CEM Liberty Blue User Manual

Liberty Blue

TM

Automated Microwave Peptide Synthesizer

Manual

Contents

Introduction

About the Instrument 1

Common Abbreviations and Units 1

How To Obtain Support

Applications Support 2

Technical Support 2

Requested Information 2

CEM Corporation Headquarters 2

CEM International Subsidiaries 3

Safety

Safety Notations 5

Personal Laboratory Safety 5

Waste Disposal 5

Fume Ventilation 5

Operating Precautions 6

System Requirements

Bench and/or Fume Hood Space 7

System Components Space Requirements 7

Environmental Conditions 7

Inert Gas Source 7

Electrical Requirements 7

Fuse Replacement 7

Introduction To The Liberty Blue

Components and Parts 8

Quick Setup Guide

Liberty Method Editor 22

Calculators 28

Edit Users and User Group 30

Setting up a Synthesis

Loading a Method 33

Standard Reagents and Concentrations 33

Recommended Reagents and Strategies for Microwave

SPPS on the Liberty Blue 33

Preparing Reagents 36

Setting up the Liberty Blue 37

Running the Liberty Blue 39

Generating A Run History Report 40

Cleavage 40

Maintenance of the Liberty Blue

Recommended Routine Maintenance Schedule 42

Maintenance Procedures 43

Maintenance Screen 47

Using the Change Bottle Operations 47

Calibration Screen 48

Advanced Features

Cycle Rules 50

Reagent Library 50

Bottle Setup 52

Rell Reagents Button 53

Diagnostics Screen 53

Settings Screen 53

Reaction Vessel Camera Option 54

Create and Load the Liberty Method 10

Prepare and Load Reagents 11

Run the Method 12

Operation of the Liberty Blue

Software Terminology 14

Liberty Blue Software Main Screen 14

Microwave Editor 16

Cycle Editor 18

Warranty

Limited Warranty Information 55

Introduction

About the Instrument

This manual is intended for use by both novice and experienced users for operation and maintenance of the
Liberty Blue Automated Microwave Peptide Synthesizer. Installation of the Liberty Blue must be completed by a
CEM certied service technician. Additional information, including, but not limited to: training notes and videos,
application notes, software updates, and parts can be viewed on CEM’s website at http://cem.com/peptide­synthesis. A registered account is required for certain downloads.

This manual refers to Liberty Blue Software version 2.2 for all software information, including screen shots and
technical information.

Common Abbreviations and Units

Abbreviation Denition Abbreviation Denition

°C degrees Celsius mL milliliter

AA amino acid mm millimeter

ACP acyl carrier protein 65-74 mmol millimole

DIC N,N’-Diisopropylcarbodiimide MW molecular weight

DMF N,N’-dimethylformamide OD outer diameter

Fmoc 9-uoroenylmethyloxycarbonyl Oxyma Pure ethyl 2-cyano-2-(hydroxyimino)acetate

g gram PN Part Number

Hz Hertz psi pounds per square inch

ID inner diameter RV reaction vessel

L liter s seconds

m meter VAC volts of alternating current

mg milligram W Watts

Introduction

1

How To Obtain Support

Applications Support

For the latest Liberty Blue applications information, go to http://www.cem.com/liberty-blue.html. The CEM Liberty
Blue pages contain downloadable applications notes, a listing of recent microwave peptide synthesis publications,
and more. A registered account is required for download.

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 Blue 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 Blue from a team of specially trained Service Technicians.
For technical support in the US and Canada, call [phone] or [phone] and ask for “Liberty Blue
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 Blue Serial Number
Liberty Blue Firmware Version
Discover Serial Number
Discover Firmware Version
Liberty Blue Software Version Number and Build Number
The report for the synthesis that was running when the error occurred
Troubleshooting Bundle (see below)

Firmware versions (both Liberty Blue and Discover) and Liberty Blue software version can be found within Liberty
Blue Software from the About Liberty Blue menu (Help Tab). Serial numbers can be found on the silver tags on the
rear of the Liberty Blue and on the side of the Discover.

In the event of a crash, the software will automatically create a Troubleshooting Bundle to be emailed to CEM
support for diagnosis. A Troubleshooting Bundle can be manually created from the Help Menu.

CEM Corporation Headquarters

Toll-Free Phone (US/Canada): [phone]
Phone: [phone]
Service Hotline: [phone]
Fax: [phone]

2

How To Obtain Support

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 mWaves 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]

Italy: CEM SRL

Phone: [phone]
Fax: [phone]
Address: Via Dell Artigianato, 6/8
24055 Cologno Al Serio (BG)
Italy

Web Address: http://www.cemmicroonde.it
Email: [e-mail]

Japan: CEM Japan K.K.

Phone: [phone]
Fax: [phone]
Address: 2-18-10 Takanawa
Minato-Ku
Tokyo
108-0074
Japan
Web Address: http://www.cemjapan.co.jp
Email: [e-mail]

How To Obtain Support

3

UK: CEM Microwave Technology Ltd.

Phone: [phone]
Fax: [phone]
Address: 2 Middle Slade
Buckingham Industrial Park MK18 1WA
Buckingham
Great Britain
Web Address: http://www.cemmicrowave.co.uk
Email: [e-mail]

Ireland: CEM Technology (Ireland) Ltd.

Phone: [phone]
Address: Sky Business Centre
9a Plato Business Park
Damastown Dublin 15
Ireland
Web Address: http://www.cemmicrowave.co.uk

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 CEM, and then select your region to see a list of distributors by country.

4

How To Obtain Support

Safety

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 emphasize dangerous or hazardous conditions which may result in personal
injury to the user and damage or destruction of the instrument.

Personal Laboratory Safety

Solvents and chemical reagents used on the Liberty Blue can be hazardous and should only be handled under a
fume hood. Personal protective gear, including but not limited to safety glasses, chemical resistant gloves, and a
laboratory coat are highly recommended when operating the Liberty Blue. For detailed information on the safety
requirements for the chemicals used on the Liberty Blue, refer to the appropriate SDS documents.

Waste Disposal

Waste produced by the Liberty Blue can be hazardous. For detailed information on the safety requirements for the
chemicals used on the Liberty Blue, refer to the appropriate SDS documents.

WARNING
Handle all waste under a fume hood, and wear suitable protective clothing such as safety glasses,
chemical resistant gloves, and a laboratory coat. Dispose of all waste in accordance with all applicable
local, state, and federal health and safety recommendations.

Fume Ventilation

The Liberty Blue operates as a semi-closed system, with minimal venting of any hazardous solvent fumes through
the vent lines coming from the side of the unit. The vent lines 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.

Safety

5

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.

Operating Precautions

The Liberty Blue must be grounded. In the event of an electrical short circuit, grounding reduces the risk of electric
shock by providing an escape wire for electric current. This instrument is equipped with a cord having a grounding
wire with a grounding plug. The plug must be plugged into an outlet that is properly installed and grounded.
Consult a qualied electrician or service technician if the grounding instructions are not completely understood or
if doubt exists as to whether the instrument is properly grounded. If it is necessary to use an extension cord, use
only a 3-wire extension cord that has a 3-blade grounding plug and a 3-slot receptacle that will accept the plug
from the instrument. The marked rating of the extension cord must be equal to or greater than the electrical rating
of the instrument.

Do not replace detachable main supply cord with inadequately rated cords.

The possibility of instrument-induced electromagnetic interference (EMI) is minimal if the instrument is operated as
outlined in this manual. The instrument should not be placed close to any electrical device susceptible to EMI.

This instrument utilizes high voltages and microwave radiation. Only those trained in repair and maintenance of
high voltage and microwave power systems should perform instrument service and repair.

This instrument complies with United States Code of Federal Regulations 21 CFR Part 1030.10 (C) for microwave
leakage. This instrument complies with FCC Requirements in the United States Code of Federal Regulations
(47CFR Part 18) – Industrial, Scientic and Medical (ISM) Equipment – emissions requirements.

WARNING
Only accessories which meet the manufacturer’s specications shall be used.

Do not attempt to lift or move the Liberty Blue system. Contact CEM Corporation if the Liberty Blue system
needs to be moved.

If instrument is used in a manner not specied by CEM Corporation in this manual, then the protection provided by
the equipment may be impaired.

6

Safety

System Requirements

Bench and/or Fume Hood Space

The Liberty Blue should be positioned on the bench such that access to the electrical outlets for the system is not
restricted.

System Components Space Requirements

Liberty Blue Instrument (Discover Module and Liberty Blue Module):
20 in (50.8 cm) W x 21 in (53.3 cm) D x 30 in (76.2 cm) H
(Depth includes 3” (7.62 cm) clearance behind instrument for unimpeded airow at rear fan ducts)

CEM Supplied Controller:
15 in (38.1 cm) W x 10 in (25.4 cm) D x 16 in (40.6 cm)
(Height includes 14.1” (35.8 cm) display)

Environmental Conditions

The Liberty Blue is designed for indoor use only.
Temperature Range: 50 °F – 85 °F (10 °C – 29 °C)
Relative Humidity Range: 10 – 85%

Inert Gas Source

The Liberty Blue 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 Blue requires electrical power of 120 VAC (60 Hz, 1.7 A) (or 240 VAC [50 Hz, 1.7 A] 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 module and on the side of the Discover module.

Three (3) grounded electrical connections providing a total of 10 A are required for all components:
Liberty Blue power cord
Router power cord
Controller (laptop computer) power cord

Fuse Replacement

The Liberty Blue has four operator replaceable fuses located in the power inlet module (at the rear of the
instrument, where the power cord connects to the Liberty Blue module). The fuses are rated F 250 V 2 A. The
top pair of fuses (PN BR198826) are North American style, 5 mm x 20 mm size, and are rated F 250 V 2 A. The
bottom pair of fuses (PN 188340) are North American style, 5 mm x 20 mm size, and are rated F 250 V 10 A.

NOTE
Optionally, the router can be powered directly from the Liberty Blue module without the need for an
external connection (using Router-Serial Power Cable, PN 243290).

System Requirements

7

Introduction To The Liberty Blue

The Liberty Blue is the latest generation of automated microwave peptide synthesizer. Built on CEM’s exible
Discover microwave platform, the Liberty Blue is capable of synthesizing peptides faster and more efciently than
conventional synthesizers, thanks to the system’s patented circular microwave cavity. The Liberty Blue’s efcient
Flex-Add™ technology eliminates the need for sample loops and allows innite volume delivery options for a wide
range of synthesis scales.

Amino Acid
Manifolds

Activator Bottle

Activator Base Bottle

Liberty Blue
Module

Reaction Vessel

Waste Bottle

Solvent Bottle

Deprotection Bottle

Power Switches

Calibration
Stand

Discover Module

Components and Parts

Liberty Blue Module: The Liberty Blue handles all of the uid transfer into and out of the reaction vessel. In
addition, the Liberty Blue 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
Blue.
Power Switches: There are two power switches, one for the Discover and one for the Liberty Blue. Both switches
must be on to operate the Liberty Blue.
External Bottles: Bottles for waste, main solvent, and deprotection connect to the manifold on the side of the
Liberty Blue using GL45 caps and tubing assemblies. The external bottles sit in a bottle holder magnetically

8

Introduction To The Liberty Blue

secured to the front of the Liberty Blue module. Optimal large capacity pressure rated bottles are available (PN
551240, 551245, 551250, 551255).
Amino Acid Manifolds: There are 27 positions on the manifold for amino acids, 20 corresponding to a specic
amino acid, and 7 extra positions. Each position is labeled using the position number and 3-letter abbreviations of
the amino acids. These positions are designed for use with 50 mL centrifuge tubes for the amino acids and 250
mL bottles for activator and activator base. Optional 120 mL tubes (PN 216560-M, pack of 30) are available for
the amino acid positions. Up to one liter GL45 threaded bottles can be used with optional adapters (PN 909465),
for the activator and activator base positions.

NOTE
The 7 external positions are not available with the Liberty Lite.

Reaction Vessel: The reaction vessel 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 Container: 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. An optional
large capacity (20 L) waste container is available (PN 909490).

Reaction Vessel Components

Vent Line

Wash Line

Thermowell

Glass Frit

Fiber Optic Probe

Reagent Line

Union

Drain Line

Introduction To The Liberty Blue

9

Quick Setup Guide

Create and Load the Liberty Method

NOTE
To load an existing method, skip to step 9.

Create the Method

1. Open the appropriate folder or sub folder in the Methods box for the new method.

2. Click the New Method button.

3. The method will appear in the appropriate folder. Enter a name for the method and press Enter.

4. Click into the Sequence box. A list of the amino acids in the current bottle setup will drop down. To enter the

sequence, either click the appropriate amino acid positions in the drop-down, or type the one-letter abbreviation
for the desired amino acids.

NOTE
The amino acids in the sequence should be entered from N-terminus to C-terminus.

5. Select the scale (0.005 mmol to 5.0 mmol) from the Synthesis Scale box, then select the resin type (Standard
or High Swelling) from the Resin Type box.

NOTE
The scale and resin type must be selected before changing any of the other parameters, as each scale
and resin type has specic default options that will be loaded upon selection.

6. The remaining options can now be selected.

6.1. C-Terminus: The C-terminus (acid or amide) is only used to calculate the molecular weight, and does

not affect the synthesis conditions.

6.2. Resin Type: The resin type will determine the rst coupling step of the reaction. If Preloaded is
checked, the software assumes the C-terminal amino acid is already loaded on the resin and
therefore skips that coupling. If Not Preloaded is selected, the rst coupling will proceed as normal.
If Chloride Loading is selected, a chloride coupling step will be used for the C-terminal amino acid
coupling.

6.3. Resin Name: The resin name entered in this box will appear in the Method Report, but will not affect
the synthesis conditions.

6.4. Resin Loading: The substitution value entered in this box (in meq/g) will appear in the Method
Report, but will not affect the synthesis conditions.

6.5. Resin Cycle: The resin cycle determines the swelling conditions used to prepare the resin at the
beginning of the synthesis. Make sure the amino acid cycles match the Resin Swelling Cycle (HS
vs. non HS).

6.6. Final Deprotection Cycle: By default, the N-terminal protecting group is removed at the end of the
synthesis. Selecting an alternate Final Deprotection cycle allows control of this step.

6.7. Bottle Setup: If using a bottle setup other than the standard default, it must be selected prior to
entering the sequence.

10

Quick Setup Guide

7. Assign cycles for each residue in the sequence that will not use the default cycle.

NOTE
For long peptides, clicking the Quick Jump button will open a shortcut to view all amino acids in the
sequence.

7.1. From the Amino Acid Cycles table, click on the amino acid to highlight it, then double-click the cycle
to open the drop-down of available amino acid cycles.

7.2. From the drop-down, select the desired cycle. This will change the cycle for that highlighted amino
acid only. To change the cycle for all amino acids to the selected cycle, right-click the cycle and
select “Apply this cycle to all”.

NOTE
To select multiple amino acids, hold Ctrl and left-click the desired amino acids. This will highlight multiple
rows in the Amino Acid Cycles table. When all the desired amino acids are highlighted, click the Mark Rows
button at the top of the Amino Acid Cycles table. The total number of selected rows will be listed next to
the ag icon. When multiple rows are marked (indicated by a blue highlight), any change made to one
row will be made to all selected rows. When all changes are made, click the Clear button to deselect all
rows.

8. When the method is complete, click Save to save the method, then close the Liberty Method Editor.

Load the Method

1. From the Liberty Blue application software main screen, open the appropriate folder in the Methods tab.

2. Click on the desired method, and drag the method to the resin position. Alternatively, right-click on the desired

method and select “Queue for run”.

3. The method name will appear in the Loaded Method indicator. The indicator will turn blue, meaning the method
is loaded and ready to run.

Prepare and Load Reagents

Prepare Reagents

1. To determine the amount of each reagent needed and how to prepare them, use the Usage and Reagent
Calculators.

1.1. From the Calculators tab, select the Usage Calculator.

1.1.1 If the method is not already loaded, from the Methods box at the bottom left of the Usage

Calculator, select the method to be included in the calculation and drag the method into the
table on the top left of the Usage Calculator.

1.1.2 The calculator will automatically determine the total usage for each reagent. For amino acids,
enter the desired concentration in the Amino Acid Concentration box, and the calculator will
automatically determine the mass of each amino acid to weigh out.

1.1.3 If desired, print a Usage Report.

1.2. From the Calculators menu, select the Reagent Calculator.

1.2.1 Resin: Enter the scale of the synthesis and the resin substitution to determine the mass of

resin needed.

Quick Setup Guide

11

1.2.2 Other Reagents: For the other reagents, click on the appropriate tab (Activator, Activator Base,
Deprotection) and then select the appropriate reagent from the list. Enter the concentration
and nal volume needed, and the calculator will update with the mass required.

1.2.3 If desired, print a Reagent Report.

Load the Reagents onto the Liberty Blue

1. Load all reagents onto the Liberty Blue.

1.1. Connect centrifuge tubes with amino acid solution to the appropriate positions. Connect empty

centrifuge tubes to all unused positions.

1.2. Connect activator and activator base bottles to the appropriate positions on the system.

1.3. Check the level of solvent remaining in the solvent bottle. If more solvent is required, use the Change

Bottle Main Solvent operation to replace the bottle (see Change Bottle Main Solvent in Section 4).

1.4. Check the level of deprotection solution remaining in the deprotection bottle. If more deprotection
is required, use the Change Bottle Deprotection operation to replace the bottle (see Change Bottle
Deprotection in Section 4).

Load the Resin into the Reaction Vessel

1. Load the resin (100-200 mesh only) into the reaction vessel.

CAUTION
The 30 mL reaction vessel should be used for 0.005 - 0.25 mmol syntheses (up to 1 g of resin). The 125
mL reaction vessel should be used for 0.5 - 5 mmol syntheses (up to 8 g of resin).

1.1. Remove the reaction vessel from the microwave cavity.

1.2. Unscrew the bottom port of the beige union connector on the vessel drain line. Then, unscrew the

vessel body from the attenuator.

1.3. Weigh the appropriate amount of dry resin (100-200 mesh only) into the vessel body.

1.4. Connect the vessel body to the attenuator, then connect the drain line to the vessel body using the

union connector tting.

1.5. Place the vessel back into the microwave cavity, securing the attenuator.

Run the Method

Ensure the Liberty Blue is Ready to Run

1. Verify that the waste container has sufcient capacity.

2. Verify that the ber optic probe is fully inserted into the thermowell.

WARNING
If the probe is not inserted all the way to the bottom of the vessel the Liberty Blue will not accurately
measure the temperature, and signicant overheating of the vessel will occur. This will result in poor
synthesis quality and/or serious damage to the vessel.

3. Verify that the method is correct by looking at the steps outlined in the Liberty Methods widow, and then load the
method from the Methods tab. If there are any errors, make corrections and reload the method.

12

Quick Setup Guide

3.1. Clear the method by clicking the small X at the top of the resin indicator.

3.2. To correct the method:

3.2.1 Open the Liberty Method Editor.

3.2.2 Open the folder where the method was saved, then click on the method to load it.

3.2.3 Click Save to save the method after editing, then close the Liberty Method Editor.

3.2.4 Load the corrected method as described above.

Run the Method

1. Click the Start button at the top of the Liberty Blue Software main screen.

2. The Loaded Method indicator will turn yellow to indicate the method is running.

3. The Liberty Blue will illuminate all required amino acids positions for the method. Ensure that all reagents

are connected to the correct reagent positions, empty centrifuge tubes are connected to any unused reagent
positions, and that there is sufcient solvent and deprotection solution, then click OK to continue.

4. The Liberty Blue will go through a series of initialization steps and leak checks.

5. During the run, the current step of the method is highlighted in yellow in the Cycle Steps table of the Current Run

tab. A status bar in the lower right of the main screen indicates relative progress of the run.

6. When the run is complete, the Loaded Method indicator will turn green, indicating the method was successfully
completed.

7. When the run is complete, remove the resin from the reaction vessel.

7.1. Remove the reaction vessel from the microwave cavity.

7.2. Unscrew the bottom port of the beige union connector on the vessel drain line. Then, unscrew the

vessel body from the attenuator.

7.3. Using dicholormethane (DCM) or another appropriate solvent, rinse the resin into a clean, empty
centrifuge tube.

NOTE
The Liberty Blue is not equipped to perform peptide cleavage. All cleavage must be carried out at either
room temperature or in the Razor™ Peptide Cleavage system.

7.4. Rinse any resin clinging to the thermowell into the centrifuge tube. Ensure there is no resin on the
top of the reaction vessel attenuator.

7.5. Connect the vessel body to the attenuator, then connect the drain line to the vessel body using the
beige union connector.

7.6. Place the vessel back into the microwave cavity, securing the attenuator.

8. The peptide is now ready to be cleaved and analyzed, and the Liberty Blue is ready for its next run.

Quick Setup Guide

13

Operation of the Liberty Blue

The operation of the Liberty Blue is controlled through the Liberty Blue application software. The Liberty Blue
includes an external computer controller for running the Liberty Blue Software. This computer is connected to the
Liberty Blue and the Discover through an Ethernet connection or wireless router.

Software Terminology

Microwave Method: The specic microwave parameters used in a cycle. Microwave Methods can be created or
modied using the Microwave Editor.
Cycle: The specic steps used for each residue within a given sequence, including deprotection, washing, and
coupling. Cycles can be created or modied using the Cycle Editor.
Liberty Method: The specic parameters used to synthesize a peptide. For each Liberty Method, a sequence is
entered, and then parameters (individual coupling cycles for each residue, C-terminus type, nal deprotection, etc.)
are selected. Liberty Methods can be created or modied using the Liberty Method Editor.
Run: A specic instance of a method being loaded and started in Liberty Blue Software. A Run History le is
recorded for each run.

Liberty Blue Software Main Screen

Control Buttons

Menus

Peptide Synthesis Status

Resin Indicator

Current Method Detail

Start/Resume: This button starts the rst method in the queue, or resumes a paused method.
Pause: This button pauses the current method.
Stop: This button stops the current method. Liberty Blue Software will nish the operation it is currently performing

before stopping the method.

14

Control Buttons

Operation of the Liberty Blue

System Status Box

Maintenance Tracker

Rell Reagents: This button allows for the replacement of reagent bottles (including amino acids, activator,
activator base, deprotection, and main solvent) without stopping the run.

Menus

File: This menu contains the Import and Export commands which will import and/or export a copy of selected
methods, associated cycles, and operations from the database. These les can be transferred to another Liberty
Blue database or submitted to CEM for troubleshooting purposes.
Edit: This menu contains the Liberty Method, Cycle, and Microwave editors, as well as the Reagent Library and
Bottle Setup editors, and the Notication screen.

Calculators: This menu contains Reagent and Usage Calculators.
Administration: This menu contains the View Audit Trail screen. If users are enabled, this menu also allows

administrators to create Users and User Groups.

Run: This menu contains the Control Buttons (Start/Resume, Pause, Stop).
Options: This menu contains the Maintenance, Diagnostics, Calibration, and Settings screens, and the Check Data

Integrity command (which will verify there are no problems with the Liberty Blue Software database).
Help: This menu contains the About Liberty Blue screen (which displays the software and rmware version
numbers), and allows you to create a troubleshooting bundle.

Indicators

Resin Indicator: The Resin Indicator shows the status for the currently loaded method: blue when ready to run,
yellow when running, red when stopped, green when complete.
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.
System Status Box: The System Status Box contains indicators that show Liberty Blue and Discover

communication status, current temperature and system pressure readings, microwave method parameters, sensor
status for the waste container, spill tray, and reaction vessel overow sensors, and maintenance tracker.

Tabs

Methods: From this tab, methods are loaded into the resin position.
Current Run: This tab displays the Method that is currently running. The current step of the method is highlighted

in yellow. When the “Keep Cycles table synced” box is checked, the cycles tables will automatically move to the
next cycle as the method progresses.
Run History: From this tab, detailed logs of each run can be accessed.

Operation of the Liberty Blue

15