1MassARRAY® System: Recommended Lab
Equipment and Set-up
Contents
OVERVIEW ....................................................................................................................................................................................................................... 1
LAB SET UP ..................................................................................................................................................................................................................... 1
CHECKLIST ...................................................................................................................................................................................................................... 2
POSITIVE CONTROLS.................................................................................................................................................................................................. 3
DNA/RNA EXTRACTION ............................................................................................................................................................................................. 3
DNA QUANTIFICATION .............................................................................................................................................................................................. 4
RECOMMENDED LAB EQUIPMENT AND CONSUMABLES ........................................................................................................................... 5
OPTIONAL: AUTOMATED LIQUID HANDLING................................................................................................................................................13
CUSTOMER SUPPORT ..............................................................................................................................................................................................14

OVERVIEW
The purpose of this document is to provide recommendations for optimal lab set up and equipment for use withthe Agena Bioscience MassARRAY® System. These recommendations are applicable for the MassARRAY Analyzer 4with Chip Prep Module and the MassARRAY Analyzer 4 with Nanodispenser RS1000 (96, 384, and 96/384 formats),for iPLEX ® Pro, iPLEX Gold, iPLEX HS, UltraSEEK ® , and MassCLEAVE™ chemistries. Though equivalent equipmentfrom other manufacturers may be used, please consult with your Agena Bioscience representative before
purchasing equivalent items.

LAB SET UP
It is strongly recommended to create three separate lab areas to prevent cross-contamination and sample handlingerrors during processing. Each area should have its own equipment.
LabArea
Area 1
Area 2

Area 3

Activities
Isolation, dilution, and quantitation of DNA. Isolation of RNA. cDNA synthesis. MassCLEAVE: bisulfitetreatment.
Pre-PCR preparation, including preparation of PCR cocktails and addition of PCR cocktail and DNA tothe reaction plate. Preparation of the SAP and extension cocktails.
Thermocycling the reaction plate after addition of PCR cocktails, addition of SAP and extension
cocktails or T cleavage/RNase A cocktail to reaction plate and thermocycling. Water addition, desalting,nanodispensing and data acquisition. UltraSEEK: bead conditioning and capture, cleaning, and elution
steps.

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

2CHECKLISTUse this checklist to ensure the required equipment is available in the pre- and post-PCR areas prior to instrument
installation and training on the MassARRAY System. This checklist focuses on material required for reaction set up
and MassARRAY processing and does not include the equipment required for DNA extraction and quantification.
Equipment
384-well MTP (384 systems only)
96-well MTP
Centrifuge - Mini Tube
Centrifuge - PlateDNA Away
Ethanol (RS1000 Nanodispenser only)
Freezer
Microtubes 1.5 mL
Mini Cooler
Multi-channel Pipettes & Filtered Tips
NaOH (RS1000 Nanodispenser only)
HPLC-grade Water
PCR Strip Tubes
PCR Workstation
Plate Rotator
Plate Sealing Roller Tool
Plate Seals
Reagent Reservoirs
Refrigerator
Single Channel Pipettes & Filtered Tips
Thermocycler
Tween (optional)
Type 1 or Deionized Water
VortexIsopropanol (Chip Prep Module only)
Single Tube Magnetic Stand (UltraSEEK only)
96-well Plate Magnetic Stand (UltraSEEK only)

Pre-PCR Area
 Pre-PCR
 Pre-PCR
 Pre-PCR
 Pre-PCR
 Pre-PCR
N/A Pre-PCR
 Pre-PCR
 Pre-PCR
 Pre-PCR
N/A Pre-PCR
 Pre-PCR
 Pre-PCR
N/A Pre-PCR
 Pre-PCR
 Pre-PCR
 Pre-PCR
 Pre-PCR
 Pre-PCR(for cDNA synthesis andmethylation panels only)
N/A
N/A Pre-PCR
N/A
N/A
N/A

Post-PCR
Area
N/A
N/A
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
N/A Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR
 Post-PCR

The following sections of the document provide detailed information on optimal laboratory set up and requiredequipment.

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

3POSITIVE CONTROLSGeneral Genotyping Controls•

Coriell HAPMAP Collections – Normal or wild type DNA, cystic fibrosis, PGx.

Somatic Mutations•••

ATCC Tumor Cell Panels – NIST DNA standards, purified DNA and cell lines
Horizon HDx Reference Standards – Purified genomic DNA and FFPE sectionsSeraCare Reference Standards

Controls & Custom Plasmids•

Maine Molecular Quality Controls – Cystic Fibrosis, PGx, FII, FV

DNA/RNA EXTRACTION
DNA/RNA extraction should be performed in Lab Area 1. Ensure that you have the required ancillary equipment(pipettes, vortex, mini centrifuge, etc.) for DNA extraction from samples. We recommend the following kits formanual extraction.

DNA Extraction
General Purpose Human Tissue, Serum, Plasma and Urine Samples• Qiagen QIAamp DNA Blood Mini Kit – suitable for DNA extraction from blood.
• Qiagen QIAamp Circulating Nucleic Acid Kit – suitable for DNA from plasma/serum.
• Qiagen DNeasy Blood & Tissue Kit – suitable for a wide variety of samples.
• Invitek PSP SalivaGene DNA Kit (#1035200200), using SalivaGene Swab Comfort (#1035231100).
• Macherey-Nagel NucleoSpin Tissue (#740952), using Puritan 6” Sterile Standard Polyester Swab with
Polystyrene Handle (Puritan #25-8061PD).
• Qiagen QIAmp DNA Mini Kit (#51304/51306), using Puritan 6” Sterile Standard Polyester Swab with
Polystyrene Handle (Puritan #25-8061PD).
• Omega Bio-Tek Mag-Bind® Viral RNA Xpress Kit (#M6219) - suitable for DNA extraction from urine usingautomation
Formalin-Fixed Paraffin Embedded Tissue Samples• Qiagen QIAamp DNA FFPE Tissue Kit• Zymo Research Quick-DNA™ FFPE Kit
High Throughput Kits
• Qiagen Gentra Puregene Blood Kit• Qiagen Gentra Puregene Tissue Kit• Zymo Research Quick-DNA™ Universal 96 Kit

RNA Extraction Kit•

Qiagen AllPrep DNA/RNA Mini Kit

cDNA Synthesis•

ThermoFisher SuperScriptTM VILOTM cDNA Synthesis Kit

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

4DNA QUANTIFICATION
DNA quantification should be performed in Lab Area 1. DNA should be stored at -20ºC when not in use and at 4ºC
when in use. MassARRAY assays require pure DNA template with A260/A280 ratios between 1.7 – 2.0 andA260/A230 > 1.7. and a working dilution of at least 5-10 ng/µL.

It is recommended that the samples be checked for quality and quantity of amplifiable copies using Agena
Bioscience’s Sample ID Panel. Alternatively, you may use a fluorometric-based or spectrophotometric-based
method for quantification. For oncology panels, fluorometric-based methods are recommended, because UV
spectrophotometric-based methods will measure any nucleotides present in the sample, including RNA, dsDNA,ssDNA, and free nucleotides, which can give an inaccurate measurement of gDNA.

Agena’s iPLEX® Pro Sample ID Panel
Uniquely identify each sample using 44 SNPs and quantify the number of amplifiable copies of DNA template fromas little as 500 to 18,000 copies (~1 ng to 60 ng) in a single reaction. The panel also provides gender identification.

Agena’s Exome QC Panel
Assess DNA identity, as well as quality and amplifiable template copy number, using 21 exonic SNPs, 3 markers forgender identification, and 25 competitive PCR assays in a single multiplexed reaction. The competitive PCR assays
span a broad dynamic range of 100 – 100,000 copies (0.3 – 300 ng) and monitor sample fragment size over a 100 –500 bp range.

Spectrophotometry
NanoDrop 8000 is a suitable UV-Vis spectrophotometer for DNA quantification.

Fluorometry
Qubit and PicoGreen are suitable for DNA quantification.

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.5RECOMMENDED LAB EQUIPMENT AND CONSUMABLES

PRE-PCR EQUIPMENT
Equipment
PlateCentrifuge(withappropriaterotors)

Mini TubeCentrifuge

Manufacturer &Model
Eppendorf
5430/R

Image

Specifications/Notes
Max. RCF with plate rotor:
3,486 x g

Eppendorf
5810/R

Substitutions acceptable

Eppendorf
MiniSpin

Recommend additional rotor
option for 2 x 8-tube PCR
strips.

SystemFormat
All

All

Substitutions acceptable
VortexMO BIO Vortex
Genie® 2 Vortex

Variable speed; Suitable fortubes and plates.

All

Substitutions acceptable

Thermal Cycler VeritiTM ThermalCycler
TM

SimpliAmp
Thermal Cycler

Choose appropriate block for
96/384.
Substitutions acceptable

ProFlexTM 96well PCR SystemPCR
Workstation
with UV
Irradiation

Mini Cooler

SensoQuest
Labcycler Basic
C.B.S. Scientific
P-048-202

VWR 89511-788

UV light with timer; Dual UV
bulb preferred.
Min. 36” x 24” x 24”
48”x24”x24”
Substitutions acceptable
Optional
For keeping enzymes cold
while setting up reactions.
Substitutions acceptable

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

AllOnly needed inpre-PCR areafor MassCLEAVE
or cDNA
synthesis

AllAll6PRE-PCR EQUIPMENT
Equipment
Refrigerator

Manufacturer &Model
VWR 14236-525

Image

Specifications/Notes
Refrigerator for storingworking reagents at 4 ºC.

SystemFormat
All

Substitutions acceptable

Freezer

VWR 97043-524

Min. -20 ºC for long-term DNAand reagent storage.

All

Substitutions acceptable

ElectronicMultichannel
Pipettes &Filtered Tips

ManualMultichannel
Pipettes &Filtered Tips

Integra Voyager
II 4731
Alternateoptions: Manual
multichannel
pipettes may be
used instead.
Rainin Pipet-Lite
Multi Pipette
XLS+

8- or 12-channel electronic
adjustable tip spacing pipette;
0.5 µL – 12.5 µL

All

Substitutions acceptable

8- or 12-channel pipette;
0.5 µL – 10 µL
20 µL - 200 µL

All

Substitutions acceptable
Single Channel Rainin Pipet-Lite
Pipettes &LTS
Filtered Tips
Eppendorf®

Volume ranges:
0.1 µL – 2 µL
0.5 µL – 10 µL
10 µL – 100 µL
100 µL – 1000 µL

GilsonSubstitutions acceptable

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

All7POST-PCR EQUIPMENT
Equipment
PlateCentrifuge
withappropriate
plate rotor

Mini Tube
Centrifuge

Manufacturer &Model
Eppendorf 5430/R

Image

Specifications/Notes
Max. RCF with plate rotor:
3,486 x g

SystemFormat
All

Eppendorf 5810/R
Substitutions acceptable

Eppendorf MiniSpin

Recommend additionalrotor option for 2 x 8-tube
PCR strips.

All

Substitutions acceptable
VortexMO BIO Vortex Genie®
2 Vortex

Variable speed; Suitable
for tubes and plates.

All

Substitutions acceptable
Thermal Cycler VeritiTM Thermal Cycler
SimpliAmpTM Thermal
CyclerChoose appropriate blockfor 96/384.

All

Substitutions acceptable

ProFlexTM 96-well PCR
SystemPlate/Tube
RotatorMini Cooler

SensoQuest Labcycler
BasicVWR 444-0502

VWR 89511-788

Tube rotator with 360ºrotation. Use standard
rotisserie to attach androtate plates.
Substitutions acceptable
Optional
For keeping enzymes cold
while setting up reactions.
Substitutions acceptable

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

RS1000UltraSEEK
panels (allsystems)
All8

POST-PCR EQUIPMENT
Equipment
Refrigerator

Manufacturer &Model
VWR 14236-525

Image

Specifications/Notes
Refrigerator for storingworking reagents at 4 ºC.

SystemFormat
All

Substitutions acceptable

Freezer

VWR 97043-524

Min. -20 ºC for long-term
DNA and reagent storage.

All

Substitutions acceptable

Electronic
Multichannel
Pipettes &Filtered Tips

ManualMultichannel
Pipettes &Filtered Tips

Integra Voyager II
4731
Alternate option:
Manual multichannel
pipettes may be usedinstead.
Rainin Pipet-Lite Multi
Pipette XLS+

8- or 12-channel electronic
adjustable tip spacing
pipette;
0.5 µL – 12.5 µL

All

Substitutions acceptable
8- or 12-channel pipette;
0.5 µL – 10 µL
20 µL - 200 µL

All

Substitutions acceptable
Single Channel Rainin Pipet-Lite LTS
Pipettes &Filtered Tips
Eppendorf®
GilsonSingle Tube
Magnetic
StandV&P Scientific VP772F3

Volume ranges:
0.1 µL – 2 µL
0.5 µL – 10 µL
10 µL – 100 µL
100 µL – 1000 µL
Substitutions acceptable
Suitable for 1.5 mL
microtubes with a single
magnet.
Substitutions acceptable

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

All

UltraSEEK
panels only

9POST-PCR EQUIPMENT
Equipment
96-well Plate
MagneticStand

Manufacturer &Model
ThermoFIsher
DynaMagTM-96 Side
Magnet 12331DD

Image

Specifications/Notes
Magnetic bead separation
block for 96-well plates.
Substitutions acceptable

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

SystemFormat
UltraSEEKpanels only

10CONSUMABLES
Item
Microtubes

PCR Strip
Tubes

Manufacturer &ModelVWR 62111-756

Image

VWR 82050-348

Tube RacksVWR Four-Way
Microtube Racks

Sealing Roller
Tool & Paddle

VWR Excel Scientific
Film Sealing Roller& Paddles

System Format

RNase-, DNase-, humanDNA- and PCR inhibitorfree.
Volume: 1.5 mLAll

Substitutions acceptable
Optional
8- or 12-well strips withcaps
Volume: 0.2 mL

VWR 93001-118

50 mL Tubes
15 mL Tubes
5 mL Tubes

Specifications/Notes

15 5/10 50

Substitutions acceptable
For working aliquots ofwater.
Sterile, RNase-, DNase- andhuman DNA-free.
Substitutions acceptable
Substitutions acceptable

Paddles or roller for sealing
platesAllAllAllAll

Substitutions acceptable

Reagent
Reservoir

VWR 89094-662

Wash Bottles

VWR 10111-982

Disposable pipetting
reservoirs; DNase- andRNase-freeVolume: 25 mL; sterile(50 mL for UltraSEEK only)
Substitutions acceptable
For use with ethanol andwater.

414004-226
Substitutions acceptable

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

AllAll11CONSUMABLES
Item

Manufacturer &Model
Clear Adhesive ThermoFisher
Plate Seals
Scientific AB0558

Pressure Pads

96-well
Microtiter
Plate

Bio-Rad ADR5001

Non-skirted:
AB0600Lor equivalent

Image

Specifications/Notes
Strong adhesive, -20 ºC to
120 ºCAll

Foam pad for uniform
pressure on plates (forBioRad thermal cyclers)All

Substitutions acceptableNon-skirted:
Working vol.: 0.2 mL
Max fill vol.: ≤0.3 mL

Verifycompatibility
with yourthermal cycler.

96-well
Microtiter
Plate
Verifycompatibility
with yourthermal cycler.
384-wellMicrotiter
Plate
Verifycompatibility
with yourthermal cycler.

System Format

96-format on theMassARRAY
System with
Chip Prep
ModuleFor UltraSEEK,
recommendsemi-skirted,
coloredonly

Semi-skirted:
TF4483343
or equivalentSemi-skirted, colored
Working vol.: 0.2 mL
Max. well vol.: 0.25 mL
Allows for barcoding

Non-skirted:
AB0600Lor equivalentNon-skirted:
Working vol.: 0.2 mL
Max fill vol.: ≤0.3 mL

96-format on theMassARRAY
System withRS1000
Nanodispenser

TF0384or equivalent

Full skirted:
Working vol.: 25 µL
Max vol.: 40 µL

384-format
systems

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

12

CONSUMABLES
Item
HPLC-gradewater

Ethanol

Manufacturer &ModelVWR JT4218-02

VWR 71006-012
Fisher ScientificBP2818500

Tween 20

BioRad #1610781
TFS 28320

DNA AWAY™

MBP DNA AWAY™
53509-506

Image

Specifications/Notes
Residue after evaporation≤2ppm
Sterile, nuclease- & DEPCfree.
Substitutions acceptableAbsolute (200 proof),
molecular biology grade.

System Format
All

RS1000(for cleaningtanks)

Substitutions acceptable
Nonionic detergent
solution. 10% w/v Optional;
for troubleshooting on theRS1000 Nanodispenser.

RS1000 only (fortroubleshooting)Eliminate DNase and DNA
contamination

All

Substitutions acceptable
Type 1 Water

Milli-Q® Advantage
A10 Water
Purification System

Isopropanol

EMD PX1835

NaOH

Honeywell Fluka
60-014-30

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

NCCLS, CAP or ATSM Type
1 water>18.2 MΩ
Used for supply (rinse)
water in CPM andRS 1000.
Substitutions acceptable:
DI waterMolecular biology-grade

0.1 M
For pin conditioning on theRS1000 Nanodispenser.

AllChip PrepModule(for dispense tipcleaning)
RS1000 only

13

OPTIONAL: AUTOMATED LIQUID HANDLINGThe following equipment may be used for automating the sample extraction and pre- and post-PCR liquid handlingsteps. Agena Bioscience does not provide setup, configuration, methods, or support for this equipment.

Manufacturer &Model
Qiagen QIAcube

ImageSpecifications
Sample prepSystemFormatAll

PromegaMaxwell® RSC

DNA extraction andquantification from a wide
range of sample types.

AllHamilton
Microlab NIMBUS

Pre- or post-PCR liquidhandling.

AllWith enclosed UV lightpackage for pre-PCR.

Eppendorf 5075

Pre- or post-PCR liquidhandling.
Capable of handling
streptavidin beads for
UltraSEEK chemistry.

All

Perkin Elmer
Janus

Pre- or post-PCR liquidhandling.
Capable of handling
streptavidin beads for
UltraSEEK chemistry.

All

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

14Manufacturer &Model
Biomek NX P

ImageSpecifications
Pre- or post-PCR liquidhandling.
Capable of handling
streptavidin beads forUltraSEEK chemistry.
Biomek FX P recommended
for high throughput
automation.

CUSTOMER SUPPORT
Please contact your local Agena Bioscience office for customer support.
AMERICAS
Help Desk: 1-877-4-GENOME or (+1) 858-882-2800
E-mail: helpdesk@AgenaBio.com
EUROPE
Phone: (+49) 40-899676-0
Email: support-europe@AgenaBio.com
AUSTRALIA and NEW ZEALAND
Phone: (+61) 7 3088 1600
Email: support-anz@AgenaBio.com
CHINA and ASIA PACIFIC
Phone: (+86) 21 6427 0566
Email: support-china@AgenaBio.com
Email: support-asia@AgenaBio.com[0221]USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.

SystemFormatAll15
Revision History
RevisionR06

Date
1/27/22R05

2/8/21R04

10/1/19

Changes•
Added DNA extraction kit recommended for the new Sample ID+ protocol.
•
Added “or equivalent” to plate types required.
•Added SensoQuest Labcycler Basic as a thermal cycler option.
•In DNA Extraction section, changed Stratec to Invitek (PSP SalivaGene DNA Kit) due tocompany name change.
•For plate/tube rotator, corrected System Format to RS1000 and UltraSEEK Panels (PostPCR Equipment section).
•
Updated customer support contact information.
•
Updated recommended microtiter plates.
•
Added DI water as acceptable substitute for Type 1 water.
•
Added NaOH (for pin conditioning on the RS1000 Nanodispenser).
•
Added isopropanol (for pin cleaning on the Chip Prep Module, with Customer Supportassistance).
•
Clarified lab area activities.
•
Updated checklist on page 2.
•
Added SeraCare Reference Standards for somatic mutation positive controls.
•
Updated recommended DNA extraction kits and added RNA extraction and cDNAsynthesis kits.
•Updated DNA Quantification section, including addition of recommended
fluorometers.
•Simplified thermal cycler recommendations.
•Added some additional options for some equipment and consumables.

Patents and Trademarks
MassARRAY, iPLEX, UltraSEEK, and Agena Bioscience are registered trademarks of Agena Bioscience, Inc. MassCLEAVE is a trademark of Agena
Bioscience, Inc. All other trademarks or service marks set forth herein are the property of their respective owners.
Agena Bioscience’s patented nucleic acid analysis by mass spectrometry methods and products are protected un der United States patent rights
including but not limited to; 7,019,288; 7,025,933; 7,332,275; 7,390,672; 7,501,251; 7,888,127; 7,917,301; 8,003,317; 8,315, 805; 8,349,566;
9,249,456; 9,310,378; 9,394,565; 9,669,376; 9,896,724, 10,604,791; 10,640,817 and 10,865,439, and patents pending, and foreign counterparts
including but not limited to EP1727911B1, EP1546385B1, EP1332000B1, EP1660680B1, and EP2107129B1.
[0221]The MassARRAY System, iPLEX Pro Sample ID Panel, Sample ID+, and iPLEX Pro Exome QC Panel are For Research Use Only. Not for use indiagnostic procedures.
1/27/22

USG-CUS-082 R06
For Research Use Only. Not for use in diagnostic procedures.