Fluidigm CyTOF XT User manual
FLDM-00254 Rev 03
2CyTOF XT User Guide
For Research Use Only. Not for use in diagnostic procedures.
Information in this publication is subject to change without notice.
It is Fluidigm policy to improve products as new techniques and
components become available. Therefore, Fluidigm reserves the
right to change specifications at any time. Every effort has been
made to avoid errors in the text, diagrams, illustrations, figures, and
screen captures. However, Fluidigm assumes no responsibility for
any errors or omissions. In no event shall Fluidigm be liable for any
damages in connection with or arising from the use of this
publication.
Patent and Limited License Information
Fluidigm products are covered by issued and pending patents in
the United States and other countries. Patent and limited license
information is available at fluidigm.com/legal/notices.
Limited Use Label License
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 except as approved in writing by Fluidigm.
Trademarks
Fluidigm, the Fluidigm logo, the CyTOF XT logo, CyTOF, CyTOF XT,
EQ, Helios, and Maxpar are trademarks and/or registered trademarks
of Fluidigm Corporation in the United States and/or other countries.
All other trademarks are the sole property of their respective owners.
© 2021 Fluidigm Corporation. All rights reserved. 07/2021
For technical support visit techsupport.fluidigm.com.
North America +1 650 266 6100 | Toll-free (US/CAN): 866 358 4354 | support.northamerica@fluidigm.com
Latin America +1 650 266 6100 | techsupportlatam@fluidigm.com
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CyTOF XT User Guide 3
Contents
About This User Guide 5
Chapter 1: Product Overview 7
Chapter 2: Mass Cytometry and CyTOF XT
16
Chapter 3: Annotated Figures of CyTOF XT
Components 38
Chapter 4: Maintenance 52
Contents
4 CyTOF XT User Guide
Appendix A: Troubleshooting 132
Appendix B: Recommendations for
Extended Shutdown 137
Appendix C: Preventive Maintenance,
Decontamination, and Disposal 139
Appendix D: Related Documents 141
Appendix E: Revision History 142
Appendix F: Safety 143
CyTOF XT User Guide 5
About This User Guide
This user guide describes the basic operation and maintenance of the CyTOF® XT system.
For detailed information about operating the system using CyTOF Software, click the Help
icon to access the integrated help guide, also available as the CyTOF Software v8.0
Help for CyTOF XT (FLDM-00045). The software Help also includes an end-to-end daily
workflow. For complete instrument specifications and pre-unpacking/installation
instructions, see the CyTOF XT System Site Requirements Guide (FLDM-00360).
IMPORTANT Before using the CyTOF XTsystem, read and understand the detailed
instructions and safety guidelines in this document. Failure to follow these guidelines may
result in undesirable effects, 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 information that may
require your attention. Refer to the following safety alert conventions.
Safety Alerts for Chemicals
For hazards associated with chemicals, this document follows the United Nations Globally
Harmonized System of Classification and Labelling of Chemicals (GHS) and uses indicators
that include a pictogram and a signal word that indicates the severity level:
Indicator
Description
Pictogram (see example) consisting of a symbol on a white background within a red
diamond-shaped frame. Refer to the individual safety data sheet (SDS) for the
applicable pictograms and hazards pertaining to the chemicals being used.
DANGER
Signal word that indicates more severe hazards.
WARNING
Signal word that indicates less severe hazards.
About This User Guide
Safety Data Sheets
6 CyTOF XT User Guide
Safety Alerts for Instruments
For hazards associated with instruments, this document uses indicators that include a
pictogram and signal words that indicate the severity level:
Indicator
Description
Pictogram (see example) consisting of a symbol on a white background within a black
triangle-shaped frame. Refer to the instrument user guide for the applicable
pictograms and hazards pertaining to instrument usage.
DANGER
Signal word that indicates an imminent hazard that will result in severe injury or death
if not avoided.
WARNING
Signal word that 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 minor
or moderate personal injury if not avoided.
IMPORTANT
Signal word that indicates information necessary for proper use of products or
successful outcome of experiments.
Safety Data Sheets
Read and understand the SDSs before handling chemicals. To obtain SDSs for chemicals
ordered from Fluidigm, either alone or as part of this system, go to fluidigm.com/sds and
search for the SDS using either the product name or the part number.
Some chemicals referred to in this user guide may not have been provided with your
system. Obtain the SDSs for chemicals provided by other manufacturers from those
manufacturers.
CyTOF XT User Guide 7
Chapter 1: Product Overview
CyTOF® XT is the latest in Fluidigm mass cytometers, offering single-cell high-dimensional
proteomic analysis at hundreds of cells analyzed per second for 135 discrete channels. The
instrument control software. The CyTOF XT system offers automated instrument tuning and
calibration based on beads, and improved data processing.
CyTOF XT simplifies instrument operation with an integrated 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 system.
The Autosampler enables batch acquisition of multiple samples, automates acquisition with
built-in resuspension capabilities, addition of internal standards and inter-sample cleaning.
The Autosampler and CyTOF XT software increase productivity with built-in clog detection,
automated declogging, and shutdown.
Together, the full range of new features on CyTOF XT maximizes both the breadth and
depth of information acquired per sample and accelerates high-parameter studies with
enhanced instrument productivity.
Chapter 1: Product Overview
CyTOF XT Site Requirement Specifications
8 CyTOF XT User Guide
CyTOF XT Site Requirement Specifications
Dimensions
Width
(cm/in)
Height (cm/in)
Depth (cm/in)
Weight (kg/lb)
CyTOF XT
instrument
93/37
135/53
75/30
288/635
Electrical*
Maximum
Power
Draw
(VA)
Operating Voltage
(V AC)
Operating
Frequency
(Hz)
Maximum Continuous
Current (A)
CyTOF XT instrument
4,000
200240
50/60
20
Environmental
Operating T (°C)
Humidity (%)
CyTOF XT instrument
1825
2080
non-condensing
Gas
Ultrahigh Purity Argon
Flow Rate
(L/min)
CyTOF XT instrument
85 ±5 psi (100 psi max.)
15
Vent
Hose Diameter. (mm/in)
Flow 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 200240 V AC, 50/60 Hz) is used to
provide power to the CyTOF XT instrument.
For optimal performance the temperature should be 20 ±2 °C.
CyTOF XT Specification
Instrument Specifications
Description
Specification (instrument)
Channels
135
Mass range
75209 amu
Abundance sensitivity
<0.3% for M+1 with M=159Tb
<0.3% for M-1 with M=175Lu
Instrument response
500 dual counts of 159Tb+ per
Dynamic range
4.5 orders of magnitude
Calibration
Automated
Operating system
Windows® 10 Enterprise LTSC
Sample introduction
Dual syringe drive
Maximum sustained event rate
500 events per sec
Flow rate
30 L/min
Chapter 1: Product Overview
CyTOF XT Specification
CyTOF XT User Guide 9
Workstation Specifications
Description
Specification (workstation)
CPU
Intel Core 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
.lmd
Compressed format. 520 GB/hr
(typical)
_SPR.fcs
3.82 MB/hr
_Beads.fcs
0.91 MB/hr (typical)
_BG.fcs
0.48 MB/hr
_Processed.fcs
4 bytes/channel/event
Chapter 1: Product Overview
Instrument and Computer Connections
10 CyTOF XT User Guide
Instrument and Computer Connections
Figure 1. Computer rear view
Chapter 1: Product Overview
CyTOF XT Equipment and Consumables
CyTOF XT User Guide 11
Figure 2. Right view, front-facing
CyTOF XT Equipment and Consumables
Standard Equipment
Part Number
Standard Equipment*
117002
CyTOF XTinstrument
108490
Monitor, standard 34-inch LG
118783
CyTOF XT computer, including keyboard and mouse
130069
CyTOF Software v8.0
* Standard equipment is subject to change at sole discretion of Fluidigm.
Chapter 1: Product Overview
CyTOF XT Equipment and Consumables
12 CyTOF XT User Guide
Standard Consumables
Part Number
Product Name
Unit
117424
Inner Torch CyTOF XT
1
117423
Outer Torch CyTOF XT
1
117506
Nebulizer CyTOF XT
1
117382
Injector CyTOF XT
1
130354
Autosampler Bottle Line Kits CyTOF XT contains:
Autosampler Selector Valve to Water Line (117787), 1 each
Autosampler Fill Pump to Waste Line (117783), 1 each
Autosampler Selector Valve to Waste Line (118367), 1 each
Autosampler Selector Valve to CAS Line (117786), 1 each
Autosampler Push Pump to Waste Line (117782), 1 each
Autosampler Selector Valve to Wash Line (117788), 1 each
Autosampler Push Pump to CAS Line (117781), 1 each
1 pack
130357
Torch Holder O-Ring Kit CyTOF XT contains
Torch Holder O-Ring 2-028 (905138), 5 each
Outer Torch O-Ring 2-021 (905506), 5 each
Outer Torch O-Ring 2-019 (905504), 5 each
Torch Holder O-Ring 2-027 (905137), 5 each
Torch 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-Ring 2-015 (905003), 5 each
Injector Holder O-Ring 2-010 (101922), 5 each
1 pack
130353
Autosampler Bottle Cap O-Ring Kit CyTOF XT contains:
Autosampler 500mL bottle Cap O-Ring 2-125 (130418) 5 each
Autosampler 1L bottle Cap O-Ring 2-128 (130417) 5 each
1 pack
117775
Autosampler Probe Line CyTOF XT
1
118763
Autosampler Sample Loop CyTOF XT
1
117784
Autosampler Nebulizer Line CyTOF XT
1
101815
Reducer O-Ring 2-113 CyTOF XT pack of 5
1 pack
130396
Sampler O-Ring 2-033 CyTOF XT pack of 10
1 pack
117174
Skimmer-Reducer Platinum Cones CyTOF XT
1
117172
Sampler Platinum Cone CyTOF XT
1
117486
Nebulizer Seal Washer CyTOF XT
1
Standard Reagents Consumables
Part Number
Description
Unit
201245
EQ Six Element Calibration Beads*
100 mL
201243
Maxpar® Washing Solution for CyTOF XT
500 mL
201244
Maxpar Cell Acquisition Solution Plus for CyTOF XT*
1 L
201242
Maxpar Water for CyTOF XT*
500 mL
* Store at 2–8 °C.
Chapter 1: Product Overview
CyTOF XT Customer-Orderable Parts
CyTOF XT User Guide 13
CyTOF XT Special Tools and Kits
Part Number
Description
Unit
117634
Torch Removal Tool CyTOF XT
1
118383
Torch Verification Tool CyTOF XT
1
105624
Cone Removal Tool CyTOF 2, Helios, CyTOF XT
1
105910
Nebulizer Cleaning Kit
1
130393
Autosampler Lines Cleaning Kit (brown union, Luer Adapter, 3 mL syringe)
1
CyTOF XT Customer-Orderable Parts
Part Number
Product Name
Unit
118230
Nebulizer Rest CyTOF XT
1
905883
Nebulizer Rest O-Ring 2-115 Kit CyTOF XT
1
905084
Nebulizer Rest O-Ring 2-010 Kit CyTOF XT
1
202222
500 mL Empty bottle CyTOF XT
1
118351
Autosampler Wash Bottle Cap CyTOF XT
1
132160
Autosampler Wash Bottle Cap O-Ring White 2-223 CyTOF XT
1
118712
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
1
132224
Autosampler Waste Bottle Cap O-Ring Black Size 2-224 CyTOF XT –
pack of 5
1
132161
Autosampler PCB Air Filter—Open Cell, 1/4" Thick GRAY CyTOF XT
1
118744
Autosampler Carousel Housing CyTOF XT
1
118716
Autosampler Maxpar Water Bottle Cap CyTOF XT
1
132163
Autosampler Maxpar Water Bottle Cap O-Ring Blue 2-223 CyTOF XT
1
102081
500 µL Syringe, CyTOF 2, CyTOF XT
1
118349
Autosampler Maxpar CAS Bottle Cap CyTOF XT
1
132225
Autosampler Maxpar CAS Bottle Cap O-Ring Green 2-224 CyTOF XT
pack of 5
1 pack
118734
Autosampler Probe Wash Tube CyTOF XT
1
117355
Torch Holder Assembly CyTOF XT
1
117375
Heater Assembly CyTOF XT
1
117377
Nebulizer Mount and nebulizer holder (excl. nebulizer) CyTOF XT
1
132162
Nebulizer Holder O-Ring 2-105
1
Chapter 1: Product Overview
Required Consumables from Other Suppliers
14 CyTOF XT User Guide
Part Number
Product Name
Unit
117383
Injector Cap CyTOF XT
1
117503
Nebulizer Retainer for O-Ring CyTOF XT
1
117384
Injector Holder CyTOF XT
1
117386
Spray Chamber CyTOF XT
1
132167
Autosampler Air Filter CyTOF XT
1
Required Consumables from Other Suppliers
Part
Consumable
Product Description
Source (Part Number)
Carousel tubes
5 mL polypropylene
sample tube with cap
5 mL High-Clarity Test Tubes with
Cap 12 x 75 mm Round Bottom
Polypropylene Sterile
(C352063)
Carousel tubes
15 mL skirted
polypropylene
sample tube with cap
15 mL Screw Cap Tube 20 x 76 mm
Conical Bottom Skirted
Polypropylene Sterile
Sarstedt (60.732.001)
Consumables Ordering
North America
Customers in the US and Canada who have a Fluidigm account are already registered for
online ordering. Go to fluidigm.com/catalog. New customers can set up an online account to
place orders, view past order history, and see current order confirmations.
Outside North America
To reorder parts and reagents, contact your regional Fluidigm sales representative or
distributor. Go to fluidigm.com/contacts.
Chapter 1: Product Overview
Regulatory Compliance
CyTOF XT User Guide 15
Regulatory Compliance
The following directives and harmonized standards were used to evaluate the safety and
performance of the CyTOF XT system:
General Regulations and Requirements
•2014/35/EU European Parliament Low Voltage Directive
•2014/30/EU European Parliament Directive: Electromagnetic Compatibility
•2006/42/EU Machinery Directive
Harmonized 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 the Instrument
The instrument is labeled with the following conformity markings:
Conformity Mark
Description
Indicates conformity with safety requirements for Canada and the United
States.
Indicates conformity with European Union requirements for safety and
electromagnetic compatibility
AZ
Refer to the CyTOF XT Site Requirements Guide (FLDM-00360) for more detailed
information on the recommended environmental conditions.
16 CyTOF XT User Guide
Chapter 2: Mass Cytometry and CyTOF XT
CyTOF XT Instrument Overview
Figure 3. CyTOF XT front view
Chapter 2: Mass Cytometry and CyTOF XT
CyTOF XT System Components Overview
CyTOF XT User Guide 17
CyTOF XT System Components Overview
Autosampler Module
The Autosampler Module of the 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 samples loaded into the
carousel can be automatically introduced into the system, allowing for unattended
instrument operation and sample data acquisition.
Figure 4. Autosampler Module
Chapter 2: Mass Cytometry and CyTOF XT
CyTOF XT System Components Overview
18 CyTOF XT User Guide
Carousel
Figure 5. The Autosampler carousel
The carousel housing contains a removable carousel, which can hold 16 tubes.
•Locations 112 are for polypropylene sample tubes (5 mL).
•Location 13 is for a large-volume polypropylene sample tube (15 mL).
•Location 14 is for EQSix Element Calibration Beads (EQ6) (15 mL).
•Location 15 is for EQ Four Element Calibration Beads (EQ4) (15 mL).
•Location 16 is reserved for the Autosampler wash tube.
NOTE Locations 1315 require 15 mL polypropylene screw cap tubes with a skirted bottom
[20 X 76 mm Conical Bottom Skirted Polypropylene Sterile, Sarstedt, Inc. (60.732.001)].
The carousel is insulated and chilled to 48 °C.
NOTE For instructions on turning on or off the carousel chiller, refer to the CyTOF Software
Help content. To view the Help content, click the icon in the upper right corner of the
CyTOF Software window.
NOTE We recommend adding barcoded samples to the carousel in one of the following
ways:
As a suspension in a 15 mL tube at Location 13
As an aliquot of multiple samples in 5 mL tubes at Locations 112 in pelleted form with
concatenation of the acquired FCS files
The carousel lid has 2 parts: the main carousel lid and the corner lid. The main carousel lid is
hinged and can be opened to allow access to the carousel for inserting and removing tubes.
Chapter 2: Mass Cytometry and CyTOF XT
CyTOF XT System Components Overview
CyTOF XT User Guide 19
The corner lid is fixed and is removed only when performing maintenance inside the
carousel.
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 carousel rotates to
position the tube of interest under the probe line. The probe line stirs samples during
acquisition to help keep cells in suspension.
Figure 7. The Autosampler probe line
Chapter 2: Mass Cytometry and CyTOF XT
CyTOF XT System Components Overview
20 CyTOF XT User Guide
The probe line has 3 positions:
•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 it to a horizontal
position to gain access to the carousel housing.
Figure 9. The Autosampler probe line: raised and horizontal
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