EU Dx MassARRAY Analyzer 4 User Guide MADX-USG-CUS-501 R03 · warning label shown in Figure 1.1 is located on the back of the instrument. Under normal operating conditions, no additional

MassARRAY® Dx Analyzer 4 USER GUIDE

MassARRAY Dx Analyzer 4 User Guide MADX-USG-CUS-501 R037/12/17

Copyright 2016-17. All rights reserved. No part of this publication may be reproduced, distributed, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, or stored in a database or retrieval system, for any reason other than a licensee's internal use, without the prior written permission of Agena Bioscience, Inc. Printed in the United States of America.

TRADEMARKSMassARRAY, iPLEX, and SpectroCHIP are registered trademarks of Agena Bioscience, Inc. (California). Agena Bioscience is a trademark of Agena Bioscience, Inc. All other trademarks or service marks set forth herein are the property of their respective owners.

PATENTSAgena Bioscience’s patented nucleic acid analysis by mass spectrometry methods and products are protected under United States patent rights including but not limited to; 6,440,705; 6,558,623; 6,730,517; 6,979,425; 6,994,969; 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; and 9,310,378, and patents pending including but not limited to US20130017960, and foreign counterparts including but not limited to EP1173622B1, EP1727911B1, EP1546385B1, EP1332000B1, EP1613723B1, EP1660680B1, and EP2107129B1.

[0217]

The MassARRAY Dx Analyzer 4 complies with EN 61010 3rd Edition.

Manufacturer Date of Manufacture Catalog Number Serial Number Separate Collection for Waste of Electrical

and Electronic Equipment

Consult Instructions for Use

WarningFlammable

WarningBiohazard

WarningCrush and Pinch Point

General WarningCaution

Risk of Danger

In vitro diagnostic device

Conformite Europeenne

NoteWarning

Laser Beam

European Representative Canadian Standards

Association

Agena Bioscience, Inc.4755 Eastgate MallSan Diego, CA 92121, USAPhone: 1.858.882.2800

EMERGO EUROPEPrinsessegracht 202514 AP The HagueThe Netherlands

Contents

Chapter 1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Intended Use . . . . . . . . . . . . . . . . . . . . . . . 1

The MassARRAY Dx Analyzer 4 Instrument . . . . . . . . . . . . . 1

Installation Procedures and Special Requirements. . . . . . . . . . 2

Limitations, Warnings and Precautions, and Hazards . . . . . . . . . 4

Customer Support . . . . . . . . . . . . . . . . . . . . 7

Chapter 2 Principles of Operation . . . . . . . . . . . . . . . . . . . . 9

MassARRAY Dx Analyzer 4 . . . . . . . . . . . . . . . . . 9

MassARRAY Software . . . . . . . . . . . . . . . . . . . 12

Chapter 3 Operating Instructions . . . . . . . . . . . . . . . . . . . . 15

Setting up the Experiment in MassARRAY Typer Software . . . . . . . 16

Starting the MassARRAY Dx Analyzer 4 Software . . . . . . . . . . 18

Loading SpectroCHIP Arrays . . . . . . . . . . . . . . . . . 19

Creating and Importing an Input File . . . . . . . . . . . . . . 22

Setting Up the Automatic Run . . . . . . . . . . . . . . . . 26

Checking the Barcode Report . . . . . . . . . . . . . . . . 30

Starting the Automatic Run . . . . . . . . . . . . . . . . . 31

Unloading SpectroCHIP Arrays . . . . . . . . . . . . . . . . 33

Viewing Acquired Data . . . . . . . . . . . . . . . . . . . 34

Chapter 4 Analyzing Data . . . . . . . . . . . . . . . . . . . . . . . 37

Viewing Results in TyperAnalyzer . . . . . . . . . . . . . . . 37

Generating Reports in TyperAnalyzer . . . . . . . . . . . . . . 39

Report Types . . . . . . . . . . . . . . . . . . . . . . 40

Chapter 5 Service and Maintenance . . . . . . . . . . . . . . . . . . . 41

Maintenance . . . . . . . . . . . . . . . . . . . . . . 41

Repairs . . . . . . . . . . . . . . . . . . . . . . . . 41

Shutting Down the MassARRAY Dx Analyzer 4 . . . . . . . . . . . 41

Removal From Operation . . . . . . . . . . . . . . . . . . 42

Appendix A Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . 43

MADX-USG-CUS-501 R03MassARRAY® Dx Analyzer 4 User Guide

ii

Appendix B Manually Acquiring Spectra . . . . . . . . . . . . . . . . . 45

Manually Acquiring Spectra . . . . . . . . . . . . . . . . . 45

Saving Manually Acquired Spectra . . . . . . . . . . . . . . . 47

Saving and Loading a Shot File . . . . . . . . . . . . . . . 48

Appendix C Recalling Plate Data . . . . . . . . . . . . . . . . . . . . . 51

Appendix D Licensing . . . . . . . . . . . . . . . . . . . . . . . . . 53


Chapter 1

Overview

Intended Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1The MassARRAY Dx Analyzer 4 Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1Installation Procedures and Special Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2Limitations, Warnings and Precautions, and Hazards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4Customer Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.1 Intended Use

The MassARRAY® Dx Analyzer 4 is a benchtop MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) mass spectrometer intended for analysis of nucleic acids.

The MassARRAY Dx Analyzer 4 is intended to be used only in combination with Agena BioscienceTM Panels indicated for use with the MassARRAY Dx Analyzer 4 for the applications described in the panel Instructions for Use.

The MassARRAY Dx Analyzer 4 is intended for use by professional users, such as technicians and physicians trained in molecular biological techniques and the operation of the MassARRAY Dx Analyzer 4.

1.2 The MassARRAY Dx Analyzer 4 Instrument

Instrument Components

The MassARRAY Dx Analyzer 4 includes the items listed in Table 1.1.

Table 1.1 MassARRAY Dx Analyzer 4 Components ( 40400; part of 40010)Component Description

MassARRAY Dx Analyzer 4 Benchtop MALDI-TOF mass spectrometer for highly accurate, sensitive analysis of nucleic acids. 2 96-pad SpectroCHIP® Array capacity per run. Integrated camera for sample positioning and barcode reading. Includes a chip holder for holding SpectroCHIP Arrays when they are loaded into the MassARRAY Dx Analyzer.


Chapter 1 Overview2

NOTEThe MassARRAY Dx Analyzer 4 instrument should only be used with Agena Bioscience Dx panels for diagnostic use.

1.3 Installation Procedures and Special Requirements

An Agena Bioscience Service Engineer will install and align the MassARRAY Dx Analyzer 4. Please contact Agena Bioscience Customer Support (page 7) if there are any questions or concerns about the installation.

Instrument Location The instrument must be placed on a work surface capable of supporting its weight. The work surface must not subject the instrument to vibration. There must be adequate clearances around the instruments as described in the MassARRAY Dx System Site Requirements document.

Integrated computer For data management; Windows operating system. Includes the following software:

• Chip Linker - For creation of input files that contain the information needed for plate and SpectroCHIP Array processing.

• SpectroACQUIRE - Instrument control software that provides the graphical user interface. Enables user to set up and start an automatic run or perform manual data acquisition.

• AnalyzerControl - Enables communication between the Analyzer 4 and the SpectroACQUIRE software.

• MassARRAY Caller - Analyzes data as it is acquired: identifies and calls the spectra peaks and exports the data to the MassARRAY database when the automatic run is completed.

• MassARRAY Typer - For set up of the experiment in the database, and display of results and generation of reports.

• MassARRAY Oracle Database - For analysis and storage of the exported data.

Accessory Kit Includes Clean Resin dimple plates and scraper.

Component Description


Chapter 1 Overview 3

CAUTION

After the Agena Bioscience Service Engineer has installed and aligned the MassARRAY Dx Analyzer 4, do not relocate the instrument. Moving the instrument improperly can impact the optical alignment and compromise data integrity. If you need to relocate the instrument, contact Agena Bioscience Customer Support.

Specifications and Requirements

Physical Dimensions and Weight

Table 1.2 MassARRAY Dx Analyzer 4 Dimensions and Weight

Environmental Requirements

Table 1.3 Optimal Environmental Conditions

Physical Clearance Requirements

Table 1.4 Minimum Space Requirements Around the MassARRAY Dx Analyzer 4

Electrical Requirements and Specifications

CAUTION

Only use the detachable power cord provided by Agena Bioscience.

Dimension Measurement

Width 45 cm (18 in)

Height (closed) 110 cm (43 in)

Height (open) 145 cm (57 in)

Depth (closed) 68 cm (27 in)

Depth (open) 113.4 cm (45 in)

Weight 95 kg (210 lb)

Item Optimal Recommended Range

Temperature 16-24°C (61-75°F)

Humidity 30-75% relative humidity

Direction Minimum Clearance Reason

Above 12 inches (30 cm) To allow instrument cooling.

Sides 24 inches (61 cm) To allow access for maintenance.

Behind 8 inches (20.3 cm) To allow access to power switch and space for power cable and ventilation.


Chapter 1 Overview4

Table 1.5 MassARRAY Dx Analyzer 4 Power Supply and Consumption Characteristics

Storage Requirements

Table 1.6 Acceptable Storage Conditions

1.4 Limitations, Warnings and Precautions, and Hazards

The MassARRAY Dx Analyzer 4 conforms to European Directive 98/79/EC for in vitro diagnostic medical devices and can be used (in the EU and in countries where approved for this purpose) for in vitro diagnostic use.

This device complies with IEC 61326-2-6:2005. This device has been designed and tested to CISPR 11 Class A. The electromagnetic environment should be evaluated prior to operation of the device. Do not use this device in close proximity to sources of strong electromagnetic radiation (e.g., unshielded intentional radio frequency sources), as these may interfere with proper operation.

Limitations of the Procedure

• The MassARRAY Dx Analyzer 4 is designed to deliver qualitative (i.e., genotype) and quantitative (i.e., allelotype) results.

• Biochemistry reaction by-products (such as ion adducts) and the presence of other peaks in close proximity to a targeted peak on the mass spectrum may affect the ability of the MassARRAY Dx Analyzer 4 to make accurate genotype calls in a multiplexed test.

• It is recommended that all genotyping and allelotyping tests run on the MassARRAY Dx Analyzer 4 include an appropriate external control for each targeted locus in the test, as applicable.

Item Description

Site Power (for each instrument) 100-240VAC/15A/50-60Hz, single phase voltage.

Uninterruptable power supply.

Properly grounded.

It is recommended that the receptacle providing power to the instrument be on a dedicated circuit.

Receptacle must be within 4 feet of instrument.

Voltage detection Instrument automatically detects and selects proper voltage within the range stated above.

Power Consumption 8.4 A maximum.

Item Description

Temperature 2-45 °C (36-113°F)

Humidity 20-85% relative humidity



Warnings and Precautions

• Handle all biological specimens as if they are potentially infectious agents.

• Follow Good Laboratory Practices and all laboratory safety precautions to prevent PCR products from contaminating reagents, instrumentation, and genomic DNA samples. PCR contamination may cause inaccurate and unreliable results.

• Wear personal protective clothing such as disposable gloves, laboratory coat and eye protection.

• Failure to follow the procedures outlined in the User Guide may result in erroneous results.

• Do not operate the MassARRAY Dx Analyzer 4 with any of the panels removed. Operating the instrument with any of the panels removed may create potential exposure to DC voltage.

• The MassARRAY Dx Analyzer 4 weighs approximately 95 kg and could cause serious injury if dropped or mishandled.

Hazards MassARRAY Dx Analyzer 4 SafetyRead and understand all of the safety and operating instructions before you operate the MassARRAY Dx Analyzer 4. To obtain accurate results, you must follow the User Guide instructions. Non-compliance with these instructions may void any warranty covering this product.

WARNINGWARNING! The MassARRAY Dx Analyzer 4 must only be used as specified by Agena Bioscience in this User Guide and other supporting documents. Any other use may impair the protections provided by the instrument.

Degree of Protection

The MassARRAY Dx Analyzer 4 is IPX0 per IEC 60529 standard.

Proper Grounding

The MassARRAY Dx Analyzer 4 must be connected to a properly grounded power source.

WARNINGWARNING! Connecting the instrument to a non-grounded power source creates an electrical hazard that can damage the instrument or cause personal injury. Do not disrupt or disconnect the power cord ground connector. Disabling the power cord ground connector creates an electrical hazard that can damage the instrument or cause personal injury.


Chapter 1 Overview6

Laser Safety

The MassARRAY Dx Analyzer 4 is a Class 1 Laser Product per IEC 60825 standard. The warning label shown in Figure 1.1 is located on the back of the instrument. Under normal operating conditions, no additional safety measures are necessary.

Mechanical Safety

Contact Agena Bioscience Customer Support (page 7) if it becomes necessary to remove the instrument cover. There are no user-serviceable components beneath the instrument cover. The warning label shown in Figure 1.2 is located on the back of the instrument.

Laboratory Safety

Biological samples such as blood, other bodily fluids, or tissue from humans and other animals, as well as microbiological cultures can transmit infectious diseases. Personal protective equipment (PPE), including protective clothing, eye wear and gloves must be worn. Applicable local, state/provincial, national and international regulations must be followed.

Waste Handling

WARNINGWARNING! Hazardous or biohazardous waste may be produced, depending on the specific application, substrates, and reagents used. Precautions must be taken to ensure health and safety of all laboratory staff. Instrument waste must be disposed of in accordance with local, state/provincial, national and international regulations.

Figure 1.1 Safety Label: Laser Warning

Figure 1.2 Safety Label: Crush and Pinch Point Warning



1.5 Customer Support

For customer support please contact:

Agena Bioscience GmbHMendelssohnstrasse 15DD-22761, HamburgGermanyPhone: (+49) 40-899676-0Fax: (+49) 40-899676-10Order Desk: [email protected]: [email protected]


Chapter 1 Overview8

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Chapter 2

Principles of Operation

MassARRAY Dx Analyzer 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9MassARRAY Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

2.1 MassARRAY Dx Analyzer 4

MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) produces, separates, and detects gas phase ions. Analyte transferred onto a SpectroCHIP Array cocrystallizes with the pad matrix. During MALDI-TOF MS, crystals are irradiated with a nanosecond light pulse from an ultraviolet laser (wavelength 337 nm). The laser energy causes structural decomposition of the irradiated crystals and generates a particle cloud from which ions are extracted by an electric field. This results in the disintegration of the crystal. After accelerating through the electric field, the ions drift through a field-free path, then reach a detector and generate a spectrum for analysis (Figure 2.1).

The MassARRAY Dx Analyzer 4 is a bench top MALDI-TOF mass spectrometer (Figure 2.2).

Figure 2.1 General schematic of MALDI-TOF MS

High voltage and grounded electrodes

Tray with SpectroCHIP Array and sample at high potential


Chapter 2 Principles of Operation10

*Note: Previous models of the instrument may look slightly different and will have different MA4front panel indicator lights. See Figure 2.3 and Table 2.2

The front control panel of the MassARRAY Dx Analyzer 4 consists of a vertical LED display that shows the status of the MassARRAY Analyzer 4 (Table 2.1).

Table 2.1 MA4 Front Panel Indicator Lights

Previous ModelSome users may have a previous model of the MassARRAY Analyzer 4 with a slightly different cover and MA4 front panel indicator lights. See Figure 2.3 and Table 2.2.

Figure 2.2 MassARRAY Dx Analyzer 4*

Manual stage control button

Sample chamber (stage out) with sample chamber lid open

Chip

Front panel indicator lights

Indicator Light Meaning When Lit

Blue, slowly flashing Instrument is not ready.

Green Instrument is ready.Instrument is ready and processing (but laser not currently firing).

Yellow, with a block of blue lights moving from bottom to top

Instrument is ready and processing (the laser is firing).

Red flash; may occur in conjunction with any of the lights described above

Error; contact Agena Bioscience Customer Support.


Chapter 2 Principles of Operation 11

Table 2.2 Front Control Panel (previous model)

Power SwitchThe main power switch of MassARRAY Dx Analyzer 4 is located on the back of the instrument at the middle left.

Figure 2.3 Front Control Panel (previous model)

Indicator/Button Meaning When Lit

Power Instrument power is on.

Ready The required vacuum pressure has been reached in the sample chamber (5.0 x 10-6 mbars), and the instrument is ready for measurement.

Error A system error occurred.

Laser The laser is firing.

Figure 2.4 Main Power Switch

Power switch

l = On, O = Off

Power cord



Input/output ports on the back of the instrument provide connections to the integrated computer.

2.2 MassARRAY Software

Typer Software MassARRAY Typer is a suite of software applications that allows for set up of the experiment in the database, and for viewing of results and generating reports.

Typer Assay Editor is used to import the assay design file into the MassARRAY database,. The assay design file contains all the essential assay design specifications for genotyping and allelotyping analysis.

Typer PlateEditor is used to create a virtual plate in the MassARRAY database. This virtual sample plate represents the physical sample plate with the analytes.

TyperAnalyzer is used to view the data and to generate reports.

Figure 2.5 Input/Output Ports

Keyboard (PS2)

Mouse (PS2) Network (Ethernet)

Monitor (VGA)

USB

Figure 2.6 MassARRAY Typer


Chapter 2 Principles of Operation 13

Chip Linker Software Chip Linker software is used to create an XML input file that links the virtual plate to a SpectroCHIP Array, and provides the information that the Analyzer 4 needs to process the SpectroCHIP Array and save data to the MassARRAY database.

SpectroACQUIRE Software

SpectroACQUIRE is the instrument control software that provides the graphical user interface enabling users to set up and start an automatic run or perform manual data acquisition.

The Automatic Run Setup tab allows the user to select the SpectroCHIP Arrays to be processed and set the acquisition parameters.

Figure 2.7 Chip Linker window



Figure 2.8 SpectroACQUIRE, Automatic Run Setup Tab


Chapter 3

Operating Instructions

Setting up the Experiment in MassARRAY Typer Software . . . . . . . . . . . . . . . . . . . . . . . . 16Starting the MassARRAY Dx Analyzer 4 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Loading SpectroCHIP Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19Creating and Importing an Input File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22Setting Up the Automatic Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26Checking the Barcode Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30Starting the Automatic Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Unloading SpectroCHIP Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33Viewing Acquired Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

This chapter explains how to process SpectroCHIP Arrays on the MassARRAY Dx Analyzer 4 instrument using the automatic run mode. Spectra may also be manually acquired from user-specified wells; see Appendix B for instructions.

Before using the MassARRAY Dx Analyzer 4, personnel must be trained by Agena Bioscience on operation of the instrument. The instrument will be installed by an Agena Bioscience Field Service Engineer, who will provide training on system start up, sample loading, and software operation. Agena Bioscience Applications and Technology Support personnel will then provide detailed software and applications training, including training on chemistry and sample workflow procedures.

Users must follow the instructions in this User Guide as well as good laboratory practices to ensure that test results are reliable.

The MassARRAY Dx Analyzer 4 is powered on at installation. Agena Bioscience strongly recommends leaving the instrument powered on.

During processing, the Analyzer 4:

• Acquires and displays spectra in real time

• Identifies and calls peaks in real time

• Saves the data to the MassARRAY database


Chapter 3 Operating Instructions16

Table 3.1 Processing SpectroCHIP Arrays on the MassARRAY Dx Analyzer 4 (Automatic Run)

3.1 Setting up the Experiment in MassARRAY Typer Software

Importing the Assay Design File with Typer AssayEditor

The assay design file must be imported into the MassARRAY database, using Typer AssayEditor. The assay design file contains all the essential assay design specifications for genotyping and allelotyping analysis.

The assay design file only needs to be imported once, prior to running your panel for the first time.

To import an assay design file:

1. Download the assay design file for your panel from AgenaCx.com.

2. Open Typer AssayEditor.

3. Create a new assay project in the Database Browser by right-clicking the root node and selecting Project Administrator.

4. Add a new Assay Project with an appropriate name. The new Assay Project will appear in the database browser. The assay design file will be stored in this project.

5. Right-click on the newly created Assay Project and select Import Assay Group in Designer format.

6. Remove the checkmarks next to Design Summary and SNP Group. Make sure that there is a checkmark next to Assay Group.

7. Click the Browse button next to Assay Group.

8. Navigate to the folder where the assay design file was saved, select it, and click Open.

Step See Page

1. Set up the experiment in MassARRAY Typer software. 16

2. Start the MassARRAY Dx Analyzer 4 software. 18

3. Load SpectroCHIP Arrays. 19

4. Create an input file. 22

5. Set up the automatic run (Automatic Run Setup tab of SpectroACQUIRE).

• Select the input file.

• Enter acquisition parameters.

• Make appropriate selections in Geometry section

• Check Turn off HV after last Chip is complete option in Instrument section.

26

6. Check the Barcode Report (Automatic Run Setup tab of SpectroACQUIRE) and correct any errors.

30

7. Start the Automatic Run (Automatic Run tab of SpectroACQUIRE).

31

8. Unload the SpectroCHIP Arrays. 33


Chapter 3 Operating Instructions 17

9. Click the Import button to import the file.

Creating a Virtual Plate in Typer PlateEditor

Once the assay design file has been imported, a virtual sample plate must be created in the MassARRAY database. This virtual sample plate represents the physical sample plate with the analytes. Use Typer PlateEditor to:

• Create a sample group and enter it into the database.

• Create a virtual sample plate.

• Apply assays to the plate.

• Apply samples to the plate.

Creating a Sample Group

1. Create a text file (.txt) of sample descriptions in a spreadsheet application such as Microsoft® Excel. The file must contain the sample ID in column A, and may contain a description in column B.

2. Each sample group belongs to a sample project, and each sample project belongs to a sample customer. Create a sample customer and sample project in the database, if you haven’t already done so.

a. Open the Plate Editor software and click on the Sample tab.

b. To create a sample customer, right-click the root-node and select Add New Sample Customer. Enter a sample customer ID and additional optional information and click OK. The new sample customer will appear in the Sample tab.

c. To create a sample project, right-click the sample customer that the sample project will be under and select Add New Sample Project. Enter a sample project ID and optional additional information and click OK. The new sample project will appear in the Sample tab.

3. Create a sample group.

a. Right-click on the sample project that you want to add the sample group to and select Add New Sample Group.

b. Enter a sample group ID and click the folder button in the toolbar to browse to the location of your sample group text file, and click Open, then click OK.

Creating a Plate

1. Each plate belongs to a project, and each project belongs to a customer. Create a customer and project in the database, if you haven’t already done so.

a. In the Plate Editor software click on the Plate tab.

b. To create a customer, right-click the root-node and select New Customer. Enter a customer ID and additional optional information and click OK. The new customer will appear in the Plate tab.



c. To create a project, right-click the customer that the project will be under and select New Project. Enter a project ID and optional additional information and click OK. The new project will appear in the Plate tab.

2. Create a Plate.

a. Right-click on the project that you want to add the plate to and select New Plate.

b. Enter a plate ID and select 96 as the plate size and click OK. The new plate will appear in the Plate tab and a plate layout will be created automatically.

Applying Assays to the Plate

1. In the Plate tab, select the plate that was just created.

2. Select the Assay tab, and locate the assay design file you imported earlier.

3. In the plate layout, select the wells of interest.

4. In the Assay tab, right-click the plex or assay that you want to assign to the selected wells and select Add plex or Add assay.

Applying Samples to the Plate

1. Click on the Sample tab.

2. In the plate layout, select the wells of interest.

3. Right-click the sample or sample group that you want to assign to the selected wells and select Add Samples from Group or Add Sample.

4. Select File > Save from the toolbar.

3.2 Starting the MassARRAY Dx Analyzer 4 Software

The MassARRAY Dx Analyzer 4 software includes three applications:

• AnalyzerControl — Enables communication between the Analyzer 4 and the SpectroACQUIRE software. The AnalyzerControl software must be running in order for SpectroACQUIRE to control the MassARRAY Dx Analyzer 4.

• MassARRAY Caller — Analyzes the data as it is acquired. Identifies and calls the spectra peaks. Exports the data to the MassARRAY database when the automatic run is completed.

• SpectroACQUIRE — Instrument control software that provides the graphical user interface. Enables you to set up and start an automatic run or perform manual data acquisition.

Double-click the Analyzer 4 instrument icon on the desktop to launch AnalyzerControl, MassARRAY Caller, and SpectroACQUIRE. The SpectroACQUIRE window appears on the desktop (Figure 3.1).



NOTEIt is recommended that you leave the software and the workstation on. If it is necessary to restart the software, use the Analyzer 4 instrument icon on the desktop. If you need to start the software independently, start the applications in the following order: AnalyzerControl, MassARRAY Caller, and SpectroACQUIRE.

You will also use Chip Linker software to create and import an input file (see page 22).

3.3 Loading SpectroCHIP Arrays

1. Move the Chip holder to the sample chamber ("sample out" position) by clicking Probe Sample In/Out on the SpectroACQUIRE toolbar (Figure 3.2). Alternatively, press the manual stage control button on the front of the Analyzer 4.

CAUTIONWhen the Chip holder is moving in or out of the Analyzer 4, do not start or quit the SpectroACQUIRE software or start acquisition. Do not move the Chip holder during spectra acquisition. Wait until acquisition is completed, or abort the run. For more details on stopping a run, see page 32.

It takes approximately one minute for the Chip holder to move to the load position. The vacuum is then eliminated and the lid may be opened and the Chip holder recovered (Figure 3.3).

Figure 3.1 SpectroACQUIRE Window



2. Open the sample chamber lid (Figure 3.3) and take out the Chip holder. Remove the previously run SpectroCHIP Arrays from the Chip holder.

NOTEIt is important that the Chip holder always contains two SpectroCHIP Arrays during a run. If you only want to process one SpectroCHIP Array, place it in SpectroCHIP Array position 1 and leave the previously run SpectroCHIP Array in position 2.

3. Place the SpectroCHIP Arrays to be processed in the Chip holder. Make sure that the Agena Bioscience logo on the SpectroCHIP Array is next to the bottom edge of the Chip holder (Figure 3.4) and that each SpectroCHIP Array is properly seated so that the Chip holder and SpectroCHIP Array surface are flush. Also make sure that the samples are dried and no liquid or dust is on the SpectroCHIP Array before loading.

NOTEAlways wear gloves and use the supplied tweezers when handling SpectroCHIP Arrays.

4. Firmly press down on the sample chamber lid and click Probe Sample In/Out on the SpectroACQUIRE toolbar.

The Chip holder moves to the "sample in" position. The Analyzer 4 ready light illuminates when the required vacuum pressure (5 x 10-6 mbars) is reached. This takes approximately two minutes.

Figure 3.2 SpectroACQUIRE toolbar

Click to move the Chip holder in or out of the Analyzer 4.



NOTEOnly use the Chip holder that was supplied with the MassARRAY Dx Analyzer 4. The Chip holder design is instrument-specific and Chip holders are not interchangeable between instruments.

Figure 3.3 Sample Chamber

Figure 3.4 Chip Holder

Sample chamber lid

Chip holder

Sample chamber O-ring

Bottom edge of Chip holder

Top edge of Chip holder Beveled edge of Chip holder

Place an old or previously run Chip in position 2

SpectroCHIP Array in Chip holder position 1

Barcode



3.4 Creating and Importing an Input File

An input file must be created linking the virtual plate created earlier in Typer PlateEditor to a SpectroCHIP Array, and providing the information that the MassARRAY Dx Analyzer 4 needs to process the SpectroCHIP Array and save data to the MassARRAY database.

Start Chip Linker

1. Double-click the Chip Linker icon on the workstation desktop.

2. In the dialog box that appears (Figure 3.5), enter your user name, password, and server.

3. Click Connect.

The Chip Linker window appears (Figure 3.6).

Specify the Input Information

1. Select a plate in the Chip Linker directory tree (Figure 3.7).

2. Select iPLEX for the terminator chemistry.

Figure 3.5 Connect to Database

Figure 3.6 Chip Linker window



3. Select the process method specified in the Instructions for Use for the panel you are running. For more details, see Table 3.2.

4. Select Nanodispenser 96 to 96 for the dispenser method. For more details, see Table 3.2.

5. Enter an experiment name.

6. Enter the SpectroCHIP Array barcode.

7. Click Add.

The input information appears in the Chip Linker table (Figure 3.7).

8. If a second SpectroCHIP Array will be processed, repeat step 1 to step 7 for the second SpectroCHIP Array.

9. Click Create to generate an input .xml file. This file will be selected for use when you set up the automatic run (page 26).

Figure 3.7 Chip Linker

See Table 3.2 for details on these items.

Chip Linker table with information for two SpectroCHIP Arrays

Directory tree of plates created using Typer PlateEditor

Select a plate in the directory tree. (Click a +/- sign to expand or collapse a node.)

To search for a plate:

• Expand a node in the directory tree

• Enter all or part of the plate name

• Click Find Next Plate.



Table 3.2 Chip Linker Window

Editing Information in the Chip Linker TableYou can edit or remove information in the Chip Linker table before the input file is generated.

Item Description

Terminator Chemistry

Specifies the type of chemistry used in your experiment.

Process Method

Specifies the MassARRAY Caller algorithm:

Genotype - Calls genotypes.

Allelotype - Calls samples polymorphic or non-polymorphic, and computes allele frequencies.

Genotype + Area - Calls genotypes and computes peak areas.

Gene Expression - Calls cDNA frequency against competitors and computes gene expression concentrations.

DispenserNOTE

If the dispenser mapping selected here does not match the plate size selected in Plate Editor, an error occurs at the start of an autorun and SpectroCHIP Array processing will not proceed.

Nanodispenser 384 to 384 – Samples transferred from a 384-well microtiter plate to a 384-well SpectroCHIP Array using the Nanodispenser.

Single Pin 384 to 384 – Samples transferred from a 384-well microtiter plate to a 384-well SpectroCHIP Array with a single pin using the Nanodispenser.

Nanodispenser 96(4) to 384 – Samples transferred from four 96-well microtiter plate to one 384-well SpectroCHIP Array using the Nanodispenser.

Nanodispenser 96 to 96 – Samples transferred from a 96-well microtiter plate to a 96-well SpectroCHIP Array using the Nanodispenser or the Chip prep module.

Nanodispenser 96 to 384 (x4D) – Samples from one 96-well microtiter plate transferred to a 384-well SpectroCHIP Array (four replicates) using the Nanodispenser.

Single Pin 96 to 96 – Samples transferred from a 96-well microtiter plate to a 96-well SpectroCHIP Array using the Nanodispenser or to a 24-pad SpectroCHIP Array using the manual dispense method.

Experiment Name

User-specified experiment name. Name may use the following characters only: A-Z,0-9, _ & -

Chip Barcode

The SpectroCHIP Array barcode or other user-specified SpectroCHIP Array identifier. Name may use the following characters only: A-Z,0-9, _ & -



NOTEAfter information is added to the Chip Linker table, the selected plate cannot be changed. If you want to change the plate, remove the row (select the row in the table and click Remove), then repeat step 1 to step 7 on page 23.

1. Select the row that you want to edit.

2. Enter the SpectroCHIP Array barcode (or other SpectroCHIP Array identifier) that is associated with the input information.

3. Edit any of the following: Terminator Chemistry, Process Method, Dispenser, or Experiment Name.

4. Click Change.

The updates are applied to the selected plate

5. Click Add.

The updated information appears in the Chip Linker table.

Removing Information From the Chip Linker Table

1. Select a row in the table.

2. Click Remove.

Create the Input Files

1. After you are finished adding input information to the Chip Linker table, click Create.

An input file (.xml) is generated for each SpectroCHIP Array.

Figure 3.8 Chip Linker

Enter a SpectroCHIP Array barcode, then edit the information.



3.5 Setting Up the Automatic Run

Selecting the Input Files

1. In SpectroACQUIRE, click the Automatic Run Setup tab.

2. Check the box located next to Chip 1 and, if acquiring data from a second SpectroCHIP Array, Chip 2.

Figure 3.9 SpectroACQUIRE, Automatic Run Setup Tab



Setting acquisition parameters

Acquisition parameters need to be specified for the particular type of data being analyzed (Figure 3.10). See Table 3.3 for a description of these parameters. SpectroACQUIRE will automatically select the appropriate parameter file and load the default values for you. Make sure that the Filter Saturated Shots box is selected.

Figure 3.10 Acquisition Parameters in SpectroACQUIRE Automatic Run Setup Tab



Table 3.3 Acquisition Parameter Description

Parameter Description Default Value

Shots (n) The number of laser shots attempted per acquisition per raster position. 20

Maximum acquisitions

Specifies the number of raster positions from which to acquire data. Acquisition begins at the center of the pad. This means if the maximum acquisitions is set to one, the laser does not raster and spectra are only acquired from the center of the pad. If the maximum acquisitions is set to 5, the Analyzer 4 attempts acquisition at the center of the pad plus raster positions 2-5.

NOTEThe Analyzer 4 may not attempt acquisition at all of the specified raster positions. The maximum acquisition value specifies the maximum number of raster positions from which to attempt acquisition. The Analyzer 4 moves on to the next well when the required number of

“good spectra” are acquired or the maximum number of raster positions has been attempted. For multiplexed assays, these criteria are applied to each assay individually. This means that the Analyzer 4 moves on when good spectra are acquired or the maximum number of rasters has been attempted for each assay in the multiplex.

5

Minimum good spectra

The minimum number of spectra to acquire before starting analysis. 3

Maximum good spectra

The maximum number of good spectra to collect. Acquisition stops after the specified number of spectra is acquired.

3

Filer Saturated Shots

This option removes any acquisitions (“shots”) with intensities above the instrument’s detection limit.

Selected

1

2 3

45

6

7

8

9

Acquisition begins at the center of the SpectroCHIP Array pad, then the laser moves (rasters) around the pad to up to 9 different raster positions.

Example raster positions



Selecting Geometry Settings

Geometry settings must be selected in the Automatic Run Setup tab (Figure 3.11).

Use Calibration WellsSelect this option to acquire spectra from calibration pads (recommended). Make sure that at least one of the calibration pads contains calibrant. If this option is chosen, but there is no calibrant in the calibration pads, the software uses the last good calibration values.

Auto Teach GeometrySelect this option to enable autoteaching (recommended). Autoteaching is the process that the SpectroACQUIRE software uses to check the position of a SpectroCHIP Array and correct small variations in the SpectroCHIP Array position.

For each pad used in autoteaching, the software determines the difference between the actual location of the pad (indicated by the autoteaching cross-hairs ) versus the desired location (indicated by the laser cross-hairs +) (Figure 3.12). The software computes the average difference and uses this value as an offset to correct the SpectroCHIP Array position. The autoteaching cross-hairs disappear after the offset is determined.

Figure 3.11 Geometry Settings in SpectroACQUIRE Automatic Run Setup Tab



Chip TypeSelect the type of SpectroCHIP Array you are using from the drop-down menu.

Turn Off HV After Last SpectroCHIP Array is Complete

Choose this option to automatically turn off the high voltage after data acquisition is completed. This option is useful if the Analyzer 4 will operate unattended and is strongly recommended.

3.6 Checking the Barcode Report

The barcode report confirms that each SpectroCHIP Array is properly associated with an experiment in the MassARRAY database.

CAUTIONGenerating a barcode report is optional. However, it is strongly recommended because a SpectroCHIP Array will not be processed if it is not associated with an experiment in the database. During a run, each SpectroCHIP Array is checked just before it is processed. Both SpectroCHIP Arrays are not checked at the beginning of the run. If the first SpectroCHIP Array has an error status, the analysis stops and the second SpectroCHIP Array will not be processed.

1. Click Barcode Report in the Automatic Run Setup tab.

2. In the report that appears, check the status of each SpectroCHIP Array.

Figure 3.12 Autoteaching and Laser Cross Hairs in the SpectroACQUIRE Video Display



Found - The SpectroCHIP Array is properly associated with an experiment in the database.

Error - The SpectroCHIP Array is not associated with an experiment in the database.

3. Click Close.

4. If any errors are found, correct them and perform another barcode report.

3.7 Starting the Automatic Run

1. In SpectroACQUIRE, click the Automatic Run tab.

Figure 3.13 Barcode Report



2. To start the run, click the button on the SpectroACQUIRE toolbar.

The software:

• Confirms that the SpectroCHIP Array is associated with an experiment in the MassARRAY database. If there is no experiment associated with the SpectroCHIP Array, the run stops and an error message will appear. No spectra are acquired from this SpectroCHIP Array or the next SpectroCHIP Array.

• Confirms that the dispenser method selected in Chip Linker matches the plate size selected in Plate Editor. If they do not match, an error message will appear and the automatic run will not proceed.

• Checks the position of the SpectroCHIP Array in the Chip holder (i.e., performs auto teaching).

• Acquires calibration spectra if the "Use Calibration Wells" option is chosen.

• Acquires spectra.

Stopping an Automatic Run

It is recommended that you allow an automatic run to finish. However, if necessary, you can stop an automatic run before acquisition is completed.

1. Click the button on the SpectroACQUIRE toolbar.

2. If any data has been collected from the current SpectroCHIP Array, choose an option in the dialog box that appears and click OK.

Figure 3.14 SpectroACQUIRE Automatic Run Tab



Table 3.4 Stop Automatic Run Options

3.8 Unloading SpectroCHIP Arrays

Do not unload SpectroCHIP Arrays while SpectroACQUIRE is acquiring spectra. Wait until the data acquisition is completed.

1. In the SpectroACQUIRE software, click the Automatic Run Setup tab.

2. Press the manual stage control button on the front of the Analyzer 4 (see Figure 2.2) to extend the target. It takes approximately one minute for the Chip holder to move to the load position.

Figure 3.15 Stop Autorun Options

Option Description

Continue with the automatic run

Resumes the acquisition from where it was interrupted.

Stop and discard the data that has been collected on the currently running chip

Stops the run and discards any spectral data acquired from the current SpectroCHIP Array.

NOTESelect this option if you want to reanalyze the SpectroCHIP Array later and save the data to the experiment that is currently associated with the SpectroCHIP Array.

Stop and store the data from the current chip

Stops the run and saves any data acquired from the current SpectroCHIP Array to the associated experiment in the MassARRAY database. If you want to reanalyze the SpectroCHIP Array at a later time, you will need to re-associate the SpectroCHIP Array with the experiment.

Stop the automatic run after completing the current chip

Stops the run after completing data acquisition from the current SpectroCHIP Array. This is useful if the second SpectroCHIP Array that was set up in the autorun will not be analyzed.



CAUTIONWhen the Chip holder is moving in or out of the Analyzer 4, do not start or quit the SpectroACQUIRE software or start acquisition. Do not move the Chip holder during spectra acquisition. Wait until acquisition is completed, or abort the run.

3. Open the sample chamber lid and take out the Chip holder. Remove the SpectroCHIP Arrays from the Chip holder. Replace Chip holder onto the Chip carrier. Press the manual stage control button on the front of the Analyzer 4 to retract the Chip carrier.

NOTEAfter SpectroCHIP Array processing is completed, it is recommended that you leave the Analyzer 4 and workstation on. If you need to shut down the system, contact Agena Bioscience Customer Support.

3.9 Viewing Acquired Data

During acquisition The spectrum from each pad is displayed in real time during acquisition and can be viewed in the SpectroACQUIRE window, along with a color-coded map of the SpectroCHIP Array which shows each pad’s call status, a real-time video of the SpectroCHIP Array surface, and a list of the call status of each assay (Figure 3.16).



Figure 3.16 SpectroACQUIRE Window During SpectroCHIP Array Processing (Automatic Run tab)

Real-time video of the SpectroCHIP Array surface from the MassARRAY Dx Analyzer camera. The red crosshair (+) indicates where the laser is aimed.

The call status of the assays per SpectroCHIP Array pad as the spectra are acquired.

The spectrum from each pad is displayed in real-time during acquisition. If multiple shots are taken, the average of the spectra is shown.

Color-coded well map (for more details, see Table 3.5 and Table 3.6)

Color indicates SpectroCHIP Array status:

Currently being processed

Waiting to be processed

Empty position in the Chip holder.

Processed

Bad SpectroCHIP Array name. Double-click the SpectroCHIP Array to view the error details.



Table 3.5 Automatic Run Tab, Genotyping or Genotyping+Area Application

Table 3.6 Automatic Run Tab, Allelotyping Application

After acquisition SpectroACQUIRE processes the spectra and saves the data to the MassARRAY database on a per SpectroCHIP Array basis. The data from the first SpectroCHIP Array may be available in the database before both SpectroCHIP Arrays have been processed. Review the data using MassARRAY Typer software Chapter 4.

Well Color Description

Purple Waiting to be processed.

Gray Well will not be processed.

Green(with plus symbol)

Conservative or moderate call. (In multiplexed assays, all assays must yield a moderate or better call.)

Red(with minus symbol)

Aggressive call, no call, bad spectrum, or no spectrum. (In multiplexed assays, just one assay yielding an aggressive call, no call, or bad spectrum will cause the well to be marked red.)

Well Color Description

Purple Waiting to be processed.

Gray Well will not be processed.

Turquoise Non-polymorphic.

Green Polymorphic.

Yellow Uncertain. (The average frequency of one allele is less than or equal to 3 times the standard error of the frequencies before averaging.)

Red Bad spectrum.

(+) or (-) In addition to a color code, each well shows a (+) or (-) sign:(+) indicates the area of the unextended primer or contaminant peak is less than 20% of the combined areas of the peaks for unextended primer, first allele, and second allele.(-) indicates the area of the unextended primer or contaminant peak is greater than or equal to 20% of the combined areas of the peaks for unextended primer, first allele, and second allele.


Chapter 4

Analyzing Data

Viewing Results in TyperAnalyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37Generating Reports in TyperAnalyzer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Report Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

This chapter describes how to view data and generate reports in Typer Analyzer. For more detailed information on data analysis and reporting, see the Instructions for Use for the panel you are running.

4.1 Viewing Results in TyperAnalyzer

1. Open TyperAnalyzer and double-click the SpectroCHIP Arrays of interest in the Project Explorer pane.The SpectroCHIP Arrays will be added to the Chip List.

2. To select the results to display, put a checkmark next to the SpectroCHIP Array in the Chip List. If more than one SpectroCHIP Array is checkmarked, click on the SpectroCHIP Array name to select it. The active SpectroCHIP Array will be highlighted.

3. You may now view and manage data in a number of different panes in the TyperAnalyzer window (see Figure 4.1), allowing you to:

• Display data in table and graphical formats.

• Automatically check results for errors.

• Apply cluster analysis to results.

• Highlight results in call cluster plots according to user-specified metadata.

• Exclude user-specified unusable results from the TyperAnalyzer windowpanes.

• Manually call a genotype.

• Restore the original genotype call.


Chapter 4 Analyzing Data38

Figure 4.1 TyperAnalyzer Default Window Layout

Traffic Light paneA plate map of the active SpectroCHIP Array. Selecting a well updates the Call Cluster Plots, Details pane, and Sample Plot.

A list of the assays on the SpectroCHIP Arrays that are checkmarked. Selecting an assay updates the:• Active SpectroCHIP Array• Selected well in the Traffic

Light pane• Call Cluster Plots• Chip and Assay Summaries• Sample Plot

TyperAnalyzer displays the results from the active SpectroCHIP Array that is checkmarked and highlighted. Changing the active SpectroCHIP Array updates the:• Traffic Light pane• Chip Summary• Call Cluster Plots• Post Processing

Clusters• Details pane• Plate Data pane• Sample Plot

Click a tab to view a pane:Post Processing ClustersCluster analysis (using a Gaussian mixtures approach) of the selected assay results on all SpectroCHIP Arrays that are checkmarked.Call Cluster PlotResults of the selected assay on the active SpectroCHIP Array plotted in a user-selected format:• High mass peak height vs. low mass

peak height (linear or log axes)• Yield vs. skew• High mass yield vs. low mass yieldSelecting a point in a graph updates the:• Spectrum in the Details pane• Selected well in the Traffic Light paneHistogramIncludes the results of all assays on the SpectroCHIP Arrays that are checkmarked. Selecting an assay in the histogram (clicking a histogram bar) updates the:• Call Cluster Plots• Details pane

Click a tab to view a pane:Automated Data Error CheckingSummary of errors detected by the software:• Positive control error• Negative control error• Mendelian error• Discordance errorChip Summary Information about the active SpectroCHIP Array.Assay Summary Information about the assays on the active SpectroCHIP Array.

Directory tree of results in the MassARRAY database.

Sample Plot Results of the selected assay in two graphs:• SNR vs. Sample ID• Height vs. Sample ID


Chapter 4 Analyzing Data 39

4.2 Generating Reports in TyperAnalyzer

1. Open TyperAnalyzer and in the Project Explorer pane double click on the SpectroCHIP Arrays of interest.The SpectroCHIP Arrays will be added to the Chip List.

2. Load the SpectroCHIP Arrays by checking the box next to the SpectroCHIP Array names in the Chip List.

3. Once the SpectroCHIP Arrays are loaded, select File > Reports in the TyperAnalyzer menu bar.TyperAnalyzer will generate the report directly into Excel readable format, and save it in the Typer-4\bin\TyperReports folder.

Figure 4.2 Generating Reports


Chapter 4 Analyzing Data40

4.3 Report Types

Table 4.1 lists the different types of reports generated by TyperAnalyzer. The reports that are available depend on the type of experiment.

Table 4.1 Report typesReport Name Description

Plate Summary Provides basic information about a SpectroCHIP Array (for example, ID, date, user) and brief statistics about the number of assays, samples, plexing level, number of calls, call rate, and status of calls.

Allelotype Includes allelotyping data such as average frequency of allele 1 and 2, frequency error, assay status, primer frequency, and pause frequency.

Allelotype Correction Includes the same data as the allelotype report and also corrections for heterozygous skewing.

Assay Type Count Lists the number of assays for the selected data.

Best Call Probability Shows the best score for the same sample and assay across multiple results. The Score column in the report indicates how good the call was on a scale from 0 to 1.

Call Probability Provides the same information as the Plate Result report and includes the call for each well. The Score column indicates how good the call was on a scale from 0 to 1.

Description Count Provides a count of each call status (A. Conservative through O. Unknown genotype) for the selected data.

Genotype Area Includes genotyping data for the selected experiment(s) and additional information derived from peak area data.

Plate Definition Lists the assays and samples in each well of the plate.

Plate Result Lists the calls for each well of the plate.

Primer Adjustment Indicates the primers that require volume adjustment to compensate for the inverse relationship between analyte mass and signal-to-noise ratio.

AllPlateSummary Provides the results of the Plate Summary Report for all the selected SpectroCHIP Arrays in the Chip View in one single report.

QC Report Summarizes data and post processing results for a user-selected well, assay, and SpectroCHIP Array.


Chapter 5

Service and Maintenance

Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Repairs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Shutting Down the MassARRAY Dx Analyzer 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41Removal From Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

5.1 Maintenance

Only qualified personnel should perform instrument maintenance and repair.

WARNINGWARNING! The instrument interface, ion source, vacuum chamber, tubing, and filter may be hazardous and/or biohazardous. Observe Universal Precautions when cleaning or replacing potentially contaminated parts.

5.2 Repairs

Contact Agena Bioscience Customer Support (page 7) if your instrument requires repair. There are no user-serviceable components.

If you notice a damaged or malfunctioning component (for example, damaged power cord), disconnect the instrument from its power source and contact Agena Bioscience.

5.3 Shutting Down the MassARRAY Dx Analyzer 4

It is recommended to leave the instrument and integrated computer powered on. If you need to turn them off, follow the steps below.

1. Move the Chip holder to the load position by pressing the manual stage control button (Figure 2.2).

2. Shutdown the integrated computer.

3. Turn off the instrument power switch on the rear of the instrument (see Figure 2.4).


Chapter 5 Service and Maintenance42

5.4 Removal From Operation

Temporary Removal From Operation

Shut down the MassARRAY Dx Analyzer 4 according to the instructions above. Contact Agena Bioscience Customer Support (page 7) before turning the instrument back on.

Perform additional procedures as required by your internal Quality Control procedures, and in accordance with local/provincial, state, and national and international regulations or accreditation requirements.

Permanent Removal From Operation

Contact Agena Bioscience Customer Support (page 7) if storing the instrument longer than 30 days or permanently removing it from operation.

Contact Agena Bioscience Customer Support before turning the instrument back on. Perform additional procedures as required by your internal Quality Control procedures, and in accordance with local/provincial, state, and national and international regulations or accreditation requirements.

This device is marked with the "crossed out wheelie bin" (Figure 5.1) in accordance with European Directive 2012/19/EU. This symbol indicates that the equipment carrying this mark shall NOT be disposed into general household waste, but should be collected separately and properly processed under local regulations.

Figure 5.1 Crossed Out Wheelie Bin Symbol


Appendix A

Troubleshooting

Table A.1 TroubleshootingProblem Possible Reason Possible Solution

The Analyzer 4 takes longer than three minutes to reach the required vacuum pressure (5 x 10-6 mbars)

Sample chamber does not properly seal.

Wipe the mating surface of the sample chamber lid with a lint-free tissue that is moistened with 50% isopropyl alcohol or ethanol. Leave the sample chamber lid open until the surface is dry (Figure A.1).

Remove the sample chamber O-ring. Wipe the O-ring with a lint-free tissue and replace it in the O-ring groove after cleaning out the groove with a lint-free tissue moistened with alcohol as above (Figure A.1).

NOTEDo not allow the O-ring to come in contact with alcohol. Allow the groove to dry before reinserting the O-ring.

Peak intensities are too low.

Laser energy is too low. Before running the SpectroCHIP Array on the Analyzer 4, fire on one of the calibrant pads and check that the calibrant peaks are 100 +/- 25%. Contact Agena Bioscience Customer Support if low.

SpectroCHIP Arrays are over- or under-dispensed.

Perform a volume check to make sure correct volumes are dispensed on the SpectroCHIP Array. See the MassARRAY Dx Nanodispenser RS1000 User Guide for instructions.

Peak shape is too wide. MassARRAY Dx Analyzer 4 is not properly tuned.

Contact Agena Bioscience Customer Support.

Peaks are not aligned to the expected calls.

Calibration may not be enabled in the SpectroACQUIRE software.

Ensure that calibrant was dispensed to the SpectroCHIP Array.

Ensure calibration is enabled. See page 29 for more information.

MassARRAY Dx Analyzer 4 is not properly tuned.



Appendix A Troubleshooting44

No calls. SpectroCHIP Array improperly linked to a plate/dispenser method.

Verify that the SpectroCHIP Array is properly linked to an experiment in the database.

Peaks are present in the spectra but not at the expected masses.


Figure A.1 Sample Chamber Lid and O-Ring

Problem Possible Reason Possible Solution

Mating surface of the sample chamber lid

O-ring seated in the O-ring groove


Appendix B

Manually Acquiring Spectra

Manually Acquiring Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Saving Manually Acquired Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Saving and Loading a Shot File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Spectra can be manually acquired from user-specified wells; for example, in order to generate a test signal of both calibrant and sample before starting an autorun. This chapter describes how to manually acquire spectra, how to save that data, and how to save and re-use manual acquisition parameters using a shot file.

B.1 Manually Acquiring Spectra

1. Start the MassARRAY Dx Analyzer 4 software and load SpectroCHIP Arrays as described in Chapter 2 (page 18 and page 19).

2. Click the SpectroACQUIRE Manual Control tab (Figure B.1).

Figure B.1 SpectroACQUIRE Manual Control Tab

[Peak Info and Calibration settings are reserved for use by Agena Bioscience Customer Support.]

Stage Position Map


Appendix B Manually Acquiring Spectra46

3. Enter the SpectroCHIP Array number (1 or 2) and select 96 SpectroCHIP Array format from the Format drop-down list.

4. To select the SpectroCHIP Array pad, click a well in the stage position map.

5. In the video display, adjust the laser cross hairs (+) on the SpectroCHIP Array pad.

To move a pad beneath the cross hairs, double-click the location where you want to position the cross hairs. For example, to center the cross hairs on a pad, double-click the center of the pad (Figure B.2).

Alternatively, click the jogging arrows to move the pad beneath the laser cross hairs (Figure B.3).

NOTEIf you need to reset the shot information for the SpectroCHIP Array, right-click the stage position map, and select Reset Shot Information on the shortcut menu.

6. Enter the number of shots.

Figure B.2 Video Display Window Pane

Figure B.3 Manual Controls

Double-click a location on the SpectroCHIP Array pad

The SpectroCHIP Array position is adjusted so that the pad is located beneath the cross-hairs.

Click the jogging arrows to adjust the position of the laser cross-hairs


Appendix B Manually Acquiring Spectra 47

7. Enter the number of shots to skip. For example, if Skip (n) is set at 1, the software discards the first two spectra that are acquired and computes the average of the remaining spectra.

8. Click Acquire.

When acquisition is finished, the corresponding well in the stage position map in the Automatic Run tab changes color. Put the mouse arrow over the well to show a tooltip that displays the number of acquisitions and well location.

9. To acquire data from another pad on the SpectroCHIP Array using the same acquisition parameters, repeat step 4 and step 5, and click Acquire.

10. To acquire data from another pad on the SpectroCHIP Array using different acquisition parameters, repeat step 4 to step 8.

NOTEThe manual acquisition information (SpectroCHIP Array format and the pads to acquire data from, including shots and spectra to skip for each pad) can be saved to a shot file. A shot file provides a convenient way to manually acquire data from the same pads on another SpectroCHIP Array of the same format. For more details on creating a shot file, see page 49.

B.2 Saving Manually Acquired Spectra

Manually acquired spectra can be saved (as a .prn file). Alternatively, spectra can be temporarily stored in a buffer that is cleared at the end of a SpectroACQUIRE session (a session ends when you close the SpectroACQUIRE software). Storing spectra in the buffer provides a useful way to view and compare manually acquired spectra.

To automatically save spectra

1. Put a check mark next to Automatic save.

2. Enter the Root Filename (folder where the file will be saved).

Figure B.4 Manual Control Tab



To manually save spectra

1. Click Current to save only the current spectrum, or click Buffer to save all spectra that are in the buffer. (Figure B.4).

2. In the Save As dialog box that appears, select a destination folder, enter a file name (.prn), and click Save.

To store spectra in the buffer

1. After an acquisition, click Add to Buffer.

The spectrum appears in the SpectroACQUIRE window.

2. Manually acquire another spectrum and click Add to Buffer.

The previously acquired spectrum is displayed in orange and the most recently acquired spectrum is displayed in black (Figure B.5).

• View Buffer - Displays the spectra that are stored in the buffer (in orange).

• Analyze Buffer - Uses the spectra in the buffer for signal analysis. This is reserved for use by Agena Bioscience Customer Support.

• Clear Buffer - Removes all spectra from the buffer.

B.3 Saving and Loading a Shot File

A shot file provides a convenient way to save a record of the manual acquisition parameters from a SpectroCHIP Array. The shot file specifies the pads from which data was acquired and the number of acquisitions per pad. A shot file provides a convenient

Figure B.5 SpectroACQUIRE Manual Control Tab

Black = Most recently acquired data

Orange = previously acquired data


Appendix B Manually Acquiring Spectra 49

way to replicate acquisition for a particular SpectroCHIP Array. It may be helpful if you need to repeat acquisition using a different Analyzer or from a different Chip holder position.

To save a shot file 1. Right-click the Stage Position map and select Reset Shot Information on the shortcut menu.

This clears acquisition information from the stage position map.

2. Manually acquire spectra from the pads of interest.

3. Right-click the stage position map and select a save option on the shortcut menu (Figure B.6).

QuickSave - Saves the manual acquisition information to a shot file (quick.shot) in the SpectroACQUIRE directory. The QuickSave command overwrites the quick.shot file.

Save Shot Info to File - Opens a dialog box that enables you to save the acquisition parameters to a shot file (.shot). The .shot file is not overwritten by the QuickSave command.

To load a shot file 1. Load a SpectroCHIP Array.

2. Right-click the stage position map and select a load option on the shortcut menu (Figure B.6).

• QuickLoad - The manual acquisition information is displayed in the stage position map.

• Load Shot Info From File - Opens a dialog box that enables you to select a shot file (.shot) to use for acquisition.

Figure B.6 Stage Position Map and Shortcut Menu

Save a shot file

After manually acquiring spectra, choose a save option on the shortcut menu.

Load a shot file

After a SpectroCHIP Array is unloaded, the acquisition history can be viewed the next time you load the SpectroCHIP Array.

Right-click the stage position map and select QuickLoad on the shortcut menu. This loads the shot file for the SpectroCHIP Array and displays the acquisition information.



Table B.1 Stage Position Map Shortcut MenuItem Description

QuickSave Saves the manual acquisition information to a shot file (quick.shot) in the SpectroACQUIRE application directory. Note: The QuickSave command overwrites the quick.shot file.

QuickLoad The manual acquisition information is displayed in the stage position map.

Save Shot Info to File Opens a dialog box that enables you to save the acquisition data to a shot file (.shot). Note: This shot file is not overwritten by the QuickSave command.

Load Shot Info From File Opens a dialog box that enables you to select a shot file (.shot) for the SpectroCHIP Array.

Reset Shot Information Removes all of the acquisition information from the stage position map.


Appendix C

Recalling Plate Data

This chapter explains how to recall raw data (the spectra associated with a plate) and associate the data with a new plate. This process uses Chip Linker software. Recalling data may be helpful, for example, in cases where:

• Additional alleles need to be analyzed.

• Samples names are incorrect.

1. Double-click the Chip Linker icon .

2. In the dialog box that appears (Figure C.1), enter your user name, password, and server.

3. Click Connect.The Chip Linker window appears (Figure C.2).

4. In the Chip Linker directory tree, select a new plate for the data.

Figure C.1 Connect to Database

Figure C.2 Chip Linker window

Directory tree of plates created using Typer PlateEditor


Appendix C Recalling Plate Data52

5. Enter the barcode of the SpectroCHIP Array with the data that you want to recall.

6. Ensure that the information in the Chip Linker window (Terminator Chemistry, Process Method, Dispenser, Experiment Name, and Chip Barcode) are correct.

7. Click Recall.

8. In the dialog box that appears, select the SpectroCHIP Array with the data that you want to recall and click Recall.

NOTEIf the Recall button is not available, the MassARRAY Caller software is not set to use the Typer 4.0 software. For assistance, contact Agena Bioscience Customer Support.


Appendix D

Licensing

Warranty. Standard Agena warranties shall apply as set forth in the Agena MassARRAY® Product Warranty documentation provided with each Product. EXCEPT AS SET FORTH IN THIS SECTION 5, AGENA MAKES NO REPRESENTATIONS, WARRANTIES, GUARANTEES, OR CLAIMS, OF ANY KIND OR NATURE, AS TO THE ACCURACY OF, RELIABILITY, UTILITY, PERFORMANCE, EFFECTIVENESS, OR OTHERWISE, OF THE PRODUCT PROVIDED HEREIN OR THE RESULTS OBTAINED THEREFROM, NOR DOES AGENA ASSUME ANY RESPONSIBILITY FOR THE RESULTS, QUALITY OF RESULTS, OR LACK OF RESULTS THE PRODUCT AND REAGENTS ARE PROVIDED "AS IS" AND WITHOUT WARRANTY OF ANY KIND, WRITTEN OR ORAL, EXPRESS OR IMPLIED, DIRECT, INDIRECT, BY ESTOPPEL, OR OTHERWISE, AND SPECIFICALLY EXCLUDING ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT OF ANY THIRD PARTY PATENT OR OTHER INTELLECTUAL PROPERTY RIGHTS, AND ANY OTHER WARRANTIES PROVIDED FOR BY THE UNIFORM COMMERCIAL CODE, USAGE IN THE INDUSTRY, OR COURSE OF DEALING BETWEEN THE PARTIES.

License. Agena’s patented nucleic acid analysis by mass spectrometry methods and products are protected under United States patent rights and patents pending, and foreign counterparts. With the purchase of Agena SpectroCHIP® arrays and reagent kit products Customer is granted a limited right to practice Agena’s patented methods and use its products. The licensed rights are not transferable, are for the benefit of Customer only, and expire with the consumption of the SpectroCHIP® arrays purchased. Transfer or resale of products and their components, purchased from Agena, is prohibited. The license rights granted are limited to one-time use only for each element per SpectroCHIP® array purchased. Re-manufacture or re-use of Agena’s SpectroCHIP® arrays and/or elements in conjunction with performing Agena’s patented nucleic acid analysis methods, is prohibited. Reverse engineering Agena products is prohibited. Except as expressly licensed with the purchase of chips and reagent kit products as set forth herein, Agena reserves all rights and no additional license rights are granted or implied.

Software License. For purposes of this Agreement, “Software” means computer software or programs supplied by Agena to Customer including but not limited to such software that is embedded in or forms an integral part of Agena’s hardware products in addition to separately provided software for application specific purposes. For purposes of this Agreement, Software does not include Oracle Corporation software products provided by Agena as such Oracle products are separately governed by the attached Oracle End User License Terms.

(a) Agena grants Customer a non-exclusive and non-transferable license to use the Software for processing data exclusively in conjunction with specially designated SpectroCHIP® arrays and reagents or reagent kit products purchased from Agena. Customer shall not permit another party to use the Software and Customer shall effect and maintain adequate security measures to safeguard the Software from access or use by unauthorized persons. Customer shall not transfer, rent, lease, sublicense, loan, copy, modify, adapt, merge, translate, reverse engineer, decompile, or disassemble the Software or create derivative works based on the whole or any part of the Software.


Appendix D Licensing54

(b) The Software license shall not be deemed to extend to any of Agena’s intellectual property rights, including rights in source code. No copies may be made of the Software without the prior written consent of Agena, except that Customer may make a single back up or archival copy. The Software license shall apply to any copy as it applies to the Software.

(c) With specific reference to application Software and including any associated report tools, Customer is provided a royalty-free, non-exclusive and non-transferable license to use the Software subject to the terms and conditions in subsections (a) and (b) above, solely upon the condition that such Software is used exclusively in conjunction with specially designated SpectroCHIP® arrays and reagents or reagent kit products purchased from Agena.

(d) All Software licenses shall terminate automatically and immediately if Customer fails to abide by any of the terms and conditions of this Agreement. Except as expressly licensed herein, Agena reserves all rights. Other than as expressly set forth herein, no license rights are granted or implied.

Indemnity. Customer will indemnify and hold harmless Agena Bioscience, Inc., its subsidiaries, and all officers, directors, employees and agents of the foregoing, (the “Agena Indemnified Parties”) from and against any and all losses, damages, liabilities, expenses and costs, including responsible legal expense and attorneys’ fees (“Losses”), to which a Agena Indemnified Party may become subject as a result of any claim, demand, action or other proceeding by any third party to the extent such Losses arise from acts or omissions by Customer resulting in (a) personal injury or harm from the use, sale or other disposition of any product or service or information provided to a third party by Customer and/or its contractual partners, customers, or collaborators; or (b) a claim that a Customer product, assay, test analysis, method, or procedure infringes any patent, trade secret or other intellectual property rights of any third party, unless such claim is solely based on Customer’s non-assay-specific use of Agena’s products according to the authorized and intended use for such product and in compliance with user operating manuals and package inserts provided with such products. The foregoing shall not apply where such Losses are caused by Agena’s gross negligence or willful misconduct. In the event an Agena Indemnified Party seeks indemnification under this provision, Agena will notify Customer in writing of a claim as soon as reasonably practicable after it receives notice of the claim, will permit Customer to assume direction and control of the defense of the claim (including the right to settle the claim) and will cooperate as requested (at the expense of Customer) in the defense of the claim. This Section will survive the expiration or termination of this Agreement.


Appendix D Licensing 55

Oracle end user license terms

ORACLE CORPORATION ("ORACLE") SOFTWARE PRODUCTS

(a)The Customer shall limit its use of Oracle's products to the scope of the application package and to its business operations;

(b)The Customer shall not transfer Oracle's products except for temporary transfer in the event of computer malfunction;

(c)The Customer shall not assign Oracle's products or any interest in Oracle's products. If a security interest is granted in Oracle's products, the secured party has no right to use or transfer Oracle's products;

(d)The Customer shall not operate a timeshare, hosting, subscription service, or rental use of Oracle's products;

(e)Title to Oracle's products remains with Oracle and shall not pass to the Customer or to any other party;

(f)The Customer shall not reverse engineer, disassemble or decompile Oracle's products unless required for interoperability and then only to the extent so required for such interoperability;

(g)The Customer shall not duplicate Oracle's products except for a sufficient number of copies for the Customer's licensed use and a single back up or archival copy;

(h)Oracle shall not be liable for any damages whether indirect, incidental, special, punitive, or consequential arising from the use of its products;

(i)Where the license which is granted by Agena in respect of Oracle products expires or terminates and is not renewed, the Customer shall discontinue use and destroy or return all copies of Oracle's products and documentation to Agena;

( j)The Customer shall not cause to be publicized any results of benchmark tests run on Oracle's products;

(k)The Customer shall comply fully with all relevant export laws and regulations of the United States and other applicable export and import laws to assure that neither the Oracle products themselves nor any direct products thereof are exported, directly or indirectly in violation of applicable laws;

(l)Oracle is not required to perform any obligations other than to the extent agreed by Agena and Oracle;

(m)Agena has the right to audit Customer's use of Oracle's products and report such use to Oracle, or to assign such right to another person;

(n)Oracle is a third party beneficiary of these Customer license terms;

(o)The Uniform Computer Information Transactions Act shall not apply; and

(p)To the extent that Oracle source code is included with any application package, such source code is similarly governed by the terms above.

[August 2015]


Appendix D Licensing56

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Documents

EU Dx MassARRAY Analyzer 4 User Guide MADX-USG-CUS-501 R03 · warning label shown in Figure 1.1 is located on the back of the instrument. Under normal operating conditions, no additional