CEM liberty User manual

600178
Rev. 5
Operation Manual

Liberty™Automated Microwave Peptide Synthesizer
600178 • Revision 5 • October 2009
Contents
Section 1: Introduction
Introduction 7
About This Manual 7
Common Abbreviations and Units 8
How to Obtain Support 10
Applications Support 10
Technical Support 10
Requested Information 10
Contact CEM 11
CEM Corporation Headquarters 11
CEM International Subsidiaries 11
CEM Distributors 12
Safety Information 13
Safety Notations 13
Safety Information 14
Fume Ventilation 14
Waste Disposal 14
System Requirements 14
Bench and/or Fume Hood Space 14
Environmental Conditions 15
Inert Gas Source 15
Electrical Requirements 15
Section 2: Operation of the Liberty
Introduction to the Liberty 16
Components and Parts 18
Reaction Vessel Components 19
Introduction to PepDriver 20
PepDriver Main Screen 21
Control Buttons 22
Menu Buttons 22
Indicators 22
Tabs 23

Liberty™Automated Microwave Peptide Synthesizer
600178 • Revision 5 • October 2009
Editors 25
Microwave Editor 25
Microwave Method Folders 25
Microwave Method Types 25
Creating a New Microwave Method 26
Editing an Existing Microwave Method 27
Cycle Editor 28
Cycle Folders 28
Copying and Modifying an Existing Microwave Method 28
Cycle Types 29
Creating a Cycle 29
Editing an Existing Cycle 30
Copying and Modifying an Existing Cycle 31
Sequence Editor 32
Creating a New Sequence 32
Modifying a Sequence 33
Using the External Amino Acid Positions 33
Importing a Sequence 34
Method Editor 36
Creating a New Method 36
Modifying an Existing Method 38
Calculators 39
Usage Calculator 39
Reagent Calculator 40
Resin Calculator 40
Deprotection Calculator 41
Activator Base Calculator 41
Activator Calculator 42
Amino Acid Calculator 42
Cleavage Calculator 43
Setting up a Synthesis 44
Conguring Methods to Run 44
Loading a Method 44
Loading Multiple Methods 45
Preparing Reagents 45
Standard Concentrations 45
Preparing Activator Solution 46
Preparing Activator Base Solution 46
Preparing Amino Acids 46
Preparing Deprotection Solution 47
Preparing Capping Solution 47
Preparing Cleavage Solution 48

Liberty™Automated Microwave Peptide Synthesizer
600178 • Revision 5 • October 2009
Setting up the Liberty 48
Loading Reagents onto the Liberty 48
Loading Resin onto the Liberty 50
Changing the Reaction Vessel 50
125 mL Reaction Vessel 50
10 mL Reaction Vessel 50
Running the Liberty 51
Preparing the Liberty to Run 51
Running the Liberty 52
Generating Reports 54
Method Reports 54
Creating a Method Report 54
Sample Method Report 55
Run History Reports 56
Creating a Run History Report 56
Sample Run History Report 56
Section 3: Quick Setup Guide
Peptide Setup 57
Create and Load the Method 57
Prepare Reagents 58
Ensure the Liberty is Ready to Run 59
Section 4: Mainteance of the Liberty
Routine Maintenance 61
Daily Maintenance 61
Weekly Maintenance 61
Biweekly Maintenance 61
Monthly Maintenance 61
Semiannual Maintenance 62
Standby Procedure 62
Maintenance Screen 63
Cleaning Tab 63
Using the Change Bottle Command 65
Performing a Backush 66
Performing a System Check 67

Liberty™Automated Microwave Peptide Synthesizer
600178 • Revision 5 • October 2009
Sample System Check File 69
Volume Calibration Tab 70
Performing a Volume Calibration 70
Importing and Exporting Volume Calibration Values 72
Performing a Large Scale Calibration 73
Sensor Calibration Tab 76
Performing a Sensor Calibration 76
Importing and Exporting Sensor Calibration Values 79
Pressure Calibration Tab 79
Performing a Pressure Calibration 80
Section 5: Advanced Features
Default Cycle Editor 82
Changing Default Cycles 82
Options Menu 83
Program Options Tab 83
Defaults Tab 85
Run History Tab 85
Test System Screen 86
Pressure Adjustment 87
Main Pressure Adjustment 87
Low Pressure Adjustment 88
Leak Check 88
Test Rotary Valves 89
Internal, Nitrogen, and Liquid Delivery Tests 90
Setting Up the Liberty for a Delivery Test 90
Performing a Delivery Test 91
Test Sensors 91
Reagent, Amino Acid, and External Amino Acid Addition 93
Leak Check Reaction Vessel 94
Flow Performance 94
Diagnostics Screen 95
Commands Tab 95
Sensors Tab 95

Liberty™Automated Microwave Peptide Synthesizer
600178 • Revision 5 • October 2009
Valves Tab 96
Status Tab 96
Delay Times Tab 97
Section 6: Troubleshooting
Tips for Recovering from Errors 99
Section 7: Spare Parts and Consumables
Reaction Vessel Parts 100
Filters 101
Solvent Keg 101
Bottles 102
Bulk Tubing and Fittings 103
Bottle Tubing Assemblies 104
Bottle Caps 105
Dip Tubes 106
O-Rings 106
Valves and Valve Wiring 107
Liquid Sensors 108
Waste Container 109
Accessories and Tools 109
Computer Accessories 110
Circuit Boards 111
Regulators 111
Documentation 111
Section 8: Index

Liberty™Automated Microwave Peptide Synthesizer
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Liberty™Automated Microwave Peptide Synthesizer
600178 • Revision 5 • October 2009 7
Section 1: Introduction
Introduction
About This Manual
This manual (PN 600178) describes the operation and maintenance of the Liberty™ Automated
Microwave Peptide Synthesizer. The manual is intended for use by both novice and experienced
users.
This introductory section contains a list of common abbreviations and units used throughout the
manual, as well as important information for the safe operation of the unit. The manual assumes
that the Liberty was installed by a CEM certied service technician.
This manual refers to PepDriver™ version 2.5.4 Build 2 for all software information, including
screenshots and technical information. The latest version of PepDriver can be downloaded from
CEM’s website at http://www.cem-technet.com. Aregistered account is required for download.
Additional information is available in the Appendicies (PN 600183), which can be found on the
included CD-ROM (PN 900105).

Liberty™Automated Microwave Peptide Synthesizer
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8
Common Abbreviations and Units
Abbreviation Definition
°C degrees Celsius
°F degrees Fahrenheit
AA amino acid
ACP acyl carrier protein 65-74
Amp amphere
Boc tert-butyloxycarbonyl
tBu tert-butyl
DCM dichloromethane
DIEA diisopropylethylamine
DMF N,N’-dimethylformamide
DODT 3,6-dioxa-1,8-octane dithiol
Ea energy of activation
EDT ethanedithiol
Fmoc 9-uoroenylmethyloxycarbonyl
g gram
h height
HATU N-((dimethylamino)-1H-1,2,3-triazolo-4,5-bi-
pyridin-1-yl-methylene) N-methylmethan-
aminium hexauorophosphate N-oxide
HBTU 2-(1 H-benzotriazol-1-yl)-1,1,3,3-
tetramethyl-uronium hexauorophosphate
HCTU O-(6-chlorobenzotriazol-1-yl)-N,N,N’,N’-
tetramethyluronium hexauorophosphate
HF hydrouoric acid
HOAt 1-hydroxy-7-azabenzotriazole
HOBt 1-hydroxybenzotriazole
Hz Hertz
ID inner diameter
L liter
l length
m meter

Liberty™Automated Microwave Peptide Synthesizer
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Abbreviation Denition
meq milliequivalent
mg milligram
MHz megahertz
mL milliliter
mm millimeter
mM millimolar
mmol millimole
MW molecular weight
NMP 1-methyl-2-pyrrolidone
OAt 7-azabenzotriazole
OBt benzotriazole
OD outer diameter
PN part number
psi pounds per square inch
PyAOP (7-Azabenzotriazol-1-yloxy)
tripyrrolidinophosphonium
hexauorophosphate
PyBOP (Benzotriazol-1-yloxy)
tripyrrolidinophosphonium
hexauorophosphate
RV reaction vessel
s seconds
TBTU O-(Benzotriazol-1-yl)-N,N,N′,N′-
tetramethyluronium tetrauoroborate
TFA triuoroacetic acid
TIS triisopropylsilane
Trt trityl
VAC volts of alternating current
W Watts
w width

Liberty™Automated Microwave Peptide Synthesizer
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How to Obtain Support
Applications Support
For the latest Liberty applications information, go to http://www.cem.com/bioscience. The CEM
Bioscience website contains downloadable applications notes, a listing of recent microwave
peptide synthesis publications, and more.
CEM is proud to provide applications support for any peptide synthesis related questions from
a team of trained chemists with a complete peptide synthesis lab. For applications support, call
[phone] (inside the US) or [phone] and ask for “Peptide Applications”, or email
CEM Liberty applications support at [email protected].
Technical Support
For the latest technical support information, go to http://www.cemservice.us. The CEM Service
website provides access to the CEM Knowledge Base, which contains helpful troubleshooting
information. From the website requests for phone or email support can also be submitted.
CEM is proud to provide technical support for the Liberty from a team of specially trained Service
Technicians. For technical support in the US and Canada, call [phone] or [phone]
and ask for “Liberty Service”. For technical support outside the US and Canada, contact your
local CEM Subsidiary or Distributor.
Requested Information
When contacting CEM for support, please provide the following information about the instrument:
Liberty Serial Number•
Liberty Firmware Version•
Discover Serial Number•
Discover Firmware Version•
PepDriver Version Number•
A recent System Check report (see p. 67)•
The Run History report for the synthesis that was running when the error• occurred (see p. 56)
Serial numbers, rmware versions, and software version can be found within PepDriver by
clicking the Help Menu (not the Help Button) and selecting About PepDriver.

Liberty™Automated Microwave Peptide Synthesizer
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Contact CEM
CEM Corporation Headquarters
Toll-Free Phone (US/Canada): [phone]
Phone: [phone]
Service Hotline: [phone]
Fax: [phone]
Mailing Address: PO Box 200
Matthews, NC 28106-0200
Physical Address: 3100 Smith Farm Rd
Matthews, NC 28104
Email (Applications Support): [email protected]
Email (Technical Support): [email protected]
CEM International Subsidiaries
France: CEM mWave S.A.S.
Phone: [phone]
Fax: [phone]
Address: Immeuble Ariane Domaine Technologique de Saclay
4, rue René Razel
91892 ORSAY Cedex
France
Web Address: http://www.cemfrance.fr
Email: [email protected]
Germany: CEM GmbH
Phone: [phone]
Fax: [phone]
Address: Carl-Friedrich-GauB-Str. 9
47475 Kamp-Lintfort
Germany
Web Address: http://www.cem.de
Email: [email protected]

Liberty™Automated Microwave Peptide Synthesizer
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Italy: CEM SRL
Phone: [phone]
Fax: [phone]
Address: Via DellArtigianato, 6/8
24055 Cologno Al Serio (BG)
Italy
Email: [email protected]
UK and Ireland: CEM Microwave Technology Ltd.
Phone: [phone]
Fax: [phone]
Address: 2 Middle Slade
Buckingham Industrial Park MK18 1WA
Buckingham
Great Britain
Email: [email protected]
CEM Distributors
For a complete list of distributors of CEM products, including contact information, go to the CEM
website (http://www.cem.com), select Contact Us, and then select Distributors.

Liberty™Automated Microwave Peptide Synthesizer
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Safety Information
Safety Notations
This manual uses three safety alert words at points in the documentation where the user should
be aware of potential hazards. The safety alerts are shown in color-coded boxes. The three
words–NOTE, CAUTION, and WARNING–indicate differing levels of observation or action as
described below:
NOTE
A NOTE is intended to provide emphasis of procedures that may be
misinterpreted or overlooked, or to otherwise clarify confusing situations.
CAUTION
A CAUTION is intended to provide essential information and to emphasize
procedures which, if not strictly followed, may result in improper instrument
operation.
WARNING
A WARNING is intended to provide emphasize dangerous or hazardous
conditions which may result in personal injury to the user and damage or
destruction of the instrument.

Liberty™Automated Microwave Peptide Synthesizer
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Safety Information
Fume Ventilation
The Liberty operates as a semi-closed system, with minimal venting of any hazardous solvent
fumes through the vent line coming from the Waste Reservoir. The vent line from the Waste
Reservoir must be vented into a proper chemical fume hood or exhaust line no longer than six
feet (6’)/two meters (2 m) from the instrument.
In addition, adequate ventilation should be provided for preparation of reagents and solvents for
use on the system. All solvent bottles and the Waste Reservoir should be placed into proper
secondary containers to minimize the risk of exposure.
Waste Disposal
Waste produced by the Liberty can be hazardous. For detailed information on the safety
requirements for the chemicals used on the Liberty, refer to the appropriate MSDS documents.
Product Removal
When removing tubes containing cleaved peptide in TFA from the Product Manifold following
cleavage, wear suitable protective clothing. These tubes contain a mixture of TFA, DCM, and
peptide. The centrifuge tubes should be capped immediately after removal from the Liberty to
reduce exposure to solvent fumes.
System Requirements
Bench and/or Fume Hood Space
The Liberty should be positioned on the bench such that access to the electrical outlets for the
system is not restricted. The Liberty requires the following space for system components:
Liberty Instrument (Discover Module and Liberty Module):
30” (w) x 24” (d) x 33.5” (h) [76 cm (w) x 61 cm (d) x 85 cm (h)]
(Depth includes 3” (7.62 cm) clearance behind instrument for unimpeded airow at rear fan ducts)
CEM Supplied Controller:
Laptop:
12.5” (w) x 9.9” (d) x 15.5” (h) [32 cm (w) x 25 cm (d) x 39 cm (h)]
(Height includes 14.1” (35.8 cm) display)
Desktop:
Minitower: 7.4” (w) x 17.5” (d) x 16.1” (h) [19 cm (w) x 44.5 cm (d) x 41 cm (h)]
Monitor: 16” (h) x 8” (d) x 20” (h) [41 cm (h) x 20 cm (w) 51 cm (h)]
External Reagent Bottles:
16” (w) x 16” (d) x 15” (h) [41 cm (w) x 41 cm (d) x 38 cm (h)]
(Left side of instrument, facing front of instrument)
WARNING
Handle all waste under a fume hood, and wear suitable protective clothing.
Dispose of all waste in accordance with all applicable local, state, and
federal health and safety recommendations.

Liberty™Automated Microwave Peptide Synthesizer
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Waste Reservoir:
10” (w) x 16” (d) x 18” (h) [25 cm (w) x 41 cm (d) x 45.72 cm (h)]
(Must be vented into fume hood)
Approximate overall dimensions for Liberty and external reagents:
48” (w) x 24” (d) x 33.5” (h) [122 cm (w) x 61 cm (d) x 85 cm (h)]
Environmental Conditions
The Liberty is designed for indoor used only.
Temperature Range: 50 °F – 85 °F (10 °C – 29 °C)
Relative Humidity Range: 0 – 85%
Inert Gas Source
The Liberty requires an inert gas source (either high purity grade nitrogen or argon) capable of
supplying 25 psi (20 L/min ow) within ten feet (10’)/three meters (3 m) of the right side of the
instrument.
Electrical Requirements
The Liberty requires four (4) dedicated, grounded electrical connections operating at 120 VAC
(110-140 VAC, 60 Hz, 10 Amp @ 120 VAC) (or 240 VAC [202-250 VAC, 50 Hz, 10 Amp @ 240
VAC] where applicable). Specic power requirements (120 VAC vs. 240 VAC) can be found on
the nameplate afxed to the rear of the Liberty instrument.
One (1) electrical connection is required for each of the following components:
Liberty Module power cord
Discover Module power cord
Router power cord
Controller (laptop computer) power cord
NOTE
Five (5) electrical connections are required when using the desktop
computer controller option: Liberty module, Discover module, router,
controller minitower, controller monitor.
NOTE
Optionally, the router can be powered directly from the Liberty Module
without the need for an external electrical connection (using Router-Serial
Power Cable, PN 243290).

Liberty™Automated Microwave Peptide Synthesizer
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Section 2: Operation of the
Liberty
Introduction to the Liberty
The Liberty Automated Microwave Peptide Synthesizer is the rst and only automated microwave
peptide synthesizer. Built on CEM’s exible Discover microwave platform, the Liberty is capable
of synthesizing up to twelve peptides in sequence on scales ranging from 0.05 to 5 mmol faster
and more efciently than conventional synthesizers thanks to the system’s patented circular
microwave cavity.
Liberty Module
Discover Module

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600178 • Revision 5 • October 2009 17
3-Port
Manifold
External
Amino Acid
Manifold
Amino Acid
Manifolds
Resin
Manifold
Product
Manifold
Waste Lines
Deprotection
and Capping
Filters
Solvent
Lines Power Switches

Liberty™Automated Microwave Peptide Synthesizer
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Components and Parts
Liberty Module:• The Liberty handles all of the uid transfer into and out of
the reaction vessel. In addition, the Liberty manages communications with the
computer controller and the Discover during peptide synthesis.
• Discover Microwave Reactor: The Discover microwave reactor holds the
reaction vessel and generates the microwave energy used to irradiate the
sample. The Discover is capable of operating independently of the Liberty.
Power Switches:• There are two power switches, one for the Discover and one
for the Liberty. Both switches must be on to operate the Liberty.
Solvent:• There are two bottles of Main Wash (DMF) and one bottle of Secondary
Wash (DCM) on the system (not shown). These positions are designed for use
with standard 4 L solvent bottles. The bottle caps and lines are color coded: black
for DMF and yellow for DCM. These bottles are pressurized at all times and the
Change Bottle command must be used to remove these bottles.
3• -Port Manifold: This manifold has three positions designated for activator,
activator base, and cleavage cocktail. These positions are designed for use with
250 mL glass bottles with GL45 thread.
Deprotection and Capping:• This shelf is designed to hold the Deprotection and
Capping bottles. The bottle caps and lines are color coded: blue for Deprotect
and purple for Capping. These positions are designed for use with 1 L glass
bottles with GL45 thread. These bottles are pressurized at all times and the
Change Bottle command must be used to remove these bottles.
Amino Acid Manifolds:• There are 20 positions on the manifold for amino acids,
each corresponding to a specic amino acid. Each position is labeled using the
3 letter abbreviations of the amino acids. These positions are designed for use
with 125 mL plastic bottles.
Resin Manifold:• Resin is added without liquid in standard 50 mL centrifuge
tubes to the twelve positions manifold. The resin will return to the same position
on the resin manifold after synthesis if cleavage is not done on the system.
Product Manifold:• If the peptide is cleaved on the system, the cleavage product
will be returned to an empty standard 50 mL centrifuge tube on one of the twelve
positions on this manifold. The spent resin will be ushed to waste.
• Reaction Vessel: The reaction vessel (not shown, see p. 19) is where the
synthesis takes place. Reagents are added to the vessel and washed out
throughout the synthesis of the peptide. There are different size vessels that can
be used depending on the scale of the synthesis.
Fiber Optic• Temperature Probe: The ber optic probe is inserted in the top
of the reaction vessel. It allows the system to monitor the temperature of the
reaction vessel.
• Waste Lines: The waste lines carry all of the system’s waste out into an external
waste container. The waste container is equipped with a level sensor and will
trigger the system to pause if the container is full.
Filters:• There are three in-line lters on the system. These lters should be
changed regularly as part of routine maintenance.