CEM liberty Operation Manual

Operation Manual

600178
Rev. 5

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

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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

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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

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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

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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

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Liberty™ Automated Microwave Peptide Synthesizer

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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. A registered 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).

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7

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

E

a

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

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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

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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 [e-mail].

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.

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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): [e-mail]
Email (Technical Support): [e-mail]

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: [e-mail]

Germany: CEM GmbH

Phone: [phone]

Fax: [phone]

Address: Carl-Friedrich-GauB-Str. 9

47475 Kamp-Lintfort
Germany

Web Address: http://www.cem.de
Email: [e-mail]

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Italy: CEM SRL

Phone: [phone]

Fax: [phone]

Address: Via Dell Artigianato, 6/8
24055 Cologno Al Serio (BG)
Italy

Email: [e-mail]

UK and Ireland: CEM Microwave Technology Ltd.

Phone: [phone]

Fax: [phone]

Address: 2 Middle Slade

Buckingham Industrial Park MK18 1WA
Buckingham
Great Britain

Email: [e-mail]

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.

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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.

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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.

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.

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)

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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).

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15

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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3-Port

Manifold

Amino Acid

Manifolds

External

Amino Acid

Manifold

Resin

Manifold

Product

Manifold

Waste Lines

Solvent

Lines

Deprotection
and Capping

Power

Switches

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Filters

17

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.

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Optional Features•

•

External Amino Acid Manifold: This manifold allows for the addition of non-

standard amino acids and other reagents from ve positions using standard

50 mL centrifuge tubes.

DMF • Keg: An optional 20 L steel keg (not shown) is available for the DMF

position. This keg allows for synthesis of longer peptides where total solvent
usage would otherwise be a limitation.

• 10 mL Reaction Vessel: A smaller reaction vessel assembly (shown below)

is available to allow synthesis on scales as low as 0.025 mmol.

Reaction Vessel Components

Fiber Optic

Probe

Spray Head

Thermowell

Resin Tube

Glass Frit

Filter

Drain Line

Quick

Disconnect

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Introduction to PepDriver

The operation of the Liberty is controlled through the PepDriver software package. The Liberty
includes an external computer controller (either a laptop or desktop Windows PC) for running
PepDriver. This computer is connected to the Liberty and the Discover through an ethernet
connection.

PepDriver Terminology

Throughout this manual, specic terms will be used to describe the various functions within

PepDriver.

• Microwave Method: The specic parameters used in a Microwave step

within a cycle. Microwave Methods can be created or modied using the

Microwave Editor (p. 25).

• Cycle: The specic steps used for each residue within a given sequence.

Cycles can be created or modied using the Cycle Editor (p. 28).

• Sequence: The specic peptide to be synthesized in a given method.

Sequences can be created or modied using the Sequence Editor (p. 32).

• Method: The specic parameters used to synthesize a peptide. For each

method, a sequence is selected, and then parameters (individual coupling

cycles for each residue, C-terminus type, nal deprotection, etc.) are also

selected as part of the method. Methods can be created or modied using

the Method Editor (p. 36).

• Run: A specic instance of a method being loaded and started in PepDriver.

A Run History le (p. 56) is recorded for each run.

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PepDriver Main Screen

Control

Buttons

Start

Pause

Stop

Peptide

Synthesis

Status

Resin

Positions

Menu Buttons

Methods

Sequences

Cycles

Setup

Maintenance

Calculator

Estimated Time

Remaining

Tabs

Current

Method Detail

System Status

Line

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Control Buttons

Start: • This button starts the rst method in the queue, or resumes a stopped

method.

Pause: • This button pauses or unpauses the current method.
Stop: • This button stops the current method. PepDriver will nish the operation it

is currently performing before stopping the method.

Menu Buttons

Methods:• This button opens the Method Editor. From the Method Editor, specic

parameters for each synthesis can be programmed.

Sequence:• This button opens the Sequence Editor, where peptide sequences

are entered to be used in methods.

Cycles:• This button opens the Cycle Editor. From the Cycle Editor, cycles can

be created or edited for use in any part of a method.

• This menu contains the Microwave Editor, Default Cycle Editor, Pepdriver

Setup:

Options Menu, and Communication options. From this menu, User Accounts can

also be accessed.

• Maintenance: From this menu, the Maintenance and Diagnostics screens can

be accessed. The Maintenance Screen allows for cleaning, volume calibration,
sensor calibration, and pressure calibration. The Diagnostics Screen contains
information about the sensors, valves, and delay times for the system.

• Calculators: This menu contains the Reagent and Usage calculators. The

Usage Calculator will calculate the amount of each reagent solution needed
for the currently loaded methods. The Reagent Calculator can then be used
to calculate how to make each of the stock solutions for the loaded methods
(including activator, activator base, deprotection, cleavage, and amino acids).

Indicators

Resin Positions:• The twelve positions on the screen correspond to the twelve

positions on the resin manifold of the Liberty. The resin should be loaded in the
same position on the manifold as the method has been loaded into in PepDriver.

Peptide Synthesis Status:• This displays the peptide sequence being

synthesized and indicates the status of the synthesis.

Current Method Detail: • This window displays the currently selected method.

When a method is running, the current step is indicated in yellow.

• System Status Line: The left box indicates the specic command the Liberty

is currently executing. The current temperature and pressure readings are
displayed next to the command indicator. Two indicators shows the computer’s
communication status with the Liberty and the Discover. The waste full and spill

tray warnings are also seen here. On the right, there is an indicator that shows

whether the microwave is running.

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Tabs

• Methods: From this tab, methods are loaded into one of the twelve resin

positions to be run.

• Queue: This tab shows all currently loaded Methods. From this tab, the order

that each Method is run in can be changed.

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23

• Current Run: This tab displays the Method that is currently running.

• Run History: From this tab, detailed logs of each Method that has been run can

be accessed. In addition, Method Reports can be generated for each Method
that has been run.

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Editors

Microwave Editor

The Microwave Editor allows for the control and customization of the microwave steps of any

cycle. By editing the power and duration of a microwave step difcult peptides can be synthesized

with higher purity and yield.
The Microwave Editor can be accessed by clicking the Setup Button on the PepDriver main

screen and selecting Microwave Editor from the menu.

Microwave Method Folders

The Microwave Editor contains separate folders for each type of microwave method. Within each
method folder, there are subfolders for each scale, allowing for the development of optimized
microwave methods for each scale. A microwave method will only appear in the Cycle Editor
when creating a cycle of the same scale.

PepDriver comes with optimized default microwave methods for deprotection, coupling, capping,
and cleavage.

Microwave Method Types

• Standard: A Standard method applies a set microwave power until the set

temperature is reached, and then turns off the microwave until the temperature
drops to 5 °C below the set temperature. The total agitation time can also be
selected.

• Multi-Step: Multi-Step methods allow for a single microwave method to use

multiple power, temperature, or time settings.

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25

Creating a New Microwave Method

Microwave methods allow for detailed control of the microwave heating and reaction time for
each step in the synthesis. The Microwave Editor allows the user to select the microwave time,
microwave power, maximum temperature, and sample agitation.

Open the folder of the appropriate method type, then open the subfolder for the 1.
appropriate scale.

NOTE

A microwave method saved in a specic scale folder will only be available

for use in Cycle Editor for cycles created in the same scale folder.

Click the New Method button.2.
The new method will appear in the selected folder. Enter a name for the method 3.

and press Enter.
Select the type of microwave method to make.4.

4.1. Standard

Enter the desired 4.1.1. microwave power setting (in Watts), maximum
temperature (in °C), and time for the microwave step (in seconds).

If 4.1.2. agitation is desired during the microwave step, check the box for
Bubbling During Microwave. Enter the amount of time to bubble and
the time between each bubbling. (Bubbling is enabled by default.

The default setting is 3 seconds On Time, 7 seconds Off Time, low

pressure)

High Pressure bubbling is not recommended as this can deposit resin on the
top of the reaction vessel. This can lead to poor synthesis quality, product
loss, and contamination between syntheses.

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Liberty™ Automated Microwave Peptide Synthesizer

CAUTION

600178 • Revision 5 • October 2009

4.2. Multi-Step

Enter the microwave power (in Watts), time (in seconds), and 4.2.1.

maximum temperature (in °C) for the rst step in the method.

Add the next step to the microwave method by clicking the Add Step 4.2.2.
button, and then enter the power, temperature, and time settings for
the second step.

Repeat step 4.2.2. for each step in the method.4.2.3.

If 4.2.4. agitation is desired during the microwave step, check the box for
Bubbling During Microwave. Enter the amount of time to bubble and
the time between each bubbling. (Bubbling is enabled by default.

The default setting is 3 seconds On Time, 7 seconds Off Time, low

pressure.)

CAUTION

High Pressure bubbling is not recommended. Bubbling at high pressure
can deposit resin on the top of the reaction vessel. This can lead to poor
synthesis quality, product loss, and contamination between syntheses.

Save the method by clicking the Save button.5.

Editing an Existing Microwave Method

The Microwave Editor allows for settings on existing methods to be modied and saved as

needed. The most common reason to modify an existing method is to increase or decrease the
microwave power to optimize peptide synthesis. To modify an existing method:

Open the folder of the appropriate method type, then open the subfolder for the 1.
appropriate scale.

Click on the microwave method to be modied.2.

Make any changes as needed.3.
Click Save to save the changes to the method.4.

Liberty™ Automated Microwave Peptide Synthesizer

600178 • Revision 5 • October 2009

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Copying and Modifying an Existing Microwave Method

Often, it is easier to copy and modify an existing microwave method rather than creating an
entirely new method. Methods can easily be duplicated and modied within the Microwave

Editor, and then be moved to different scale folders as needed. To copy an existing method:

Open the folder of the appropriate method type, then open the subfolder for the 1.
appropriate scale.

Right click on a microwave method and select Copy Method.2.
The new method will appear named “Copy of (method name)”. Type a new name 3.

and press Enter.
Any settings in the method can be changed. If the copied method was a Multi-4.

Step method, steps can also be added or deleted by using the Add Step and
Delete Step buttons.

When all changes have been made, click Save to save the modied method.5.
If the new method is to be used at a different synthetic scale, drag the method 6.

from the folder it was created in to the appropriate folder.

Cycle Editor

The Cycle Editor allows for the full control and customization of any step of a synthesis. This
allows for optimization of each step of a given peptide synthesis.

The Cycle Editor can be accessed by clicking on the Cycles Button on the main screen of
PepDriver, or by clicking the Cycle Editor button from the Method Editor.

Cycle Folders

The Cycle Editor contains separate folders for each type of cycle. Within each cycle folder, there
are subfolders for each scale, allowing for the development of optimized cycles for each scale. A
cycle will only appear in the Method Editor when creating a method of the same scale.

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Liberty™ Automated Microwave Peptide Synthesizer

600178 • Revision 5 • October 2009