Covaris E220 evolution User manual

E/LE-series User Manual 1
For research use only
E and LE-Series
USER MANUAL
an automated, batch system for
high performance sample preparation
using adaptive focused acoustic energy
Product Name: E/LE-series running SonoLab 6.2.4 or later
Product Number: E220, E220x, LE220, E220R, LE220R

E/LE-series User Manual 2
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.
Information subject to change without notice
For Research Use Only
Not for use in diagnostic procedures
Publication P/N 010119 Rev J
October 2017
Covaris products are covered by Patent No. US 6,719,449, US 6,948,843, and other pending applications
Copyright ©2014 Covaris, all rights reserved.
Covaris, Inc.
14 Gill Street, 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

E/LE-series User Manual 3
Warnings
For safety of operating personnel:
1. Make sure that the equipment is properly grounded. DO NOT operate if it is not properly
grounded.
2. 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.
3. DO NOT attempt to operate the equipment without the safety door closed. When the safety door
is open, the mechanical positioning system and the acoustic wave system will not run. If there is
any indication that the safety system is not functioning properly, DO NOT operate the equipment
and contact Covaris immediately.
4. 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:
1. The instrument is designed to operate in ambient laboratory conditions e.g., 15 to 32°C (60 to
90°F). 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
temperatures.
2. 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. The system will not allow the
acoustic wave treatment to start unless an adequate volume of water is present.
3. ONLY distilled or deionized water should be used to fill the water bath.
4. Empty the water bath and wipe dry EVERY day. DO NOT leave water in the tank for extended
time as there is no water filtration or water cleaning system with the apparatus. Drain the
degassing lines (see section 4.5 Shutdown Procedure).
5. Establish a standard of operation and periodically test equipment, as described in the
Maintenance section of this manual.
6. Be advised that loading third party software onto the computer may interfere with the
performance of the Covaris SonoLab™ software. Please consult 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. 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, 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 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:
Installation and Training – Setup and installation of the equipment and operator training can be purchased
at time of initial acquisition of the equipment. Both will be performed by a qualified Covaris service
representative. One half day will be scheduled to perform the installation and on-site training.
•The operators’ training will include valuable hands-on time with the equipment.
•Preventative maintenance and troubleshooting tips will also be covered.
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 4:00pm, 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 and cables) for normal operation of
equipment are provided on a priority basis. Shipping charges are included. Failure due to accident, abuse,
or improper operation is not covered.

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TABLE OF CONTENTS
1.0 INTRODUCTION...........................................................................................................................6
1.1 Overview of the Manual............................................................................................................................6
1.2 Purpose of the Equipment........................................................................................................................6
1.3 Main Components .....................................................................................................................................6
1.4 Principle of Operation ...............................................................................................................................7
1.5System Distinctions – E, Ex and LE.......................................................................................................8
2.0 INSTALLATION.............................................................................................................................9
2.1 Unpacking and System Setup.................................................................................................................9
2.2 Placement of Equipment..........................................................................................................................9
2.3 Power Requirements ................................................................................................................................9
2.4 Set-up Procedures ....................................................................................................................................9
3.0 SYSTEM DESCRIPTION............................................................................................................11
3.1 General Overview....................................................................................................................................11
3.2 Treatment System...................................................................................................................................11
3.3 Computer..................................................................................................................................................13
3.4 Safety System..........................................................................................................................................13
3.5 Water Bath Temperature........................................................................................................................13
3.6 Application Software ...............................................................................................................................14
4.0 SYSTEM OPERATION...............................................................................................................18
4.1 Start-Up Procedures ...............................................................................................................................18
4.2 Creating and Modifying a Method in the Method Editor Panel.........................................................19
4.3 Running a Method Manually in the Main Panel..................................................................................20
4.4 Manual Overrides....................................................................................................................................20
4.5 Shut-Down Procedures ..........................................................................................................................21
5.0 SYSTEM SPECIFICATIONS ......................................................................................................21
6.0MAINTENANCE..........................................................................................................................22
6.1 Water Bath................................................................................................................................................22
6.2 Transducer ...............................................................................................................................................22
6.3 Safety System..........................................................................................................................................22
6.4 Degassing the System............................................................................................................................23
6.5 Relocation of the System .......................................................................................................................23
7.0 TROUBLESHOOTING................................................................................................................25
APPENDIX A: SonoLab 7 And 6.2 Software Installation on a Windows XP Or 7 Computer ....................26
APPENDIX B: Covaris 220 Series Instrument Driver Update Procedure for Windows 7 ..........................28
APPENDIX C: Site Preparation and Installation Requirements..............................................................................31
APPENDIX D: Humidity and Water Management in Covaris E and LE Systems.......................................34
APPENDIX E: “R” version of E220 and LE220 (E220R and LE220R) ........................................................36

E/LE-series User Manual 6
1.0 INTRODUCTION
1.1 Overview of the Manual
This manual contains operation and maintenance instructions for the Covaris E and LE-series
instruments (the E220, E220x and LE220). It contains background information essential to the
proper use and care of this equipment.
The following definitions apply in this manual:
NOTE: Inconvenience only if disregarded – no damage or personal injury
CAUTION: Equipment damage may occur, but not personal injury.
WARNING: Personal injury may occur – DO NOT DISREGARD.
There is also a PDF version of this manual on the system computer (if a computer was supplied
with your order). Open the manual by double clicking the manual icon on the desktop.
1.2 Purpose of the Equipment
The E and LE Series instruments are used for high-throughput, sample preparation and
extraction. The technology uses controlled and highly focused nonlinear acoustic waves that are
delivered to each sample. The systems are designed to work with a variety of closed or open
sample vessels including vials, tubes, and multi-well plates. Contact Technical Support for more
information. The instruments are not intended for use in diagnostic procedures; for research use
only.
CAUTION: The system is designed to work primarily with closed sample holders. Open
vessels may be used; however, the energy should be dramatically reduced as
there is potential for leakage and spilling into the water tank. Please contact
Covaris Technical Support for guidance in this area if open vessel processing is
required.
1.3 Main Components
The main components of the E and LE Series instruments include:
•acoustic transducer
•temperature sensing device
•sample positioning system
•degassing pump
•water bath
•user manual
External components include a notebook computer.
The user is expected to provide a recirculating chiller/heater. Covaris can provide specifications
for recommended recirculators.

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Figure 1
1.4 Principle of Operation
The Covaris Process generates acoustic shock waves to cause controlled cavitation and
acoustic streaming at the focal point within the sample treatment vessel. Acoustic energy has
been utilized for many years for a variety of diagnostic, therapeutic and research purposes. Well-
known uses of sonic or acoustic energy in materials processing include "sonication", an
uncontrolled process of mechanical disruption involving the direct immersion of an unfocused kHz
range (e.g., 15,000 cycles per second) ultrasound source into a fluid suspension of the material
being treated. There are also specific clinical examples of the utilization of therapeutic ultrasound
(e.g. lithotripsy) and of diagnostic ultrasound (e.g., fetal imaging).
Typically, when ultrasound is applied to a bulk biological sample solution (as for the extraction of
intracellular constituents from tissue), the treatment causes a complex, heterogeneous, mixture of
sub-events that vary during the course of a treatment dose. In other words, the ultrasonic energy
may be partitioned between various states. For example, the energy may directly treat a sample;
the energy may displace the target and shift the target out of the optimal energy zone; the energy
may result in interference, (i.e., a “bubble shield”), that reflects the acoustic energy; or the large
particles may move to low energy nodes thereby leaving the smaller particles with more dwell-
time in the high energy nodes. In addition, the sample viscosity, temperature, and uniformity will
vary during the ultrasonic process, resulting in gradients during the process. The current low
frequency, unfocused sonicator-type processes are random and non-uniform. This limits the use
of ultrasound in high throughput applications where treatment standardization is required.
In contrast, focused, nonlinear acoustic waves are computer generated and delivered to
individually-addressable samples with the E and LE series systems. The mechanical energy
imparted on the sample results in a controlled series of compression, rarefaction events. The E
and LE-series instruments were designed to provide the researcher with methods and systems to
control the delivery of mechanical energy into a biological sample for high-throughput sample
preparation applications.

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1.5 System Distinctions – E, Ex and LE
All E Series instruments employ an XYZ motion system to move sample plates or racks over the
acoustic transducer according to user-programmed methods. E Series instruments, however, are
available in several configurations:
•The E220 employs a single focal point transducer to sequentially treat samples as they
are positioned over the transducer by the motion system. The E220 may be programmed
to a maximum Duty Cycle (acoustic power on/off ratio) of 20.0%.
•The E220x operates identically to the E220, except that Duty Factor may be programmed
to a maximum value of 50.0% percent to provide additional treatment power.
•The LE220 operates identically to the E220x, except that a line transducer is employed,
producing a line of focused power rather than a single point. Acoustic power is thus
applied across the sample plate or rack, treating an entire row of tubes or wells in
parallel. The acoustic power is divided approximately across all the samples in a row, so
treatment power must be increased accordingly in order to obtain results similar to those
obtained with a focused point transducer.
SonoLab operating software automatically detects the type of instrument and adjusts its
programming parameters accordingly. The plate or rack graphic seen in the Main and Method
Editor screens will also illustrate the point versus line treatment configurations, as illustrated in
Figure 2.
Figure 2 – E and Ex (left) versus LE (right)
Graphics employed in this manual will show the LE well plate configuration, but all instructions
are applicable to either E, Ex, or LE systems.

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2.0 INSTALLATION
2.1 Unpacking and System Setup
The Covaris system is shipped in one crate, containing the instrument, the instrument supplies,
optionally purchased notebook computer, and the selected accessory kit. Remove all wrappings,
taking care not to inadvertently discard any parts, accessories, or documents.
Normal precautions in unpacking and reasonable care in handling should be exercised to avoid
possible damage to the unit. Visually inspect all external controls, indicators and surfaces to
detect any damage that may have occurred during shipment.
The shipping company is responsible for damage to equipment during shipment. If damage has
occurred, notify the shipping company immediately to establish proper basis for a claim.
NOTE: In case of damage do not discard packing material until Covaris has inspected for
cause of damage.
WARNING: Risk of back injury. The instrument weighs approximately 110 pounds (50
kilograms).
2.2 Placement of Equipment
The area required for the instrument (see Figure 1) is approximately 23” wide by 30” deep by 19”
high (59 cm x 76 cm x 48 cm). Space on or adjacent to the bench is required for a notebook
computer. Additional space may be required for a user-supplied recirculator.
Two fans maintain a safe operating temperature in the instrument by circulating air over the
internal components. Therefore, place the instrument so that there is a minimum of 1” (3cm)
between the rear panel and any wall or obstruction for airflow.
2.3 Power Requirements
The instrument draws a maximum of 500 VA. The Covaris E and LE-Series instrument are
configured with a universal power supply. Refer to label on left side of instrument for specific
power requirements
In case of a power interruption, the system will halt. The equipment will then need to be
restarted. As files or data not saved prior to the power interruption will be lost, the use of an UPS
(Uninterrupted Power Supply) is recommended with this system if your site has frequent power
surges or loss of power. The UPS should be capable of supplying full 5 amperes at the voltage
used.
WARNING: To prevent the possibility of electrical shock, always plug the system into a
grounded power source.
2.4 Set-up Procedures
2.4.1 Connections
Ensure that the user-supplied chiller is connected to the CHILLER IN and OUT ports on the
left side of the instrument using the Covaris supplied hoses. The hoses are setup with quick
disconnect fitting to be attached to the instrument and hose clamps for the user supplied
chiller
Ensure there is a USB cable connected from a USB port on the computer to the USB port on
the instrument (located above the power switch on the right side, near the back of the
instrument).

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2.4.2 Powering Up the System
Power up the Covaris system by moving the power switch to the “1” position. If the computer
is supplied by Covaris, turn it on. Open the SonoLab software by double clicking the
SonoLab icon on the desktop.
NOTE: To ensure connection between the laptop and instrument, please wait 30 seconds
after powering the system on before starting SonoLab 6.2.
Re-home the system daily by closing and restarting SonoLab. This will correct any
accumulated misalignments in the system.
2.4.3 Control Buttons
There are two control buttons located on the right side of the
instrument as shown in Figure 3. The red STOP button can be
depressed and held for 1 second at any time to halt operation.
The green DOOR button, when lit, can be depressed to allow
the operator to open the safety enclosure door (See section
3.4).
Figure 3
2.4.4 Water Bath
Configuration
The water bath tank needs to be
oriented properly when inserted into
the system. The bath should be
oriented with the label “Insert this
end” at the back of the tank (see
Figure 4). The "waterline" label will
be displayed on the front side of the
tank.
Figure 4
CAUTION: The magnetic safety interlock will not allow the instrument to operate if the water
tank is not oriented properly and fully inserted.
Fill the water bath to the water line on the side of the tank, as the water level will rise when
the transducer is submerged. Only distilled or deionized water should be used to fill the
water bath.
CAUTION: Never run a method without a water bath. This will permanently damage the
transducer.

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CAUTION: Using anything besides distilled or deionized water in the water bath is a
misapplication of the equipment and will void the warranty.
The system includes a water level sensor. If the water level is too low, a warning massage
will be issued by the software. In addition, the degas pump will not operate for more than 10
seconds if a low water level is detected. This is to protect the pump from running without
water.
Prior to running a method, the water bath should be degassed for 45 minutes. Degas the
system by lowering the transducer (click the START HOMING button in the Initiation
Sequence or click the LOAD PLATE button on the MAIN PANEL of SonoLab). Then click the
DEGAS ON button.
NOTE: The DEGAS ON button will not engage the degassing pump if the transducer is in
the SERVICE BATH position
NOTE: The degas pump will turn off after 10 seconds if the water tank is not filled with
water to the fill line.
3.0 SYSTEM DESCRIPTION
3.1 General Overview
The Covaris E and LE220 systems, as shown in Figure 1, are custom instruments for high-
throughput sample preparation and compound management. The system is comprised of the
Treatment System which delivers the energy to the sample, the Safety System which provides
intelligent interruption during the “treatment”, and the Computer and the Application Software
which provide the user interface to the entire system.
This instrument is a very powerful, high-energy system. It is designed to disrupt and homogenize
biological tissue, extract biochemicals, and accelerate reagent dissolution.
3.2 Treatment System
3.2.1 Acoustic Transducer
The acoustic transducer delivers a high intensity, focused, computer-controlled acoustic
shock wave to a sample. This is called the “treatment”. The treatment of all samples in a
tube rack or well plate is called a method.
WARNING: Objects at the focal point of the transducer will be exposed to high energy
when the system is activated.
3.2.2 Temperature Sensors and Temperature Control
The water bath sensor, a 5cm metal probe, monitors the temperature of the water bath. The
water bath temperature limits can be set to values between 0º C and 45º C. The water bath
temperature is controlled by connecting an external recirculating chiller/heater to the ports in
the back of the system. The recirculator will pump a temperature-controlled fluid through a
stainless steel loop immersed in the water bath.
NOTE: Although the instrument reports the bath temperature via the Temperature
Sensor, it does not control the recirculating chiller. Typically, for most applications (e.g., gene
expression, proteomics, compound dissolution, and drug metabolism studies) the temperature of

E/LE-series User Manual 12
the recirculating chiller is set to 15 degree C with the temperature of the water bath equilibrating
at 18 degree C.
CAUTION: A recirculating chiller is required for efficient and controlled operation of the E and
LE-series instruments.
3.2.3 Sample Positioning System
The major components of the system include:
The sample positioning system (x, y, z axes)
The transducer positioning system (z’ axis)
The sample holder plate
The robotic interface
Figure 5 shows the sample holder plate with the A1 position identified.
Figure 5
3.2.4 Water Bath and Degassing System
The water bath holds approximately 1.3 gallons
(4.92 liters) of distilled or deionized water. The
water level is indicated by a label on the front
wall of the water bath. The left side of the label
(“FILL”) indicates the water level when filling the
bath. The right side of the label (“RUN”)
indicates the water level when the transducer is
submerged.
The water level will be dictated by the tube rack.
If Covaris has provided an Instruction for Use
(IFU) for your tube rack, please refer to it for the
recommended water level. If no water level is
specified, fill the water bath to the “0” level.
WARNING: The water bath is heavy when filled. Use caution when moving it.
The degassed, temperature controlled water provides an efficient energy couplant from the
transducer to the sample to be processed. The water bath must be degassed for
A1 positionA1 position

E/LE-series User Manual 13
approximately 45 minutes to ensure proper operation of the instrument. The degassing pump
will start automatically as the transducer is submerged. Its ON status is indicated by a green
indicator on the SonoLab main screen. If the degas pump has been turned OFF, it can be
restarted by clicking the DEGAS ON button.
The degassing system consists of a dip tube with six small holes, a positive displacement
pump, and an outlet nozzle. Dissolved gasses and vapors are reduced in the water by
pulling the water through the small holes in the dip tube and pumping the resulting coalesced
bubbles out the outlet nozzle before they can re-dissolve. During normal operation, there
should be an intermittent stream of bubbles coming from the outlet nozzle. If no bubbles are
visible for several minutes, the six small holes in the dip tube may be plugged. If this occurs,
the dip tube may be removed and the holes cleared with a fine wire (e.g., 26 Gauge needle).
3.3 Computer
The computer uses the Microsoft™ WindowsXP Operating System or Windows 7 with
SonoLabapplication software.
3.4 Safety System
The safety system protects the user from hazards associated with the acoustic treatment system
and the moving parts in the sample positioning system.
The safety system prevents operation of the instrument if the front door is open, the water tank is
not in place, or the robotic interface is not enclosed. The front door can only be opened when the
green light on the DOOR button is lit. Once lit, pressing the button will allow the door to be
opened. There is also a red STOP button on the right of the safety enclosure (see Figure 3).
Depressing the STOP button for one second (or clicking on the STOP button in SonoLab) halts all
operations. The Process Stopped Dialog Box appears, which allows the user to either Resume
or Abort the current operation as shown in Figure 6. Note that Resume is viable only when the
SonoLab STOP button has been used. Methods halted with the safety enclosure STOP button
cannot be restarted.
Figure 6
NOTE: The door may be opened in the event of a power failure by inserting a special tool
provided with the instrument into the hole in the enclosure above the safety interlock and
rotating clockwise 90 degrees. The instrument will not operate if the safety interlock is
disabled. The tool is stored in a clip on the back of the instrument.
3.5 Water Bath Temperature
The software monitors water bath temperature. If the bath temperature is beyond user defined
limits, while a method is running, the method is halted and the following dialog box will appear:

E/LE-series User Manual 14
Figure 7
3.6 Application Software
3.6.1 Main Panel
Software Panel 1: MAIN PANEL (LE220 application shown)
Motion Buttons
The motion buttons move the sample holder and the transducer. They operate as follows:
DEGAS ON starts the degas pump
DEGAS OFF turns the degas pump off

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LOAD PLATE lowers the transducer from a raised position (SERVICE BATH position) and
moves the sample holder to the manual load position.
SERVICE BATH raises the transducer and sample holder out of the water bath.
METHOD EDITOR button will take the operator to the Method Editor Panel which allows the
user to create and/or modify a method.
START button starts running a method. After selecting the button, a warning dialog box
opens to ensure the system is ready to proceed. The warning reminds the user to check that
there is water in the water bath, that the system has been degassed, and that there are
samples in the sample holder. See the warning screen below:
Figure 8
If the user is ready to proceed, click the START button.
STOP halts the operation of the sample positioning system. (Methods may then be aborted
or resumed.)
NOTE: The STOP button on the instrument and the STOP button on the display perform the
same function, however methods halted with the instrument STOP button cannot be resumed.
The EXIT button will exit the program.
The Status Indicator Lights
ACOUSTIC POWER indicates that the transducer is active.
LOW WATER LEVEL indicates that the water sensor and transducer are not immersed.
INTERLOCK OPEN indicates the software senses that the mechanical safety interlock is in
the open position.
BATH or SIDE DOOR FAULT indicates that the water tank or the side door (robotic systems
only) is not in place or properly secured.
DEGAS indicates the degassing pump is on. (Located below the DEGAS ON button.)
While a method is running, the following indicators display current treatment parameters:
BATH TEMPERATURE displays the temperature of the water bath. The thermometer
graphic, normally blue, will turn red if bath temperature exceeds the temperature limits
set by the user in the method.
DUTY FACTOR, PIP (PEAK INCIDENT POWER), and CYCLES PER BURST show the
parameters for the current well being processed. (Refer to section 3.6.2)

E/LE-series User Manual 16
ACOUSTIC POWER GRAPH shows the acoustic power being delivered to the sample for
each treatment.
Plate Map Graphic
Each row of wells is represented in the plate map.Untreated wells are yellow. A well
undergoing treatment is green and once completed the color changes to blue. If a treatment
is aborted, the row will appear red.
Acoustic Treatment Graph
The DUTY FACTOR, INTENSITY, and CYCLES/BURST indicators display the treatment
parameters being applied to each well during a method run. These parameters are
programmed into each method by use of the Method Editor Panel (see section 3.6.2).
Progress Bar
Indicates the percent completed of the currently running method (as a percent of the total
calculated time).
3.6.2 Method Editor Panel
Software Panel 2: METHOD EDITOR PANEL
This screen allows the user to select either a previously created method (and its associated
parameters) or to create a new method. On the left side of the screen are the controls to set-
up the well plate.

E/LE-series User Manual 17
Left clicking on a table entry highlights that entry. The shift and control keys may be
employed to highlight multiple entries. The Treatment Parameters may be edited for all
highlighted table entries.
SELECT ALL and DESELECT ALL manipulate highlighting of steps in the Method Table.
The MOVE Buttons move highlighted entries within the table.
The FILL PLATE button creates multiple sequences per well by applying the treatments
highlighted in one or more rows in the table using the ordering of the selected sequence.
SELECT ALL will highlight all entries in the list of treatments. Edits made to acoustic
parameters will apply to all highlighted entries.
DESELECT ALL will remove highlighting from all entries in the list of treatments.
MOVE SELECTION DOWN will move the highlighted entries down one position in the list.
MOVE SELECTION UP will move the highlighted entries up one position in the list.
REMOVE SELECTED will delete highlighted entries from the list.
Note that edits to method parameters will cause the METHOD CHANGED indicator to
illuminate until these edits are either undone or saved.
Treatment Parameters
For a new or an existing method, the user may define and edit the individual row parameters
or sequence in the control panel.
ROW/COL is the current treatment position in the well plate. The set of parameters
defined for the well is a treatment.
TIME is the amount of time (sec) to apply the parameters or to treat a sample.
Acoustic energy is produced in bursts and the system allows the user to modify this energy to
maximize the effects on the treatment of samples for any particular application. Contact
Covaris Technical Support for recommendations regarding these settings.
DUTY FACTOR is defined as a percentage. This is the percentage of time that the
transducer is “on” and creating acoustic waves. Average acoustic power will increase
with greater Duty Cycle. Minimum is 0.1%. Maximum is 20.0% for E and 50.0% Ex and
LE.
PIP (PEAK INCIDENT POWER): The instantaneous power in Watts transmitted to the
acoustic transducer during the “on” time of each acoustic burst. The larger the number,
the more energy each acoustic wave has. Minimum is 3.0 and maximum is 500.0 Watts.
CYCLES PER BURST: The number of waves generated by the transducer in a burst.
For example, 100cpb at 10% duty factor is a wavetrain of 100 “on” energy cycles followed
by 900 “off” energy cycles. Minimum is 50 and Maximum is 1,000.
Dithering is the controlled horizontal circular movement of the treatment vessel around a
center point during processing to mix the sample. For horizontal dithering, the following
parameters can be set:
RADIUS is the radius (in mm) the vessel moves in a circular motion.
VELOCITY is the speed (in rpm) of this movement of the vessel.
DWELL is the time the vessel remains at the center point between dithering operations.

E/LE-series User Manual 18
CAUTION: Method progress will halt if these values exceed the maxima allowed by each well
plate definition. Test dithering functions before using them in on valuable
samples. Contact Covaris for guidance if needed.
Method Parameters
FREQUENCY SWEEPING: The acoustic frequency sweeps through a range during
processing. This is the default setting for the E and LE-series instruments. As plastic readily
absorbs acoustic energy, this lower power setting is more appropriate for method
development with plastic vessels. Frequency sweeping is both preferred and recommended
for plastic sample vessels.
VERTICAL SWEEP moves the sample up/down during processing.
VERTICAL +/- is the vertical movement in mm.
VERTICAL RATE is the frequency in cpm (cycles per minute).
MAX and MIN TEMPERATURE allow the user to select water bath temperature limits for the
treatment. The temperature limits can be set to a value in the range of 0º C and 45º C. If the
water temperature is beyond the specified limit, the BATH thermometer on the main panel will
turn red and processing will be halted. It can be restarted by selecting OVERRIDE in the
temperature warning dialog box.
General Operation Buttons
The following buttons are employed for creating, importing, exporting and saving methods.
Note that edits to method parameters will cause the Method Changed indicator to illuminate
until these edits are either undone or saved.
NEW METHOD opens a new method with no treatments yet defined for any wells.
LOAD METHOD opens an existing method (*.e1proc file) and displays it on the Method
Editor panel.
IMPORT CSV FILE and EXPORT CSV FILE features have not been implemented.
SAVE METHOD AS saves the currently displayed method parameters to a new or
existing method (*.pro) file.
SAVE METHOD saves the currently displayed method parameters to the method
(*.e1proc) file name displayed in Method Name.
RETURN closes the Main Panel. Note that you may be prompted to save or discard any
unsaved edits before returning to the Main Panel.
4.0 SYSTEM OPERATION
4.1 Start-Up Procedures
Chiller Connection
The recirculating chiller (required) should be connected to the treatment system using the hoses
supplied. The chiller inlet is connected to the fitting labeled “IN” and the chiller outlet is connected
to the fitting labeled “OUT” located on the left side of the instrument.
Water Bath
Special care needs to be taken when changing the water bath. First, select the SERVICE BATH
button to raise the transducer. Then carefully pull out the acrylic water tank from the instrument
base plate and empty it. Fill the water tank and place it back into its position, ensuring that it is
oriented properly in the instrument and the water is at the correct level (see section 2.4.3).

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WARNING: The water bath is heavy when filled. Use caution when moving it.
CAUTION: Never run a method without a water bath; the system should detect this and
refuse to operate, but a lack of water risks permanent damage to the transducer.
Degassing
The Covaris system requires that the water bath be degassed to maintain repeatable acoustic
energy coupling, therefore, the pump should be running whenever samples are being treated.
This is especially critical for high intensity applications such as solid tissue homogenization. At
room temperature, the water bath should be degassed for at least 1/2 hour prior to running a
treatment method. Select the DEGAS PUMP button on the Main Panel. Ensure the water bath is
filled to the water level before turning on the pump; otherwise, damage to the pump may occur.
NOTE: The degassing pump will turn off after 10 seconds if the water tank is not filled
with water.
Manual Loading of the Multi – Well Plate Holder
Select the LOAD PLATE button on the Main Panel to raise the multi-well plate holder. The
system will position the stage above the water bath.
Fill the tube rack with the sample vessels to be run. If required, place the hold-down plate over
the vessels. The hold-down plate ensures that the vessels stay in place for correct processing.
The plate should be loaded on the multi-well plate holder with the A-1 position in the upper right
corner. See Figure 5.
If not all the wells are filled with samples to be treated and the method is high intensity, load the
unused positions with empty vessels to reduce splashing.
NOTE:Ensure the well-plate is seated flush onto the well-plate holder to insure the
samples are correctly aligned with the focal point of the transducer.
4.2 Creating and Modifying a Method in the Method Editor Panel
To open an existing method to run or to modify, select METHOD EDITOR, click on LOAD
METHOD and choose from the list of previously saved set-ups.
To create a new method, select the METHOD button.
Select the Well Plate Configuration from the PLATE NAME menu.
Parameters may now be selected in the Treatment Parameters area.
Select the Current Well Parameters
Click on any well; a treatment can be configured using the Treatment Parameters.
Treatment parameters for additional wells may be programmed by clicking on those wells and
using the Treatment Parameters controls. Well treatments may be copied across an entire plate
by employing the FILL PLATE button. This feature also allows several choices for the order in
which wells are listed in the method. Wells will always be treated in order as displayed in the
treatment entry list.
Save the method by selecting the SAVE METHOD button. The system will prompt the user to
name the METHOD.

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4.3 Running a Method Manually in the Main Panel
Load the samples first by selecting the LOAD PLATE button. The motion system will move the
sample holder tray to the front of the enclosure and the green DOOR button will illuminate. Press
the DOOR button to open the door and position the samples on the tray.
Click the pull-down menu button under the Method Name. Select from the list of defined
methods.
Click the START button. The system will run the treatment displayed in the Method Name box.
CAUTION: If the computer loses connection with the instrument during processing, the
method will stop.
The following Main Panel indicators provide system status information:
The green indicator between the DEGAS buttons will illuminate when the degas pump is on. This
pump should be run for at least 45 minutes prior to running a method.
On the WELL PLATE MAP, each well will appear yellow prior to treatment, green during
treatment and blue following treatment.
The CURRENT STEP, TOTAL STEPS and ESTIMATED TIME TO COMPLETION displays
monitor progress through the method.
The ACOUSTIC POWER indicator and graph indicate when acoustic treatment is being applied,
and its approximate power.
The DUTY FACTOR, PIP, AND CYCLES PER BURST graphics show the treatment parameters
being applied to a well when the Acoustic Power indicator is illuminated.
INTERLOCK OPEN will illuminate when human access is occurring in the acoustic treatment
area. Acoustic power and internal motion will be suppressed whenever an INTERLOCK
OPEN condition is detected. Specifically, this will occur either when the front door is
open, and/or when the side robot interface door is open with no robot interface in place.
4.4 Manual Overrides
There is a STOP Button on the main SonoLab screen. This will halt the current method. The
method may also be stopped by pressing and holding the red STOP button on the instrument for
one second. The green DOOR button will light once the method has stopped.
To restart, the system will prompt the user with a message to either RESUME or ABORT the
method. If the door is not closed, selecting RESUME will prompt the user again to RESUME or
ABORT. Selecting RESUME with the safety system closed will continue the method where it was
interrupted. Selecting ABORT terminates the method.
NOTE:Methods stopped with the safety enclosure STOP button cannot resume via
the RESUME function in SonoLab. To pause and resume a method, use the
SonoLab STOP button.