaches the syringe drive st...

Page 107: ...enance CyTOF XT User Guide 107 15 Hold the plunger button in the channel with both thumbs and tighten the thumbscrew into the plunger using both index fingers 16 Initialize the fill pump and push pump...

Page 108: ...e guard and tighten screw 19 Reconnect all color coded the Autosampler fluidic lines as shown below 20 Restart the Maxpar CAS Plus flow No leaks should be observed Continue with acquisition Nebulizer...

Page 109: ...r Assembly Maintenance CyTOF XT User Guide 109 1 In CyTOF Software click Instrument Configuration Click Autosampler to open the Autosampler tab 2 In the Autosampler tab under the Actions Continuous CA...

Page 110: ...zer line from its NEB position on the switching valve of the pump and valve unit 5 Turn clockwise to install the new nebulizer line on the nebulizer assembly Take care not to leave an air gap between...

Page 111: ...rument using an adjustable wrench 3 Replace the line with a new nebulizer gas line and tighten it using an adjustable wrench 4 Push to connect the quick connect end of the nebulizer gas line to the ne...

Page 112: ...ne hand With the other thumb on the flat surface of the spring assembly gently turn the pin to align it with the slot to release the spring assembly from the nebulizer mount 3 Remove the spring assemb...

Page 113: ...ring block assembly can now be easily removed from inside the nebulizer mount 5 Using the smaller diameter end of the torch removal tool align the 4 pins with the holes in the spring block assembly ca...

Page 114: ...s not required 8 Clean the seal washer by wiping the accessible surface with a Kimwipe moistened with isopropanol 9 Replace the threaded cap on the spring block assembly and tighten it using the torch...

Page 115: ...ock The pin on the spring block fits into the smaller slit on the nebulizer mount 10 Insert the spring assembly into the nebulizer mount and secure it by engaging both pins to lock it in place Place y...

Page 116: ...r the plasma has been shut off Allow sufficient time at least 20 min for these items to cool to room temperature before you handle them Remove and Disassemble Torch Assembly Table 8 Cleaning equipment...

Page 117: ...remove it CAUTION Finger cut hazard Broken glass may cause injury or cutting of fingers or hands To avoid breakage keep the torch assembly straight while removing and replacing 3 Carefully turn the wh...

Page 118: ...sembly 118 CyTOF XT User Guide NOTE The torch removal tool has 2 ends one to remove the outer torch and the other to remove the inner torch 4 Line up the 2 pins on the larger diameter end of the torch...

Page 119: ...uide 119 5 Pivot the torch removal tool left and right to loosen the outer torch 6 Once the outer torch is loosened lift the torch removal tool which is now attached to the outer torch from the torch...

Page 120: ...Assembly 120 CyTOF XT User Guide 7 Line up the 4 pins of the smaller diameter end of the torch removal tool with the 4 notches on the inner torch 8 Using the torch removal tool turn counterclockwise...

Page 121: ...outer torch in 10 Contrad Decon with caution Do not allow the 2 O rings to contact the detergent 3 Scrub the inner and outer torch with the appropriately sized glassware brush Refer to Table 8 4 Rins...

Page 122: ...orch removal tool larger diameter end with the 2 pins to return the outer torch to the torch holder 3 Check the torch assembly alignment using the torch verification tool a Insert the torch verificati...

Page 123: ...the retaining ring Turn the torch assembly clockwise until hand tight IMPORTANT Do not overtighten the retaining ring 5 Repeat Step 3a to check the alignment once more using the torch verification to...

Page 124: ...time at least 20 min for these items to cool to room temperature before you handle NOTE Wear goggles gloves and a lab coat IMPORTANT The following procedure should be done when the instrument plasma...

Page 125: ...Chapter 4 Maintenance Fill the Chiller with Coolant CyTOF XT User Guide 125 2 Loosen the level sensor 3 Remove the level sensor...

Page 126: ...Chapter 4 Maintenance Fill the Chiller with Coolant 126 CyTOF XT User Guide 4 Insert tubing into the opening of the level sensor and fill coolant to max line 5 Reinstall the level sensor...

Page 127: ...the plasma has been shut off Allow sufficient time at least 20 min for these items to cool to room temperature before you handle them IMPORTANT The following procedure should be done when the instrum...

Page 128: ...ent Configuration Alignment 3 Loosen the 2 thumb screws on the air filter bracket 4 Pull on the air filter bracket to remove the air filter 5 If air filter is dirty contact Fluidigm technical support...

Page 129: ...cated on the right side of the bottle station 1 In CyTOF Software click Instrument Configuration Click Autosampler Carousel to open the Carousel tab 2 Disable the Carousel Chiller Under Carousel Chill...

Page 130: ...Chapter 4 Maintenance Check the Autosampler Air Filter 130 CyTOF XT User Guide 4 Pull to remove the magnetic cover 5 Pull the air filter bracket straight out to remove the air filter...

Page 131: ...ter is dirty replace it with a new one Otherwise return the air filter to its original position 7 Place the magnetic Autosampler air filter cover back in its original position 8 Return the Maxpar Wate...

Page 132: ...ight side of the instrument to ensure that the Vacuum button is illuminated Plasma does not ignite or does not stay lit RFG power circuit breaker is off Check the RFG power circuit breaker red on the...

Page 133: ...f the torch due to heat from the plasma Use torch verification tool to check the alignment of the inner and outer torch Refer to Reassemble the Torch Assembly If the torch is not aligned disassemble a...

Page 134: ...spray with a flashlight It should appear as a fine aerosol that leaves the nebulizer in an even symmetrical V pattern If it is not clean the nebulizer or replace it if necessary If the nebulizer pres...

Page 135: ...Check that EQ6 beads are loaded in the correct location of the carousel Add beads or replace if necessary IMPORTANT Be sure to vigorously shake the bottle of EQ6 beads before transferring the beads to...

Page 136: ...ent sample Check that the sample is present in the correct location in the carousel Poor event detection Observed antibody streaking in rain plot Stop acquisition wash sample and continue acquisition...

Page 137: ...edure 1 Confirm that the system is connected to the argon supply so that the vacuum chamber is filled with argon when vented NOTE Plasma must be off before beginning the shutdown procedure 2 Turn off...

Page 138: ...nstrument to achieve the necessary vacuum levels 2 Turn on the system circuit breaker located on the right side of the instrument 3 Press the illuminated Vacuum button located on the right side of the...

Page 139: ...rument or system use appropriate personal protective equipment and adhere to Biosafety in Microbiological and Biomedical Laboratories BMBL a publication from the Centers for Disease Control and Preven...

Page 140: ...posed of in accordance with federal state regional and local laws for hazardous waste management and disposal Do not dispose of this product in unsorted municipal waste This equipment may contain haza...

Page 141: ...uide 141 Appendix D Related Documents Go to fluidigm com to download these related documents Title Document Number CyTOF XT System Site Requirements Guide FLDM 00360 CyTOF Software v8 0 Help for CyTOF...

Page 142: ...Bottle Cap O Ring White 2 223 CyTOF XT 132224 905266 Autosampler Waste Bottle Cap O Ring Black Size 2 224 CyTOF XT 5 pack 132161 118323 Autosampler PCB Air Filter Open Cell 1 4 Thick GRAY CyTOF XT 13...

Page 143: ...ld be serviced by authorized personnel only WARNING Do not modify this instrument or system Unauthorized modifications may create a safety hazard WARNING BIOHAZARD When handling biohazardous material...

Page 144: ...time from covering the nebulizer port when the nebulizer is removed WARNING The nebulizer may be very hot Carefully remove the nebulizer from the beaker using a heat resistant glove or mitt CAUTION H...

Page 145: ...minimize negative environmental impact from disposal of electronic waste do not dispose of electronic waste in unsorted municipal waste Follow local municipal waste ordinances for proper disposal prov...

Page 146: ...precautions to ensure that the surrounding workplace is safe and that system operators are not exposed to hazardous levels of toxic substances When working with any chemicals refer to the applicable s...

Page 147: ...e regulator which vents the cylinder as necessary to prevent it from becoming a safety hazard WARNING Do not use electronic pressure regulator and auto switching valves because doing so may affect the...

Page 148: ...Fluidigm Corporation South San Francisco CA USA T 650 266 6000 For technical support visit techsupport fluidigm com...

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