Covaris M220 User manual

For research use only
M-Series
USER MANUAL
instrument developed for
high performance sample preparation
using adaptive focused acoustics
Product Name: M-Series
Model Numbers: M220
Software: SonoLab 7

M220 User Manual Page 2
Trademarks
Patented or patent pending and registered or registration-pending are trademarks of Covaris.
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 010157
Revision H, May 2017
Product covered by Patent No. US6, 719,449, US6, 948,843, and other 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 attempt to operate the equipment with the safety cover in the OPEN position or without water in the
acoustic assembly; 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
includes a solid state heater/chiller apparatus to control sample temperature.
NEVER run a method without water in the acoustic assembly; 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 detected.
AFA-grade water should be used to fill the water bath.
Empty the water bath and wipe it dry EVERY day with a lint-free cloth.DO NOT leave water in the water bath for an
extended time as there is no water filtration or water cleaning system with the apparatus.
Do not employ isopropyl alcohol, ammonia-based or abrasive cleaners on the acoustic assembly, as these will
damage the acrylic or transducer surfaces.
The Tube Holder should be stored in a dry place or in the M220 Accessories Storage Station when not in use.
Establish a standard of operation and periodically test equipment, as described in Appendix A of this manual.
DO NOT load third party hardware, software, or parts onto the system without consulting with Covaris.

M220 User Manual Page 4
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 THE 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] or [e-mail]
M220 Instrument Repair – Repair of all parts (including the laptop) from normal operation of equipment are
provided in our Service Depot. All labor charges are included. Instrument packaging and ground shipping will
be provided. 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....................................................................................................................................7
1.1 Overview of the Manual............................................................................................................7
1.2 The M220 and the Covaris Process.........................................................................................7
2.0 INSTALLATION AND SETUP ...............................................................................................................7
2.1 Assembly ...................................................................................................................................7
2.2 Installing the Tube Holder........................................................................................................9
2.3 SonoLab Installation...............................................................................................................10
2.4 Starting SonoLab ....................................................................................................................11
3.0 OPERATION........................................................................................................................................12
3.1 General Overview....................................................................................................................12
3.2 Preparing the M220 for Use....................................................................................................13
3.3 Filling the Water Bath .............................................................................................................15
3.4 Loading the Sample................................................................................................................16
3.5 Running a Method...................................................................................................................17
3.6 Instrument Light......................................................................................................................17
3.7 Draining water and cleaning ..................................................................................................17
3.8 Shutdown Procedure..............................................................................................................17
4.0 USING A PREEXISTING METHOD.....................................................................................................18
4.1 DNA shearing protocol...........................................................................................................18
4.2Chromatin shearing protocols...............................................................................................18
5.0 CREATE AND EDIT METHODS..........................................................................................................19
6.0 SonoLab™ APPLICATION SOFTWARE............................................................................................25
6.1 Run Screen ..............................................................................................................................25
6.2 History Screen.........................................................................................................................25
6.3 Setup Screen ...........................................................................................................................26
6.4 Maintenance Screen................................................................................................................32
6.5 About Tab.................................................................................................................................33
7.0 TROUBLESHOOTING.........................................................................................................................35
Appendix A: Suggested M Series IQ / OQ / PQ..........................................................................................36
Appendix B: M Series Site or Transport Preparation................................................................................42
Appendix C: Updating SonoLab Software..................................................................................................43
Appendix D: Installing SonoLab on a new computer and installing Windows Instrument Drivers.....44
Appendix E: Running the SonoLab Protocol Updater ..............................................................................45

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1.0 INTRODUCTION
1.1 Overview of the Manual
This manual contains installation, operation and service instructions for the Covaris M220 Focused-
ultrasonicator. It contains information essential to the proper use and care of this 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 a PDF version of this manual available on the computer desktop. Open the manual by
double clicking the user manual icon. A hypertext version of this manual can also be found in the
Help tab of the SonoLab Software.
1.2 The M220 and the Covaris Process
The M220 Focused-ultrasonicator is based on Covaris Adaptive Focused Acoustics (AFA)
technology. This instrument is designed to provide researchers an integrated stand-alone tool to be
used in laboratory environment. The instrument is ideal for those who work with DNA shearing and
sample preparation.
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.
2.0 INSTALLATION AND SETUP
2.1 Assembly
The following items should be found in the package of the Covaris M220 instrument:
oQuick Start User Guide
oUser Manual
oNotebook Computer with AC Adapter (# 500311)
oCables
1 USB cable
1 M220 power cord
1 Computer AC Adaptor power cord (Non US customer only)
oAccessories
Fill-Drain Kit (# 500299)

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•1 100ml wash bottle
•1 20 ml Syringe
•2 Re-sealable plastic syringe tips
Cleaning Swab Kit (# 500298)
•10 disposable swabs
AFA-grade water (125ml)
oM220 Safety Cover
oM220 Main Unit
CAUTION: Lift the M220 out of the box by its baseplate. Do not lift by the Acoustic
Assembly. Lifting the unit by its acoustic assembly may damage the instrument.
Figure 2.1- A front view of the M220 instrument.
After the instrument is unpacked, please locate the M220 on a flat surface near two power outlets.
Use both sides of the base (Figure 2.1) to lift the instrument. Do not use the acoustic assembly to
lift the instrument.
If necessary, adjust the four adjustable feet to ensure the instrument is stable and level. Do not
remove the adjustable feet. They are needed to ensure proper air flow from the system chiller.
Hinges
Tube holder
Computer Station
Acoustic Assembly
Safety Cover
M220 Main Unit
Chiller Exhaust
(On both sides)
Computer Loading
Bars
Lift Here

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1) Peel off the backing from the Velcro strips on the Computer Loading bars. Place the
computer on top of the glue side of the strips as shown in Figure 2.2. Gently press the
computer to secure it in place.
Figure 2.2- Secure the computer on top of the M220 as shown.
Figure 2.3 - The back panel of the M220 instrument
2) As shown in Figure 2.3, plug the AC power cord into the power inlet located at the back
panel of the instrument; Plug the AC power cord into the power outlet;
3) Plug the AC adaptor into the computer and into the power outlet;
4) Connect the USB cable into the USB port located at the back panel of the instrument
(Figure 2.3) and USB port on the notebook computer;
5) Place the Safety Cover on the hinges (please refer to Figure 2.1);
6) Place the Tube Holder in the Acoustic Assembly housing (refer to section 2.2 below).
The entire instrument may be relocated in this assembled configuration by disconnecting power,
lifting from the sides, relocating, and repeating the appropriate assembly steps.
2.2 Installing the Tube Holder
Power Inlet
Power Switch
USB port
To computer
Center the
computer on top of
the M220 as shown
Ventilation
fan

M220 User Manual Page 10
Open the Safety Cover and place the Tube Holder into the Acoustic Assembly. Note that the
undercut at the forward-left corner of the tube holder should be aligned with the pin on the assembly.
Figure 2.4 -Place the Tube Holder in the Acoustic Assembly
2.3 SonoLab Installation
SonoLab 7 is an application used to control a 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 7 has been pre-installed in the computer purchased with the M220 instrument. No
further installation or configuration is required if the computer is purchased with M220 instrument.
Users can directly go to section 2.4 to start the SonoLab program.
If it is necessary to install or re-install SonoLab 7 or instrument drivers on a computer, please contact
Covaris for the latest versions, downloading and installation instructions.
Pin
Undercut
Tube Holder