Covaris E220 evolution User manual

E220 evolution User Manual Page 1
For research use only
E220
evolution
USER MANUAL
Instrument and software developed for
high performance sample preparation
using adaptive focused acoustic energy
Product Name: E/LE220-Series
Model Numbers: E220 evolution
Software: SonoLab 7

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Trademarks
Patented or patent pending and registered or registration-pending trademarks of Covaris are protected.
Registered names and trademarks used in this document, even when not specifically marked as such, are not to be
considered unprotected by law.
WCS and AFA are either registered trademarks or trademarks of Covaris, Inc. in the United States and/or other
countries.
Clorox is a registered trademark of The Clorox Company.
Teflon is a registered trademark of The DuPont Company.
Information subject to change without notice
For Research Use Only
Not for use in diagnostic procedures
Publication P/N 010264
Revision E, July 2017
Product covered by Patent No. US6, 719,449, US6, 948,843, and other pending applications
Copyright © 2017 Covaris, all rights reserved.
Covaris, Inc.
14 Gill St, Unit H
Woburn, Massachusetts
01801-1721 USA Printed in U.S.A.
UNIVERSAL PRECAUTIONS
Universal Precautions should be followed on all specimen samples, regardless of whether a sample is known to contain
an infectious agent. Laboratories handling specimen samples are advised to comply with applicable parts of the following
governmental and clinical standards, or their equivalent in the country of use:
•Centers for Disease Control (CDC), Universal Precautions for Prevention of Transmission of HIV and Other
Bloodborne Infections, published 1987, updated 1996
•Clinical and Laboratory Standards Institute (CLSI), GP17-A2 Clinical Laboratory Safety; Approved Guideline -
Second Edition, published 2004, ISBN 1-56238-530-5
•Clinical and Laboratory Standards Institute (CLSI), M29-A3 Protection of Laboratory Workers from
Occupationally Acquired Infections; Approved Guideline, Third Edition, published 2005, ISBN 1-56238-5674
•Occupational Safety and Health Administration (OSHA), 29 CFR 1910.1030 Bloodborne Pathogens
•International Standards Organization (ISO) 15190:2003, Medical Laboratories – Requirements for Safety

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Warnings
For safety of operating personnel:
Make sure that the equipment is properly grounded. DO NOT operate if it is not properly grounded.
The unit is equipped with a power plug appropriate for the destination country. DO NOT, under any circumstances,
remove the grounding prong from the power cord.
Do not run an acoustic treatment with the Acoustic Assembly and sample cover in the UP position or without a water
bath - the acoustic system will not work.
If there is any indication that the Safety System is not functioning properly, DO NOT operate the equipment and
contact Covaris immediately.
If the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment
may be impaired.
To prevent damage to the equipment:
The instruments are designed to operate in ambient laboratory conditions e.g., 19ºC to 25ºC (66ºF to 77ºF). DO
NOT operate the instrument in a cold room environment; the system is designed to operate with a water bath and
re-circulating heater/chiller apparatus to control sample temperature.
NEVER run a method without a water bath; this could damage the transducer. The instrument is equipped with a
water level sensor to protect the transducer and degassing pump. The system will not allow the degassing pump to
operate or the acoustic treatment to start unless an adequate volume of water is detected.
Distilled or deionized water should be used to fill the water bath.
Unless a Water Conditioning System (WCS) is employed, empty the water bath and wipe it dry EVERY day with a
lint-free cloth.DO NOT leave water in the tank for an extended time as there is no water filtration or water cleaning
system within the apparatus (unless WCS is employed).
Do not employ isopropyl alcohol, ammonia-based or abrasive cleaners on the water tank, as these will damage the
acrylic surfaces.
Establish a standard of operation and periodically test equipment, as described in Maintenance (see section 6.0) of
this manual.
Loading third party software onto the computer may interfere with system operation. Please consult with Covaris.

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Warranty
When used in accordance with written instruction and under normal operating conditions, the Covaris
instruments are guaranteed to be free of defects in MATERIAL and WORKMANSHIP for one (1) year from the
date of original delivery by an authorized representative. Any component which proves defective during the
stated period will be repaired free of charge or replaced at the sole discretion of Covaris, F.O.B., Woburn,
Massachusetts, U.S.A. provided the defective component is returned properly packaged with all transportation
charges prepaid. The customer is expected to perform basic diagnostics and component replacement with
telephone support from Covaris personnel. If Covaris personnel are required to perform on-site repair, all travel
related costs are paid by the customer. A limited warranty as specified may apply to certain components of the
equipment.
Warranty Exceptions
This warranty is void if failure of the software or hardware has resulted from accidents, abuse, improper
maintenance, or repair, or misapplication by the customer. It is also void if damage is caused by any
unauthorized attachments or if modifications are made to the equipment. Removing or tampering with the
Safety Enclosure will void the warranty, and the customer will assume all liabilities.
This warranty is limited to the original purchaser and is not transferable.
The software will perform according to the accompanying written materials and the medium on which the
software is delivered is free of defects in materials under normal use and service. The warranty is void if
damage has resulted from third party software not intended for use with the system.
The high power focused transducer is designed to give maximal mechanical energy output in water. Permanent
damage to the transducer and electronic circuits could result if the transducer is operated without water.
Operation of the system without water in the water bath voids the warranty.
CONTACT COVARIS, INC. SHOULD YOU HAVE ANY QUESTIONS CONCERNING EQUIPMENT
Warranty Services
The purchased equipment is covered by a twelve (12) month warranty which includes all the service and
support necessary so that the customer can operate the equipment successfully. Extended warranties are
available at the end of the original 12 month warranty period.
Services included with the original purchase of the system are:
Technical Support – On-going assistance with the operation or application of the equipment and/or
troubleshooting is provided via:
•Telephone [phone]) during the hours of 9:00am to 5:00pm, Monday through Friday,
oUnited States, Eastern Standard Time (EST)
oGreenwich Mean Time (GMT-05:00)
•E-mail queries to [e-mail]
Parts Replacement – Replacement of parts (excluding consumables) from normal operation of equipment are
provided on a priority basis. All labor and shipping charges are included. Failure due to accident, abuse, or
improper operation is not covered.
An Operator’s Manual is provided with the equipment. This manual includes sections on the operating
instructions, maintenance guidelines, and troubleshooting tips.

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TABLE OF CONTENTS
1.0 INTRODUCTION................................................................................................................................6
1.1 Overview of the User Manual.........................................................................................................6
1.2 The E220 evolution and the Covaris Process................................................................................6
2.0 INSTALLATION AND SETUP............................................................................................................7
2.1 Assembly........................................................................................................................................7
2.2 Installation......................................................................................................................................8
3.0 GETTING STARTED .......................................................................................................................11
3.1 Fill the Water Bath........................................................................................................................11
3.2 Start the System...........................................................................................................................11
3.3 The SonoLab Run Screen - Running a Method...........................................................................13
3.4 System Shutdown ........................................................................................................................17
3.5 Temperature Control....................................................................................................................18
3.6 Degas System..............................................................................................................................19
4.0 SonoLab™ APPLICATION SOFTWARE.........................................................................................19
4.1 Create and Edit Methods .............................................................................................................20
4.2 Temperature Tab..........................................................................................................................25
4.3 Saving Methods in Folders...........................................................................................................26
4.4History Tab...................................................................................................................................27
4.5 Setup Screen................................................................................................................................27
4.6 Maintenance Screen ....................................................................................................................32
4.7 About Tab.....................................................................................................................................33
4.8 Motion Tab ...................................................................................................................................33
5.0 SYSTEM SPECIFICATIONS ...........................................................................................................35
6.0 MAINTENANCE...............................................................................................................................36
6.1 Cooling Air Intake.........................................................................................................................36
6.2 Water Bath ...................................................................................................................................36
6.3 Transducer...................................................................................................................................36
6.4 Safety System..............................................................................................................................36
6.5 Degassing System .......................................................................................................................36
6.6 Cleaning the System....................................................................................................................37
7.0 TROUBLESHOOTING.....................................................................................................................38
Appendix A: Suggested E220 evolution IQ / OQ / PQ ................................................................................40
Appendix B: E Series Site or Transport Preparation...................................................................................46
Appendix C: Installing SonoLab Software, Firmware and Instrument Drivers............................................48
Appendix D: Recirculating Chiller................................................................................................................53
Appendix E: Humidity and Water Management in Covaris E and LE Systems ……………………………..55

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1.0 INTRODUCTION
1.1 Overview of the User Manual
This manual contains operation and maintenance instructions for the Covaris E220 evolution
Focused-ultrasonicator. This document contains information essential to the proper use and care of
the equipment.
Should any unforeseen problems occur with the normal operation of the equipment, contact Covaris
Technical Support immediately.
The following definitions apply in this manual:
NOTE: Inconvenience if disregarded.
CAUTION: Equipment damage may occur.
WARNING: Personal injury may occur.
There is also a PDF version of this manual, typically available on the computer desktop. Open the
manual by double clicking the user manual icon.
1.2 The E220 evolution and the Covaris Process
The E220 evolution Focused-ultrasonicators are based on Covaris Adaptive Focused Acoustics
(AFA) technology. This instrument is designed to provide researchers an integrated stand-alone tool
to be used in a laboratory environment. The instrument is ideal for those who work with cell lysing,
DNA shearing, or chromatin shearing.
The system is comprised of the Treatment System which delivers the acoustic energy to the sample,
the Safety System which protects users from inadvertently contacting the high intensity acoustic
energy, and the Computer and Application Software which provides users an interface to control the
device.
The Covaris Process uses adaptive focused acoustic energy to precisely control cavitation and
acoustic streaming within the sample treatment vessel in a non-contact, isothermal fashion. Focused
acoustic energy is generated and delivered to individual samples. The mechanical energy imparted
on the sample results in a controlled series of compression and rarefaction events.

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2.0 INSTALLATION AND SETUP
2.1 Assembly
The following items should be found in the crate containing the instrument:
•Main Unit
•Quick Start User Guide
•User Manual
•Notebook Computer with AC Adapter
•Cables
oUSB cable
oInstrument power cord
oComputer AC Adaptor power cord
•Accessories
oChiller Hose Kit
oSample Tubes & Racks (varies by application)
oWater Tank (installed in main unit)
E/LE Series Focused-ultrasonicator

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2.2 Installation
2.2.1 Unpack the instrument and place it on a table or bench, with space to accommodate the
instrument and the laptop. The recirculating chiller may be placed on the floor to save
bench space.
2.2.2 Please refer to the rear of the instrument’s right side panel and identify the following
features:
The Rear Right Panel of the System
USB Port
Product Safety Label
Serial Tag,
Regulatory and
Line Power Label
AC Line (Mains) Input
and Power Switch

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2.2.3 Refer to the figure below and identify the following items:
2.2.4 Plug the instrument into a power source using the enclosed line cord. The instrument is
a “universal input” device and automatically employs any worldwide line voltage or
frequency (100 to 240 volts AC, 50 or 60 Hz). Leave the instrument power and
notebook power switched OFF at this time.
2.2.5 Plug one end of the USB cable into the USB Port, and the other end into any USB port
on the notebook computer.
2.2.6 Connect the computer to a power source. Connect the mouse or other accessories to
the computer.
2.2.7 Connect the two hoses provided for coolant flow from the chiller. The connections are
bi-directional. (There is no defined IN or OUT.)
2.2.8 Connect the hoses to the chiller. Please refer to Appendix D and your chiller operation
manual for details on chiller connection and operation.
2.2.9 Position the instrument and computer in your work space as desired.
CAUTION: When positioning the system, please keep the fan and rear panel vents
free of obstructions that may block the flow of air.
CAUTION: To prevent chiller damage, use of a 20% glycol solution in the circulating
chiller is required.Please refer to the chiller’s user manual.
Quick-connect Ports for
Chiller Hoses
Door Lock Release
Button
Stop Button
Enclosure Door
Safety Lock
Enclosure Door
Handle

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2.2.10 Power on the instrument using the power switch at the right rear, at the power entry
module.
2.2.11 Press and hold the green ‘Door’ button while pulling the door handle to open the safety
enclosure front door. Slide out the water tank and remove it from its plastic shipping
bag. Remove and discard the desiccant pack.
Safety Enclosure and Water Tank
2.2.12 If a Water Conditioning System (WCS) will be employed with the instrument, please
refer to the WCS User Manual for further instructions. The WCS removes biological
growth and particulates from the water, allowing bath water to remain in place for up to
one month.
2.2.13 The instrument is now ready to be started.
Safety Enclosure
Water Tank

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3.0 GETTING STARTED
3.1 Fill the Water Bath
The instrument’s transducer must be immersed in a water bath to transmit high-
frequency, focused acoustic energy to the sample tube. For best performance,
employ only clean, distilled or deionized water in the bath.
Open the front door, remove the tank and fill to the level specified in the protocol
to be used. Typical DNA Shearing protocols call for water level 6. Avoid filling
higher than 15, as the tank may overflow. Employ the markings on the FILL side
of the gauge. The tank holds approximately 01.25 gallons (5.0 liters).
Once the tank is in place and the Acoustic Assembly is lowered into the bath, the
water level should be read from the RUN side of the label.
3.2 Start the System
Turn the instrument power ON using the power switch located on the rear, right side
of the instrument at the power entry module. When power is ON, the green door-
lock release switch will illuminate and the ventilation fans in the rear panels will run.
Also start the external chiller, programming its set point to a few degrees below the
desired instrument bath temperature. Be sure to employ a 20% glycol solution
inside the chiller to prevent freezing. Do not use undiluted glycol solution.
Start the system computer. The computer employs a Windows®Operating System (XP, 7 or 8).
SonoLab 7 is an application used to control a Covaris Focused-ultrasonicator for processing a
biological or chemical sample. It is designed to create, edit, and run a processing program called a
method. It has provisions to run, pause or stop a method and view execution histories which contain
a record of key instrument parameter values during a run. It also contains editors for customizing
system settings and performing maintenance functions.
SonoLab 7 is installed on the computer purchased with the instrument. No further installation
or configuration is required.
Find the SonoLab 7 icon on the desktop:
If the icon is not visible, or if SonoLab 7 is not installed, please refer to Appendix C or contact
Covaris for installation instructions.
By default, there is no login required for SonoLab. To secure SonoLab by requiring users to login
and limiting user permissions, see ‘User Authentication’ in section 4 of this manual.

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Double-click on the SonoLab icon to start SonoLab. An animated splash screen will appear:
Following the splash screen, the SonoLab Run Screen will appear with the motion system homing dialog box
in front of it:
Click ‘Yes’. The transducer and sample holder mechanical assemblies will move into position and
the SonoLab ‘Run’ screen will display.

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If the instrument is powered ON and connected to the laptop via the USB cable, SonoLab will
connect to the instrument, display “E220 evolution” at the top center of the screen.
If SonoLab does not connect to the instrument, the Run Screen will not appear. SonoLab will display
the About Screen and the status “Disconnected” will be displayed in place of the instrument model.
In this case, please refer to Section 7.0 for diagnostic instructions.
3.3 The SonoLab Run Screen - Running a Method
3.3.1 Instrument Status & Basic Controls
System attributes are displayed on the Run Screen as green (acceptable) or red. The SonoLab
Run button will remain gray and inactive unless a method has been selected, the degas pump is
ON, and all Status conditions are green (acceptable) or overridden. Any method will be paused
if any status changes to not acceptable while the method is running.
The status indicators and controls are described below:

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Status Indicators
•Degas Pump is both a control and indicator for the instrument degas pump. The pump is
automatically turned ON when SonoLab starts. When ON, the degas pump removes
dissolved gas from the bath water. Clicking on the switch image will turn the pump OFF.
Clicking again will turn it ON.
•Lightbulb is also both a control and indicator. The enclosure light is automatically turned on
when SonoLab starts. Clicking on the light bulb image will turn the light OFF (eg. for treating
light sensitive samples); clicking again will turn it ON.
•Degas: To ensure properly degassed water, the degas pump should operate continuously
for at least 60 minutes. The Degas indication will turn green once this criterion has been
met. If the degas pump is turned OFF, this timer resets. Operators may click “Ignore Degas
Timer” to bypass this status check.
•Water Temperature indicates if the bath temperature is between the minimum and
maximum set for the selected method. Operators may click “Override” to bypass this status
check. See the Temperature Control later in Section 3 and Appendix D for details on using
the external chiller to maintain bath temperature within desired limits.
•Water Level indicates if there is enough water in the water tank for safe operation of the
instrument. Water levels near or below “0” on the WATER LEVEL label will cause this
indicator to turn red.
•Door Open: A green check indicates that the door is properly closed.
•Motors Enabled indicates that motion system for positioning the samples is ready.
•Water Tank: A green check indicates that the water tank is present and properly positioned
in the instrument.
•Stop Switch: A green check indicates that the red ‘Stop’ switch on the front of the
instrument is not pressed.
•Not in Motion indicates that the motion system is idle.
Controls
•Run button starts a treatment method. It will be disabled (grayed out) unless all of the
above status indicators contain the green check mark, or are overridden.
•Pause button interrupts the treatment. Details of the ‘Run’ and ‘Pause’ button operation are
described in the section, ‘Running a Method’ below.
The following buttons cause the instrument motion system to move the sample tray to
predefined positions.
•Home moves all motion axes to their initialized position, as occurs when the software starts.
•Load Position moves the tray to the front of the safety enclosure to facilitate loading
samples.
•Start Position takes the sample tray to the treatment position of the first tube of the
currently selected method. This position may be used to verify that the water level in the
bath is correct.
•Drip Position raises the sample tray above the bath water to allow excess water to drip
from the sample, if desired, prior to removing the sample from the instrument.

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•Service Position raises the sample tray and the transducer assembly allowing the water
bath to be removed from the instrument.
•Center Position moves the sample tray to the center of its travel. This position is primarily
used by service personnel.
3.3.2 Select a Method
To select and load an acoustic Method, click the pull-down menu of the “Method” combo box, as
shown below, and a list of existing method names along with their detailed information will
appear. Navigate through the list with the vertical scroll bar and click to select a Method.
If no methods appear in the pull-down menu, then a new method must be created. Please see
Section 4 for instructions on creating and editing methods.
3.3.3 Run a Method
To start an acoustic treatment, the following conditions must be met:
•There must be an acoustic method selected in the Method box
•The Degas pump must be running
•The Degas pump timer must see the pump running for 60 minutes (or override)
•Water Temperature must be within acceptable Min and Max limits (or override)
•The Water Tank must be present
•Water Level must be at or above that required for correct operation
•The front door must be closed
The Run button will remain gray and inactive until all of these conditions
are met. Once a method has been selected and all system attributes
are acceptable or overridden, the Run button will become active
(green).
Click Run to start the selected method.The sample tray will move the first sample above the
transducer and acoustic power will be applied according to the acoustic parameters specified by
the method. At the same time, the ‘Run’ button becomes a grayed out ‘Abort’ button and the
‘Pause’ button is enabled. See details on pausing the method below.
Pull down menu
Edit the selected
method
Create a new method
Run/Creation Notes
(Click to expand)

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The programmed temperature range and the acoustic treatment details will be posted on the left
side of the Run Screen:
Average acoustic power (in Watts) and water bath temperature will be displayed numerically and
graphically at the lower right corner of the Run Screen, along with a progress bar for the method
being run:
Note that the average Power values will approximate (Peak Power x Duty Factor).
The user may, at any time while running a method, click “Pause” to
interrupt a running method.
When the method is paused, the user may continue
the method by clicking the Resume button, or
terminate the method by clicking the Abort button.

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Notes
When the method ends, a Run Results box will be posted over the Run Screen.
If necessary, click the mouse in the text entry area to set the focus, then notes may be added
either via the keyboard or an alternative input device. For instance, a barcode reader may be
used to capture data directly from pre-labeled samples.
When finished adding notes, click Close.
Simply open the front door and remove the sample rack.
A new rack may then be loaded into the tray and the process repeated.
If there is additional sample processing to be done, the instrument and SonoLab may be left ON
and operating. If the system will be idle for an extended period of time (e.g. overnight or a
weekend), then please refer to the next section on System Shutdown.
3.4 System Shutdown
If the instrument will be idle for an extended period of time (e.g. overnight or a weekend), shut down
the instrument using the following procedure:
3.4.1 Empty the water tank and purge the degas pump
Turn off the degas pump and click the ‘Service Position’ button to raise the Acoustic Assembly.
Empty the water bath, place it back into the instrument and click the ‘Load Position’ button to
lower the Acoustic Assembly.
Click the Degas Pump control to restart the pump and purge the pump and water lines. The
pump will automatically stop within 10 seconds. Remove and empty the tank again, dry the tank
with a lint-free soft cloth and place it back in the system.
3.4.2 Close SonoLab
Exit SonoLab by clicking on the in the upper right corner. ”Are you sure you want to exit
SonoLab?” will appear.
“Yes” will close the application. “No” will cancel this request.

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3.4.3 Turn System OFF
To shut down the laptop, select Shutdown from the START menu on the Windows screen and
select the option SHUTDOWN. Then the computer will power down.
Power down the instrument using the switch located near the power entry module of the
instrument, at the rear of the right side.
3.5 Temperature Control
An important principal of the Covaris Focused-ultrasonicator is isothermal temperature control. The
sample is immersed in a water bath which conducts ultrasonic energy while maintaining a stable
sample temperature. Each protocol published by Covaris specifies a desired bath temperature.
The instrument does not control its own water temperature. This must be controlled by adjusting the
set point of an external chiller. This chiller pumps fluid through hoses connected to the left side of
the unit (see Setup) and then through stainless steel tubes immersed in the water bath. These tubes
are visible as part of the Acoustic Assembly, surrounding the ultrasonic transducer.
CAUTION: Leaving water in the water bath or degassing lines for an extended time
may promote algal growth in the tank and lines, This growth can interfere with water
quality and sample processing.
Change water daily and rinse with a 10% bleach solution monthly.
Chiller Tubes
Transducer

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The chiller set point should be programmed a few degrees C below the desired bath temperature.
For example, if a protocol calls for a bath temperature of 7°C, the chiller set point should be adjusted
to approximately 4°C.
During ultrasonic treatments, the instrument continuously measures water bath temperature and
displays this value in SonoLab. Each method has a minimum and maximum temperature defined,
and treatments will be paused if bath water strays beyond these limits. Using the example of 7°C,
the minimum and maximum may be set to 4°C and 10°C, respectively.
If the bath temperature exceeds the method’s programmed temperature limits (in either direction, too
cold or too warm), the Temperature Status indicator on the SonoLab Run Screen will turn red and
the method will pause (unless Temperature has its Override box checked). Such a deviation in
temperature may be indicative of a chiller malfunction or a flow failure in the chiller lines.
CAUTION: To prevent chiller damage, use of a 20% glycol solution in the chiller fluid
is required.Do not use undiluted glycol solution. Please refer to the chiller user
literature.
Use only deionized or distilled water in the instrument bath.
3.6 Degas System
The instrument is equipped with a pump that draws bath water through a degassing process.
Properly degassed water is important for efficient transfer of acoustic energy from
the instrument’s transducer to the sample being treated. If water is detected in the
tank, the pump is automatically turned on when SonoLab is started.
The pump should be allowed to run until the Degas indicator on the Run Screen
turns green (at least 60 minutes) prior to an acoustic treatment.
The pump may be switched off and on with the Degas Pump control on the Run Screen.
Note: the pump can be programmed to stop and start automatically. See ‘Degas Pump Settings’ in
section 4 of this manual.
4.0 SonoLab™ APPLICATION SOFTWARE
SonoLab is an application used to control the Covaris AFA (Adaptive Focused Acoustics) instrument
for processing a sample. It is designed to create, edit, and run a sample processing program called
a method. It has provisions to run, pause or stop a method and view execution histories which
contain a record of key instrument parameter values during a run. It also contains editors for
customizing system settings and performing maintenance functions.
SonoLab provide a series of tabs to access its various features. Each tab will highlight as the cursor
approaches, and a single mouse or touchpad click will access the new screen. Each screen has
secondary screens, indicators and controls. The choices are:

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•Run – Select methods to run, run methods, create new or edit existing methods
•History – View system history
•Setup – System setup by user (file management, User Authentication, etc.)
•Maintenance – Instrument parameters set by factory or service personnel
•Motion – Present only when an admin user is logged in. Provides for manual control of
instrument motion system.
•About – System configuration information
The Run tab is the principal user screen for the system. See details presented earlier in this section
on operating the instrument through the Run Screen.
The Run Screen
The Run screen provides access to the Create New Method and Edit Existing Method screens.
4.1 Create and Edit Methods
SonoLab supports the creation of new methods and editing of existing methods from the Run Tab. A
method consists of one or more treatments, delays and message prompts.
4.1.1 To edit or create a new method, click the “Edit…” or “New…” button in the “Method”
window. The Method Editor window will appear.