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ABI 433A Peptide Synthesizer

User Guide

Volume 2 of 2 – Appendices

DRAFT

March 19, 2004 5:39 pm, 433 AppTitle Page

© Copyright 2004 Applied Biosystems. All rights reserved.

For Research Use Only. Not for use in diagnostic procedures.

Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use of this document.

TRADEMARKS:

Applied Biosystems, and SynthAssist are registered trademarks and AB (Design), Applera, and FastMoc are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries.

All other trademarks are the sole property of their respective owners.

Part Number 904856 Rev. D03/2004

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March 2004 iii

Contents

Appendix A: Applied Biosystems Limited Warranty A-1

Appendix B: Post-Synthesis Procedures B-1

Appendix C: Chemicals and Reagents C-1

Appendix D: Amino Acid Derivatives D-1

Appendix E: Pre-defined Chemistry Modules E-1

Appendix F: Parts List and Plumbing Schematic F-1

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iv March 2004

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March 2004 Appendix A: Applied Biosystems Limited Warranty A-1

Appendix

A: Applied Biosystems Limited Warranty

Computer Configuration

Applied Biosystems supplies or recommends certain configurations of computer hardware, software, and peripherals for use with its instrumentation. Applied Biosystems reserves the right to decline support for or impose extra charges for supporting nonstandard computer configurations or components that have not been supplied or recommended by Applied Biosystems. Applied Biosystems also reserves the right to require that computer hardware and software be restored to the standard configuration prior to providing service or technical support. For systems that have built-in computers or processing units, installing unauthorized hardware or software may void the Warranty or Service Plan.

Limited Product Warranty

Limited Warranty

Applied Biosystems warrants that all standard components of its Applied Biosystems Model 433A will be free of defects in materials and workmanship for a period of one (1) year from the date the warranty period begins. Applied Biosystems will repair or replace, at its discretion, all defective components during this warranty period. After this warranty period, repairs and replacement components may be purchased from

Applied Biosystems at its published rates. Applied Biosystems also provides service agreements for post-warranty coverage. Applied Biosystems reserves the right to use new, repaired, or refurbished instruments or components for warranty and post-warranty service agreement replacements. Repair or replacement of products or components that are under warranty does not extend the original warranty period.

Applied Biosystems warrants that all optional accessories supplied with its Applied Biosystems Model 433A, such as peripherals, printers, and special monitors, will be free of defects in materials and workmanship for a period of ninety (90) days from the date the warranty begins. Applied Biosystems will repair or replace, at its discretion, defective accessories during this warranty period. After this warranty period, Applied Biosystems will pass on to the buyer, to the extent that it is permitted to do so, the warranty of the original manufacturer for such accessories.

With the exception of consumable and maintenance items, replaceable products or components used on or in the instrument are themselves warranted to be free of defects in materials and workmanship for a period of ninety (90) days.

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A-2 Appendix A: Applied Biosystems Limited Warranty March 2004

Applied Biosystems warrants that chemicals and other consumable products will be free of defects in materials and workmanship when received by the buyer, but not thereafter, unless otherwise specified in documentation accompanying the product.

Applied Biosystems warrants that for a period of ninety (90) days from the date the warranty period begins, the tapes, diskettes, or other media bearing the operating software of the product, if any, will be free of defects in materials and workmanship under normal use. If there is a defect in the media covered by the above warranty and the media is returned to Applied Biosystems within the ninety (90) day warranty period, Applied Biosystems will replace the defective media.

Applied Biosystems does not warrant that the operation of the instrument or its operating software will be uninterrupted or error free.

Warranty Period Effective Date

Any applicable warranty period under these sections begins on the earlier of the date of installation or ninety (90) days from the date of shipment for hardware and software installed by Applied Biosystems personnel. For all hardware and software installed by the buyer or anyone other than Applied Biosystems, and for all other products, the applicable warranty period begins the date the product is delivered to the buyer.

Warranty Claims

Warranty claims must be made within the applicable warranty period, or, for chemicals or other consumable products, within thirty (30) days after receipt by the buyer.

Warranty Exceptions

The above warranties do not apply to defects resulting from misuse, neglect, or accident, including without limitation: operation with incompatible solvents or samples in the system; operation outside of the environmental or use specifications

or not in conformance with the instructions for the instrument system, software, or accessories; improper or inadequate maintenance by the user; installation of software or interfacing, or use in combination with software or products, not supplied or authorized by Applied Biosystems; and modification or repair of the product not authorized by Applied Biosystems.

THE FOREGOING PROVISIONS SET FORTH Applied Biosystems’ SOLE AND EXCLUSIVE REPRESENTATIONS, WARRANTIES, AND OBLIGATIONS WITH RESPECT TO ITS PRODUCTS, AND APPLIED BIOSYSTEMS MAKES NO OTHER WARRANTY OF ANY KIND WHATSOEVER, EXPRESSED OR IMPLIED, INCLUDING WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY AND FITNESS

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FOR A PARTICULAR PURPOSE, WHETHER ARISING FROM A STATUTE OR OTHERWISE IN LAW OR FROM A COURSE OF DEALING OR USAGE OF TRADE, ALL OF WHICH ARE EXPRESSLY DISCLAIMED.

Warranty Limitations

THE REMEDIES PROVIDED HEREIN ARE THE BUYER'S SOLE AND EXCLUSIVE REMEDIES. WITHOUT LIMITING THE GENERALITY OF THE FOREGOING, IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION, ANY TRADE PRACTICE, UNFAIR COMPETITION, OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS, FOR DIRECT, INDIRECT, PUNITIVE, INCIDENTAL, MULTIPLE, CONSEQUENTIAL, OR SPECIAL DAMAGES SUSTAINED BY THE BUYER OR ANY OTHER PERSON OR ENTITY, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES, INCLUDING WITHOUT LIMITATION, DAMAGES ARISING FROM OR RELATED TO LOSS OF USE, LOSS OF DATA, FAILURE OR INTERRUPTION IN THE OPERATION OF ANY EQUIPMENT OR SOFTWARE, DELAY IN REPAIR OR REPLACEMENT, OR FOR LOSS OF REVENUE OR PROFITS, LOSS OF GOOD WILL, LOSS OF BUSINESS, OR OTHER FINANCIAL LOSS OR PERSONAL INJURY OR PROPERTY DAMAGE.

NO AGENT, EMPLOYEE, OR REPRESENTATIVE OF Applied Biosystems HAS ANY AUTHORITY TO MODIFY THE TERMS OF THIS LIMITED WARRANTY STATEMENT OR TO BIND APPLIED BIOSYSTEMS TO ANY AFFIRMATION, REPRESENTATION, OR WARRANTY CONCERNING THE PRODUCT THAT IS NOT CONTAINED IN THIS LIMITED WARRANTY STATEMENT, AND ANY SUCH MODIFICATION, AFFIRMATION, REPRESENTATION, OR WARRANTY MADE BY ANY AGENT, EMPLOYEE, OR REPRESENTATIVE OF APPLIED BIOSYSTEMS WILL NOT BE BINDING ON APPLIED BIOSYSTEMS, UNLESS IN A WRITING SIGNED BY AN EXECUTIVE OFFICER OF APPLIED BIOSYSTEMS.

THIS WARRANTY IS LIMITED TO THE BUYER OF THE PRODUCT FROM APPLIED BIOSYSTEMS AND IS NOT TRANSFERABLE.

Some countries or jurisdictions limit the scope of or preclude limitations or exclusion of warranties, of liability, such as liability for gross negligence or wilful misconduct, or of remedies or damages, as or to the extent set forth above. In such countries and jurisdictions, the limitation or exclusion of warranties, liability, remedies or damages set forth above shall apply to the fullest extent permitted by law, and shall not apply to the extent prohibited by law.

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Damages, Claims, and Returns

Damages

If shipping damage to the product is discovered,

contact the shipping carrier and request inspection by a local agent. Secure a written report of the findings to support any claim. Do not return damaged goods to Applied Biosystems without first securing an inspection report and contacting Applied Biosystems Technical Support for a Return Authorization (RA) number.

Claims

After a damage inspection report is received by Applied Biosystems, Applied Biosystems will process the claim unless other instructions are provided.

Returns

Do not return any material without prior notification and authorization.

If for any reason it becomes necessary to return material to Applied Biosystems, contact Applied Biosystems Technical Support or your nearest Applied Biosystems subsidiary or distributor for a return authorization (RA) number and forwarding address. Place the RA number in a prominent location on the outside of the shipping container, and return the material to the address designated by the Applied Biosystems representative.

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Table A-1. Flow Test Specifications* (the “Mechanical Performance”)

Flow Test Number Flow Test Value

1 DIEA (Boc) 1.9– 2.4 mL1 Piperidine (Fmoc) 0.9–1.3 mL4 Ac

2

0 (Boc) 1.8– 2.3 mL4 DMAP (Fmoc) 2.0–2.3 mL5 DMSO 0.8–1.3 mL6 MeOH 2.0– 2.5 mL9 DCM 3.2– 3.7 mL10 NMP 2.4–2.75 mL11 NMP 2.0– 2.3 g12 DCM 3.5–4.1 g

*These specifications assume both gas regulators have been properly calibrated.

Table A-2. Synthesis of Acyl Carrier Protein (65–74) (the “Chemical Performance”)

Amino Acid Fmoc Coupling Minimum Values

Boc CouplingMinimum Values

Asn 98.6 99.4

Ile 98.4 99.3

Tyr 98.5 99.3

Asp 98.6 99.2

Ile 98.6 99.3

Ala 98.5 98.2

Ala 98.5 98.5

Gln 98.4 98.4

Val 97.1 98.2

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Applied Biosystems

March 2004 Appendix B: Post-Synthesis Procedures B-1

Appendix

B: Post-Synthesis Procedures

Contents

Quantitative Ninhydrin Procedure B-2Post-Synthesis Calculations B-5

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B-2 Appendix B: Post-Synthesis Procedures March 2004

Quantitative Ninhydrin Procedure

Despite the use of highly efficient coupling techniques, we cannot assume coupling reactions are 100 percent efficient. In this ninhydrin monitoring procedure

1

, free amines react with ninhydrin to form a violet-colored compound, known as Ruhemann’s purple, which can be quantitatively measured at 570 nm.

DANGER! CHEMICAL HAZARD

.

Acetic acid (glacial)

is a flammable liquid and vapor. Exposure causes eye, skin, and respiratory tract burns. It may be harmful if inhaled, absorbed through the skin, or swallowed. Keep away from heat, sparks, and flame. Read the MSDS, and follow the handling instructions. Wear appropriate

protective eyewear, clothing, and gloves.

WARNING CHEMICAL HAZARD. Ninhydrin can irritate the skin, eyes, and respiratory system. Read the MSDS, and follow the handling instructions. Wear appropriate protective eyewear,

clothing, and gloves.

WARNING CHEMICAL HAZARD. Methanol is a flammable liquid and vapor. Exposure causes eye and skin irritation, and may cause central nervous system depression and nerve damage. Read the MSDS, and follow the handling instructions. Wear

appropriate protective eyewear, clothing, and gloves.

WARNING CHEMICAL HAZARD. Ethanol is a flammable liquid and vapor. Exposure causes eye, skin, and respiratory tract irritation and may cause central nervous system depression and liver damage. Read the MSDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing,

and gloves.

WARNING CHEMICAL HAZARD. Phenol is a highly toxic, combustible, and vesicant chemical that causes burns and is readily absorbed through the skin. It is extremely destructive to mucous membranes, eyes, and skin. Inhalation and ingestion can cause central nervous system, liver, pancreas, and

1.Sarin, V.K., Kent, S.B.H., Tam, J.P. and Merrifield, R.B. 1981.

Analytical Biochem.

117:147-157.

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spleen damage and can be fatal. Read the MSDS, and follow the handling instructions. Wear appropriate protective

eyewear, clothing, and gloves.

WARNING CHEMICAL HAZARD. Potassium cyanide is a highly toxic chemical that can cause serious damage to the eyes and skin upon contact. It can cause damage to the central nervous system when inhaled. Read the MSDS, and follow the handling instructions. Wear appropriate protective eyewear,


WARNING CHEMICAL HAZARD. 2-Methyl pyridine is a flammable liquid and vapor. Exposure causes eye, skin, and respiratory tract irritation. It is harmful if inhaled, absorbed through the skin, or swallowed, and may cause central nervous system depression and damage to the liver and kidneys. Keep away from heat, sparks, and flame. Read the MSDS, and follow the handling instructions. Wear appropriate protective eyewear,


To start the synthesis:

1. Weigh each test tube to the nearest tenth of a milligram, and then add 2–3 mL MeOH. If you are using Fmoc chemistry, also add 2–3 drops of acetic acid.

2. After the synthesis, wash with MEOH:

a. Rinse any resin off the side of the tube with MeOH.

b. After the resin has settled, remove the liquid with a pipette.

c. Wash the resin once with MeOH. Remove the MeOH with a pipette.

d. Vacuum aspirate the last few drops of MeOH off the resin as you tilt and gently turn the test tube.

3. Dry the test tubes in a centrifugal vacuum evaporator (Speed Vac) or in a vacuum desiccator for one or more hours.

4. Determine the sample weight of the dried resin in each test tube to the nearest 0.1 mg.

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5. Using a Pasteur pipette or an automatic re-pipettor, add Ninhydrin reagents to the blank (empty tube), and samples using the following proportions:

Monitor 1 Phenol/EtOH4 drops (75 µL)

Monitor 2 KCN/Pyridine8 drops (100 µL)

Monitor 3 Ninhydrin/EtOH4 drops (75 µL)

6. Incubate the test tubes in a heating block at 100°C for 7 minutes with Boc resins and for 5 minutes with Fmoc resins.

7. When the heating is completed, remove the tubes and immediately add 4.8 mL of 60% EtOH for a final volume of 5 mL.

8. Vortex the tubes to mix the solution thoroughly. Take care not to splash fluid out of the tube. Let the resin settle to the bottom of the tubes.

9. Use 60% EtOH to zero a spectrophotometer at 570 nm. Read the absorbance of each sample (including the blank) at 570 nm. Take care not to transfer any resin into the cuvette or flow cell. The presence of resin will alter the readings. If necessary, pipette the sample into the cuvette.

10. Calculate the µmol/g of amine, or use the SynthAssist software:

µmol/g =[Abs sample – Abs blank)

×

dilution (mL)] 10

6

[Extinction coeffecient

×

sample weight(mg)]

Note Dilution = 5 mL

Extinction coefficient = 15,000

m

-1

cm

-1

11. Calculate the percent coupling as follows:

Note To calculate resin substitution, after the addition of each residue, refer to “Choosing a Resin for the Reaction Vessel” in ABI 433A

Peptide Sythesizer, Volume 1, Chapter Two.

% coupled =[ 1 – amine (µmol/g) ]

103 x substitution (mmol/g)

x 100

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Post-Synthesis Calculations

This section explains how to calculate the theoretical weight of the final, protected peptide- resin, the substitution of the protected peptide-resin, and the substitution of the protected peptide-resin at the end of each coupling. These calculations can also be performed with the SynthAssist

®

Software.

First determine the substitution (loading) of the original protected amino acid-resin. If you purchased an Fmoc amino acid-resin or a Boc amino acid-PAM resin, the substitution is on the bottle. This value is usually between 0.6 to 0.9 mmol/g. If you start with an unloaded p-alkoxybenzyl alcohol resin (HMP resin) or an unloaded BHA or MBHA resin, you need to calculate the loading with the first amino acid on the resin.

SynthAssist uses the molecular weights of the amino acid derivatives (see Appendix 3) to calculate the substitution after each coupling. The residue weights for the Fmoc derivatives were calculated by subtracting 240 (H

2

O + Fmoc) from the molecular weight. The residue weights for the Boc derivatives were calculated by subtracting 118 (H

2

O + Boc) from the molecular weight.

Calculations for unloaded p-Alkoxybenzyl Alcohol Resin

1. Calculate the weight of 1 mol of resin.

2. Add 1 mol Fmoc amino acid.

3. Subtract 1 mol H

2

O.

4. Calculate new substitution.

Example:

Calculate substitution of Fmoc-Asp(OtBu) on (0.90 mmol/g) HMP resin.

1. 1000 mmol/mol = 1111 g/mol0.90 mmol/g

2. Fmoc-Asp (OtBu) = 411 g/mol

3.

4.

– H2O = –18 g/mol1504 g/mol

1000 mmol/mol1504 g/mol

= 0.66 mmol/g

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Calculations for Unloaded MBHA Resin

Note MBHA resins are stored as hydrochloride salts.

To calculate the weight of 1 mol of resin:

5. Add 1 mol Boc amino acid.

6. Subtract 1 mol H

2

O.

7. Subtract 1 mol HCl (for the hydrochloride salt).

8. Calculate new substitution.

Example 1:

To calculate the substitution of Boc-Leu on 0.65 mmol/g MBHA resin:

1.

2. Boc - Leu 231 g/mol

3. – H

2

O – 18 g/mol

4. – HCl – 36.5 g/mol

____________________

1714.5 g/mol

5.

After a coupling, substitution changes as a result of the addition of the protected amino-acid residue to the peptide-resin. To calculate the change in substitution (mmol/g), you must calculate the weight of 1 mol of the protected peptide-resin, add the residue weight, and then recalculate the substitution.

1000 mmol/mol0.65 mmol/g

= 1538 g/mol

1000 mmol/mol1714.5 g/mol

= 0.58 mmol/g

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Example 2:

Calculate the substitution after each Fmoc coupling during the synthesis of ACP (65-74), starting with HMP resin with a substitution of 1.05 mmol/g. Calculate the theoretical yield of peptide-resin.

Table B-1. Substitution Information

The theoretical yield of peptide-resin starting with 0.25 mmol resin is (0.00025)(2817) = 0.70 g. This weight includes the Fmoc group on the peptide-resin.

If the Fmoc group is removed, the theoretical yield of the peptide-resin is 0.65 g.

2817

– Fmoc = – 222

(0.00025) (2595) = 0.65 g

Cycle Amino Acid ResidueWeight

ResinEq. Wt.

Subst.(mmol/g)

1 Fmoc Gly HMP Resin 1231 1231 0.81

2 Asn(Trt) 357 1588 0.63

3 Ile 113 1701 0.59

4 Tyr(tBu) 220 1921 0.52

5 Asp(OtBu) 171 2092 0.48

6 Ile 113 2205 0.45

7 Ala 71 2276 0.44

8 Ala 71 2347 0.43

9 Gln(Trt) 371 2718 0.37

10 Val 99 2817 0.36

10001.05

= 952

Fmoc Gly = 297

– H2O – 18

1231

2595

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Example 3:

Calculate the substitution after each coupling during the synthesis of Bradykinin starting with Boc-Arg(Tos) PAM Resin with a loading of 0.66 mmol/gram.

Boc-Arg(Tos) PAM Resin1000 = 1515.66

Table B-2. Bradykinin Synthesis Substitution Information

The theoretical yield of peptide-resin starting with 0.50 mmol PAM resin is (0.0005)(2645) = 1.32 grams.

Cycle Amino Acid Residue Weight Resin Eq. Wt. Subst. mmol/g

1 Phe 147 1662 0.60

2 Pro 97 1759 0.57

3 Ser (Bzl) 177 1936 0.52

4 Phe 147 2083 0.48

5 Gly 57 2140 0.47

6 Pro 97 2237 0.45

7 Pro 97 2334 0.43

8 Arg (Tos) 311 2645 0.38

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March 2004 Appendix C: Chemicals and Reagents C-1

Appendix

C: Chemicals and Reagents

This chapter lists chemicals and their part numbers used by the various chemistries supported by the ABI 433A Peptide Synthesizer.

Contents

Fmoc Reagents and Solvents C-2Boc Reagents and Solvents C-3

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C-2 Appendix C: Chemicals and Reagents March 2004

Fmoc Reagents and Solvents

Table C-1. Chemicals for FastMoc™ Chemistry

Bottle PartPosition Number Description Quantity

1 571261* Aldrich 450 mL2 —— (empty) ——4** 400631 DMAP, (0.1 M dimethylaminopyridine/

N,N-dimethylformamide) 200 mL 5 401132 0.45 M HBTU/HOBt in DMF 200 mL

6 400470 Methanol 450 mL 7 401517 2M N,N-Diisopropylethylamine/

N-methylpyrrolidone 200 mL8 400663 1.0 M Dicyclohexylcarbodiimide/

N-methylpyrrolidone 200 mL9 400142 Dichloromethane 4 L10 400580 N-Methylpyrrolidone 8 L

*Aldrich Part Number

**Only for loading HMP resin

FastMoc Chemistry Capping Cycles Use PNA Capping Solution (GEN 063102) at position 4.

Table C-2. Chemicals for Fmoc/HOBt/DCC Chemistry

Bottle PartPosition Number Description Quantity

1 571261* Aldrich 450 mL2 —— (empty) ——4** 400631 DMAP, (0.1 M dimethylaminopyridine/

N,N-dimethylformamide) 200 mL 5 —— (empty) ——

6 400470 Methanol 450 mL 7 400662 1.0 M 1-Hydroxybenzotriazole/

N-methylpyrrolidone 200 mL8 400663 1.0 M Dicyclohexylcarbodiimide/

N-methylpyrrolidone 200 mL9 400142 Dichloromethane 4 L10 400580 N-Methylpyrrolidone 8 L

*Aldrich Part Number**Only for loading HMP resin

Fmoc/HOBt/DCC Chemistry Capping Cycles Use PNA Capping Solution (GEN 063102) at position 4.

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March 2004 Appendix C: Chemicals and Reagents C-3

Table C-3. Fmoc Amino Acids

Part Number (1 mmol cartridges) each box of ten Description

400632 410632 Alanine, Fmoc-L-Ala,400633 410633 Arginine, Fmoc-L-Arg(Mtr)400961 410961 Arginine, Fmoc-L-Arg (Pmc)401089 411089 Asparagine, Fmoc-L-Asn(Trt)400635 410635 Aspartic Acid, Fmoc-L-Asp (OtBu)400962 410962 Cysteine, Fmoc-L-Cys (Trt)401090 411090 Glutamine, Fmoc-L-Gln(Trt)400637 410637 Glutamic Acid, Fmoc-L-Glu (OtBu)400638 410638 Glycine, Fmoc - Gly400778 410778 Histidine, Fmoc-L-His (Trt)400640 410640 Isoleucine, Fmoc-L-Ile400641 410641 Leucine, Fmoc-L-Leu400642 410642 Lysine, Fmoc-L-Lys (Boc)400644 410644 Methionine, Fmoc-L-Met400645 410645 Phenylalanine, Fmoc-L-Phe400646 410646 Proline, Fmoc-L-Pro400647 410647 Serine, Fmoc-L-Ser (tBu)400648 410648 Threonine, Fmoc-L-Thr (tBu)400649 410649 Tryptophan, Fmoc-L-Trp400650 410650 Tyrosine, Fmoc-L-Tyr (tBu)400651 410651 Valine, Fmoc-L-Val

Table C-4. Fmoc Resin

Part No. Description Quantity

400957 HMP-Resin, (p-hydroxymethyl 5 gramsphenoxymethylpolystyrene resin)

Boc Reagents and Solvents

Table C-5. Chemicals Required for Boc Chemistry

Bottle Part Description QuantityPosition Number

1 400136 N,N-Diisopropylethylamine 175 mL2 400137 Trifluoroacetic acid 450 mL

5 400661 Dimethyl sulfoxide/ N-methylpyrrolidone 450 mL

6 400470 Methanol 450 mL7 400662 1.0 M 1-Hydroxybenzotriazole/

N-Methylpyrrolidone 200 mL8 400663 1.0 M Dicyclohexylcarbodiimide/

N-Methylpyrrolidone 200 mL9 400142 Dichloromethane 4 L

10 400580 N-Methylpyrrolidone 4 Lwaste 400230 Waste Neutralizer 450 mL

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C-4 Appendix C: Chemicals and Reagents March 2004

Table C-6. Boc Amino Acids

Description Part Number

2 mmol cartridge/box of tenAlanine, t-Boc-L-Ala 410149Arginine, t-Boc-L-Arg(Tos) 410150Arginine, t-Boc-L-Arg(Mts) 410409Asparagine, t-Boc-L-Asn 410151Aspartic acid, t-Boc-L-Asp(OBzl) 410152

Cysteine, t-Boc-L-Cys(4-CH3Bzl) 410153

Cysteine, t-Boc-L-Cys(4-CH3OBzl) 410412

[also called t-Boc-L-Cys(Mob)]Glutamine, t-Boc-L-Gln 410154Glutamic acid, t-Boc-L-Glu(OBzl) 410155Glycine, t-Boc-Gly 410156Histidine, t-Boc-L-His(Bom) 411016

Histidine, t-Boc-L-His(Dnp) 410659Isoleucine, t-Boc-L-Ile•1/2H

2O 410160

Leucine, t-Boc-L-Leu•H2O 410161

Lysine, t-Boc-L-Lys(Cl-Z) 410162Methionine, t-Boc-L-Met (0) 410413Methionine, t-Boc-L-Met 410164Phenylalanine, t-Boc-L-Phe 410165Proline, t-Boc-L-Pro 410166Serine, t-Boc-L-Ser(Bzl) 410167Threonine, t-Boc-L-Thr(Bzl) 410168Tryptophan, t-Boc-L-Trp(CHO) 410170Tyrosine, t-Boc-L-Tyr(Br-Z) 410171Valine, t-Boc-L-Val 410172

Table C-7. Methylbenzhydrylamine (BHA) Resin

Description Part Number

0.5 mmol 5 gramp-methyl BHA Resin 400229 400377

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March 2004 Appendix D: Amino Acid Derivatives D-1

Appendix D: Amino Acid Derivatives

Contents

Molecular Weights and Residue Weights of Protected Amino Acids D-2Amino Acid Derivatives D-3

Amino Acid See page

GlycineAlanineValineLeucineIsoleucineProline

D-3

PhenylalanineMethionineTryptophan

D-4

SerineThreonineTyrosine

D-5

Cysteine D-6

Asparagine D-7

Glutamine D-8

Apartic acidGlutamic acid

D-9

Histidine D-10

Lysine Arginine

D-11

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D-2 Appendix D: Amino Acid Derivatives March 2004

Molecular Weights and Residue Weights of Protected Amino Acids

Amino Acid Boc Derivative M.W.

Residue Wt. in ProtectedPeptide Chain Fmoc Derivative M.W.

Residue Wt. in ProtectedPeptide Chain

Alanine Boc-Ala 189 71 Fmoc-Ala 311 71

Arginine Boc-Arg(Tos) 429 311 Fmoc-Arg(Mtr) 609 369

Boc-Arg(Mts) 457 339 Fmoc-Arg(Pbf) 649 409

Fmoc-Arg(Pmc) 663 423

Asparagine Boc-Asn 232 114 Fmoc-Asn(Mbh) 581 341

Fmoc-Asn(Trt) 597 357

Aspartic Acid Boc-Asp(OBzl) 323 205 Fmoc-Asp(OtBu) 411 171

Boc-Asp(OcHex) 315 197 Fmoc-Arg(Pbf) 649 409

Cysteine Boc-Cys(4-CH3Bzl) 325 207 Fmoc-Cys(tBu) 400 160

Boc-Cys(4-CH3OBzl) 341 223 Fmoc-Cys(Trt) 586 346

Boc-Cys(Acm) 292 174 Fmoc-Cys(Acm) 414 174

Glutamic Acid Boc-Glu(OBzl) 337 219 Fmoc-Glu(OtBu) 425 185

Boc-Glu(OcHex) 329 211

Glutamine Boc-Gln 246 128 Fmoc-Gln(Mbh) 595 355

Fmoc-Gln(Trt) 611 371

Glycine Boc-Gly 175 57 Fmoc-Gly 297 57

Histidine Boc-His(Dnp) 421 303 Fmoc-His(Trt) 620 380

Boc-His(Bom) 375 257 Fmoc-His(Bum) 464 224

Isoleucine Boc-Ile 231 113 Fmoc-Ile 353 113

Leucine Boc-Leu 231 113 Fmoc-Leu 353 113

Lysine Boc-Lys(Cl-Z) 415 297 Fmoc-Lys(Boc) 469 229

Methionine Boc-Met 249 131 Fmoc-Met 371 131

Boc-Met(O) 265 147

Phenylalanine Boc-Phe 265 147 Fmoc-Phe 387 147

Proline Boc-Pro 215 97 Fmoc-Pro 337 97

Serine Boc-Ser(Bzl) 295 177 Fmoc-Ser(tBu) 383 147

Threonine Boc-Thr(Bzl) 309 191 Fmoc-Thr(tBu) 397 157

Tryptophan Boc-Trp 304 186 Fmoc-Trp 426 186

Boc-Trp(CHO) 332 214

Tyrosine Boc-Tyr(Br-Z) 494 376 Fmoc-Tyr(tBu) 460 220

Valine Boc-Val 217 99 Fmoc-Val 339 99

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Amino Acid Derivatives

G

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P

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s

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c

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asparagine

asparagineMW 132.12

N

AMINO ACID BOC PROTECTED DERIVATIVE FMOC PROTECTED DERIVATIVE

2H N CH COOH

AsnBoc-Asn-OH

N- -Boc-N- -xanthyl-L-asparagineMW 412.44

Boc-Asn(Xan)-OH

CH2

NH

C

CH2

NH CH COOHC

O

OC

CH3

CH3

CH3

NH CH COOHC

O

CH2 O

N- -Boc-L-asparagineMW 232.24

Fmoc-Asn(Trt)-OH

O2

CH2

NH

C O2

NH

C O

NH

C O

NH CH COOHC

O

O

CH2C

CH3

CH3

CH3

O

βα

Fmoc-Asn(Mbh)-OH

N- -Fmoc-N- -(dimethoxybenzhydryl)- L-asparagine

MW 580.64

Mbh also known as:Dod = dimethoxydityl

Ddm = dimethoxydiphenylmethyl

α

N- -Fmoc-N- -(trityl)-L-asparagineMW 596.69

α β

α

β

C

NH CH COOHC

O

CH2 O

CH2

NH

C O

CHO O CHH3 3C

Applied Biosystems


glutamine

N- -Fmoc-N- -(dimethoxybenzhydryl)-L-glutamMW 594.66

Mbh also known as:Dod = dimethoxydityl

Ddm = Dimethoxydiphenylmethyl

glutamineMW 146.15

Q


2H N CH COOH

Gln Boc-Gln-OH Fmoc-Gln(Mbh)-OH

N- -Boc-N- -xanthyl-L-glutamineMW 426.47

Boc-Gln(Xan)-OH

CH2

NH

C

NH CH COOHC

O

CH2 O

CH2

NH CH COOHC

O

OC

CH3

CH3

CH3

NH CH COOHC

O

O

CH2C

CH3

CH3

CH3NH CH COOHC

O

CH2 O

N- -Boc-L-glutamineMW 246.26

Fmoc-Gln(Trt)-OH

N- -Fmoc-N- -(trityl)-L-glutamineMW 610.72

O2

CH2

NH

C O2

NH

C O

CH2

NH

C O

CHOH3 3C

NH

C O

O

CH2

CH2CH2

CH2

CH2

α γ

α α

α

γ

OCH

C

γ

Applied Biosystems


a

Applied Biosystems


histidine

Applied Biosystems


l

N- -Fmoc-N- -Boc-L-lysine MW 468.55

lysineMW 146.19

K


2H N CH COOH

Lys

Boc-Arg(Tos)-OH

Fmoc-Lys(Boc)-OH

CH2

NH CH COOHC

O

CH2 O

NH CH COOHC

O

OC

CH3

CH3

CH3

N- -Boc-N -tosyl-L-arginineMW 428.51

arginineMW 174.20

2H N CH COOH

Arg

CH2

R

CH2

CH2

CH2

CH2

NH2

C O

O

NH

CH2CH2CH2CH2

C CH3H C3

CH3

CH2

NH

CHN

2NH

NH

CH2CH2CH2

Boc-Lys(Cl-Z)-OH

NH CH COOHC

O

OC

CH3

CH3

CH3

N- -Boc-N- -(2-chlorobenzyloxycarbonyl)-L-lysineMW 414.89

C O

O

NH

CH2CH2CH2CH2

CH2

Cl

CHN NH

CH3

SO2

Fmoc-Arg(Mtr)-OH

N- -Fmoc-N -(4-methoxy-2,3,6- trimethylbenzenesulfonyl)-L-arginine

MW 668.8 (IPE)

Boc-Arg(Mts)-OH

NH CH COOHC

O

OC

CH3

CH3

CH3

N- -Boc-N -(mesitylene-2-sulfonyl)-L-arginineMW 456.56

NH

CH2CH2CH2

CH3

CHN NH

SO2

CH3CH3

α

α ε α ε

α

α

NH CH COOHC

O

O

NH

CH2CH2CH2

CHN NH

CH2

CH3

SO2

CH3

CH3CH3

O

G G

G N- -Fmoc-N -(2,2,4,6,7-pentamethyldihydro-benzofuran-5-sulfonyl)-L-arginine

MW 648.8

αFmoc-Arg(Pbf)-OH

O

OCH2NH CH COOHC

NH

CH2CH2CH2

CHN NH

CH3

SO2

CH3CH3

O

CH 3C3H

G

Applied Biosystems



arginineMW 174.20

2H N CH COOH

Arg

CH2

R

CH2

CH2

NH

CHN

2NH

Fmoc-Arg(Pmc)-OHO

O

N- -Fmoc-N -(2,2,5,7,8-pentamethylchroman-6-sulfonyl)-L-arginine

MW 662.81

α

CH2NH CH COOHC

NH

CH2CH2CH2

CHN NH

CH3

SO2

CH3CH3

O

CH3C3H

G

Applied Biosystems

March 2004 Appendix E: Pre-defined Chemistry Modules E-1

Appendix E: Pre-defined Chemistry Modules

Contents

Function List E-4FastMoc™ 1.0 mmol Chemistry E-8

Module A – Activation E-8Module A – Conditional: Activation E-9Module B – Deprotection E-11Module B – Conditional: Deprotection/MonPrevPk E-13Module b – Conditional: MonDoMod(deprot/MonPrevPk) E-16Module C – Capping with Ac2O Solution E-17Module c – DCM Washes E-18Module D –NMP Washes E-19Module d – Conditional: MonDoMod (capping/wash) E-20Module E –Transfer E-21Module F – Clean cartridge, coupling, drain, and NMP washes E-23Module F – CondMonPrevPeak: Coupling etc/SkipMod E-25Module f – CondMonPrevPeak: MonDoMod (coupling) E-27Module G – Resin Sampling E-29Module g – CondMonPrevPeak: MonDoMod (resin sampling) E-30Module H – Load and Cap E-31Module H – Conditional: Load and Cap E-34Module I – Fifteen-minute wait E-36

FastMoc 0.25 mmol Chemistry E-37Module A – Activation E-37Module A – Conditional: Activation E-38Module A – Monitoring: Activation E-39Module a – Conditional: MonDoMod (activation/transfer) E-40Module B – Piperidine deprotection E-42Module B – Deprotection/Mon 1st-X E-43Module B – Deprotection/MonPrevPk E-45Module B – Conditional: Deprotection/Mon1st-X E-47Module B – Conditional: Deprotection/ MonPrevPk E-49Module B – Conditional: Deprotection/ MonPrevPk E-50Module b – Conditional: MonDoMod

(deprotection/Mon1-X) E-51Module b – Conditional: MonDoMod (deprotection/

MonPrevPk) E-52Module C –Acetic anhydride capping E-53Module c – DCM washes E-54Module D – NMP washes E-55Module d – Conditional: MonDoMod (capping/wash) E-56

Applied Biosystems

E-2 Appendix E: Pre-defined Chemistry Modules March 2004

Module E – Transfer E-57Module F – Clean, couple, drain, and wash E-58Module F – Clean, couple, drain, and wash, with feedback E-59Module F – Conditional: Coupling etc/SkipMod E-60Module f – Conditional: MonDoMod (Coupling) E-62Module G – Resin sampling E-63Module g – Conditional: MonDoMod (resin sampling) E-65Module H – Load and cap E-66Module I –Ten-minute wait E-69Module i – Cart (eject/advance)/SkipMod E-69

FastMoc 0.10 mmol Chemistry E-70Module A – Dissolving amino acid E-70Module A – Conditional: Activation E-71Module a – Conditional: MonDoMod (activation/transfer) E-72Module B – Piperidine deprotection E-74Module B – Deprotection/Mon1st-X E-75Module B – Deprotection/MonPrevPk E-77Module B – Conditional: Deprotection/ Mon1stPeak-X E-79Module B – Conditional: Deprotection/ MonPrevPeak E-81Module b – Conditional: MonDoMod (deprot/Mon1stPk-X) E-83Module b – Conditional: MonDoMod (deprot/MonPrevPeak) E-84Module C – Capping with Ac2O E-85Module c – DCM washes E-86Module D – NMP washes E-87Module d – Conditional: MonDoMod (capping/wash) E-88Module E – Transfer E-89Module F – Clean, couple, drain, and wash E-90Module F – Clean, couple, drain, and wash, with feedback E-91Module F – Conditional: Coupling etc./SkipMod E-92Module f – Conditional: MonDoMod (coupling) E-94Module G – Resin sampling E-95Module g – Conditional: MonDoMod (resin sampling) E-97Module H – Load and cap E-98Module I – Ten-minute wait E-101Module i – Cart(eject/advance)/SkipMod E-101

Fmoc/HOBt/DCC 0.25 mmol Chemistry E-102Module a – Activation E-102Module b – Piperidine Deprotection E-104Module c – DCM Washes E-106Module d – NMP Washes E-108Module e – Transfer E-110Module f – Coupling E-112Module g – NMP Washes and Resin Sampling E-113

Applied Biosystems


Module h – Loading E-115Module i – Waiting E-116

Fmoc/HOBt/DCC 0.10 mmol Chemistry E-117Module a – Activation E-117Module b – Piperidine Deprotection E-119Module c – DCM Washes E-121Module d – NMP Washes E-123Module e – Transfer E-125Module f – Coupling E-127Module g – NMP Washes E-128Module h – Loading E-130Module i – Wait E-131

Boc/HOBt/DCC 0.50 mmol Chemistry E-132Module a – Activation E-132Module b – TFA Deprotection E-135Module c – DCM Washes E-138Module d – DIEA Neutralization and NMP Washes E-140Module e – Transfer E-143Module f – Coupling in NMP and Adding DMSO E-146Module g – DIEA addition, resin sampling and capping E-148Module h – Coupling E-150Module i – Wait E-150

Boc/HOBt/DCC 0.10 mmol E-151Module a – Activation E-151Module b – TFA Deprotection E-153Module c – DCM Washes E-156Module d – DIEA Neutralization and NMP Washes E-157Module e – Transfer E-159Module F – DMSO, DIEA, & Drain E-161Module f – Coupling in NMP E-162Module G – DMSO, DIEA, Drain & R.S. E-163Module g – DMSO and DIEA Addition, Resin Sampling,

and Capping E-165Module i – Wait E-167

Applied Biosystems


Function List

There are 152 functions available, each designated by a number and name. Function names describe the action accomplished by the function, although the names are somewhat abbreviated on the Model 433A LCD, due to space limitations. In SynthAssist® Software, the names of the functions are longer, and may change depending on the contents of the reagent bottles. The table on the following four pages lists all the functions by number, followed by the names as they appear on the LCD, and on SynthAssist Software. The SynthAssist name includes a bottle number, for which you may substitute the appropriate reagent name.

Table of Functions

Function Model 433A Number Function Name SynthAssist Function Name

1 WAIT Wait 2 VORTEX ON Vortex reaction vessel on 3 VORTEX OFF Vortex reaction vessel off 4 SAVE CART Read cartridge 5 NEEDLE DWN Needle down 6 NEEDLE UP Needle up 7 EJECT CART Eject cartridge 8 ADVAN CART Advance cartridge 9 GAS T VB Flush top valve block with gas to waste10 GAS B VB Flush bottom valve block with gas to waste

11 #9 T VB Flush top valve block with #9 to waste12 #9 B VB Flush bottom valve block with #9 to waste13 #10 T VB Flush top valve block with #10 to waste14 #10 B VB Flush bottom valve block with #10 to waste15 #1 T VB Flush top valve block with #1 to waste16 #1 B VB Flush bottom valve block with #1 to waste17 #4 B VB Flush bottom valve block with #4 to waste18 #5 B VB Flush bottom valve block with #5 to waste19 #6 B VB Flush bottom valve block with #6 to waste20 MIX ACT Mix activator

21 VENT ACT Vent activator22 DRAIN ACT Drain activator to waste23 ML TO ACT Transfer measuring loop to activator24 CART TO AC Transfer cartridge to activator25 #9 T ACT Deliver #9 to activator top26 #10 T ACT Deliver #10 to activator top27 #6 T ACT Deliver #6 to activator top28 GAS T ACT Pressurize activator

Function Model 433A Number Function Name SynthAssist Function Name

Applied Biosystems


29 #9 ACT-DRN Flow #9 through activator to waste30 #10 A-DRN Flow #10 through activator to waste

31 #1 B ACT Deliver #1 to activator32 #4 B ACT Deliver #4 to activator33 #5 B ACT Deliver #5 to activator34 #6 B ACT Deliver #6 to activator35 #9 B ACT Deliver #9 to activator36 #10 B ACT Deliver #10 to activator37 ACT TO RVc Transfer activator to reaction vessel (top closed)38 ACT TO RVo Transfer activator to reaction vessel (top open)39 RELAY 0 Relay 0 pulse on40 MIX RV Mix reaction vessel

41 VENT RV Vent reaction vessel42 DRAIN RV Drain reaction vessel to waste43 ML TO RV Transfer measuring loop to reaction vessel44 CART TO RV Transfer cartridge to reaction vessel (top open)45 #9 T RV Deliver #9 to reaction vessel top46 #10 T RV Deliver #10 to reaction vessel top47 #1 T RV Deliver #1 to reaction vessel top48 GAS T RV Pressurize reaction vessel49 #9 RV-DRN Flow #9 through reaction vessel to waste50 #10 RV-DRN Flow #10 through reaction vessel to waste

51 #1 B RV Deliver #1 to reaction vessel52 #4 B RV Deliver #4 to reaction vessel53 #5 B RV Deliver #5 to reaction vessel54 #6 B RV Deliver #6 to reaction vessel55 #9 B RV Deliver #9 to reaction vessel56 #10 B RV Deliver #10 to reaction vessel57 RV TO ACTc Transfer reaction vessel to activator (top closed)58 INTERRUPT Interrupt conditional59 RELAY 1 Relay 1 pulse on60 MIX CART Mix cartridge

61 VENT CART Vent cartridge 62 DRAIN CART Drain cartridge to waste63 ML TO CART Transfer measuring loop to cartridg64 #9 CART Deliver #9 to cartridge65 #10 CART Deliver #10 to cartridge66 #9 SML N Deliver #9 to cartridge small needle67 #10 SML N Deliver #10 to cartridge small needle68 MEAS #7 Deliver #7 to measuring loop (open)69 MEAS #8 Deliver #8 to measuring loop (open)70 PURGE ML Flush bottom valve block with loop contents to waste

71 #2 B VB Flush bottom valve block with #2 to wasteFunction Model 433A

Number Function Name SynthAssist Function Name

Applied Biosystems


72 #2 B RV Deliver #2 to reaction vessel73 VENT #2 Vent #2 without gas74 FLUSH #2 Back-flush #275 GAS-VENT #2 Vent #2 with gas76 PRS #2 Pressurize #277 PRS #4 Pressurize #478 PRS #M Pressurize manifold79 PRS #1 Pressurize #180 GAS TO AUX Flush bottom valve block with gas to aux. waste

81 ACT TO AUX Drain activator to aux. waste82 RV TO AUX Drain reaction vessel to aux. waste83 CART TO AX Drain cartridge to aux. waste84 #9 TO AUX Flush bottom valve block with #9 to aux. waste85 #9 RV-AUX Flow #9 through reaction vessel to aux. waste86 #10 RV-AUX Flow #10 through reaction vessel to aux. waste87 TAKE SAMPL Take sample88 RS TO RV Resin sampler to reaction vessel89 RS TO FC Resin sampler to frac.collector90 #9 TO RS Deliver #9 to resin sampler

91 #10 TO RS Deliver #10 to resin sampler92 #1 TO RS Deliver #1 to resin sampler93 GAS TO RS Deliver gas to resin sampler94 #5 TO CART Deliver #5 to cartridge95 VENT ML Vent measuring loop96 CRT TO RVc Transfer cartridge to reaction vessel (top closed)97 #7 TO MLc Deliver #7 to measuring loop (closed)98 BEGIN LOOP Begin loop UPPER99 END LOOP End loop UPPER

100 User Fxn A User defined

101 User Fxn B User defined102 User Fxn C User defined103 User Fxn D User defined104 User Fxn E User defined105 User Fxn F User defined106 User Fxn G User defined107 User Fxn H User defined108 User Fxn I User defined109 User Fxn J User defined110 begin loop Begin loop lower

111 end loop End loop lower113 TOGGLE OFF Toggle all off114 RELAY 0 ON Relay 0 on115 RLY 0 OFF Relay 0 off

Function Model 433A

Number Function Name SynthAssist Function Name

Applied Biosystems


116 RELAY 1 ON Relay 1 on117 RLY 1 OFF Relay 1 off118 #10 TO AUX Flush bottom valve block with #10 to aux. waste119 #9 ACT-AUX Flow #9 through activator to aux. waste120 AUX TO ACT Deliver aux. solvent to activator

121 AUX TO CRT Deliver aux. solvent to cartridge122 AUX TO RV Deliver aux. solvent to reaction vessel123 AUX TO WST Flush bottom valve block with aux. solvent to waste124 #1 TO CART Deliver #1 to cartridge125 #2 TO CART Deliver #2 to cartridge126 #4 TO CART Deliver #4 to cartridge127 #6 TO CART Deliver #6 to cartridge128 Mon1stPk-X Monitoring first peak - X129 Mon1stPk Monitoring first peak130 MonPrevPk Monitoring previous peak

131 Mon Stop Monitoring stop132 Save MonPk Read monitoring peak133 MonBegLoop Begin loop monitoring134 MonEndLoop End loop monitoring135 Mon Reset Monitoring reset136 SkipModMon Do module if condition met137 Do Mod Mon Do module if condition not met138 Int MaxMon Interrupt condition not met139 IntConduct Interrupt conductivity above X”140 Int Chnl 2 Interrupt channel 2 above X”

141 Int Chnl 3 Interrupt channel 3 above X”142 MonDrain X Monitoring drain below X”143 MonRVWaste Drain reaction vessel monitored to waste144 MonRV toAux Drain reaction vessel monitored to aux. waste145 Test X´> Pk Test X’ greater than peak146 Test X´< Pk Test X’ less than peak147 SkipOnTest Do module if test false148 Do On Test Do module if test true149 Int OnTest Interrupt test true150 MATCH CART Match cartridge

151 TOGL USER Toggle user function on152 ATTENTION Attention

Applied Biosystems


FastMoc™ 1.0 mmol Chemistry

Module A – Activation

Step# Fxn# Function Name Time Add Key Events

1 2 VORTEX ON 1 02 36 #10 B ACT 2 03 20 MIX ACT 5 04 22 DRAIN ACT 5 05 98 BEGIN LOOP 2 06 21 VENT ACT 2 07 30 #10 A-DRN 5 08 22 DRAIN ACT 5 09 99 END LOOP 1 010 22 DRAIN ACT 10 011 110 begin loop 3 0 3 Amino Acid cartridges12 4 PRINT CART 10 013 6 NEEDLE UP 10 014 7 EJECT CART 10 015 8 ADVAN CART 10 016 5 NEEDLE DWN 10 017 14 #10 B VB 1 018 9 GAS T VB 2 019 65 # 10 CART 5 0 NMP to cartridge20 60 MIX CART 5 021 78 PRS #M 10 022 18 #5 B VB 1 023 94 #5 TO CART 8 0 HBTU to cartridge24 60 MIX CART 330 025 98 BEGIN LOOP 5 0 Transfer to Activator26 24 CART TO AC 4 027 1 WAIT 4 028 99 END LOOP 1 029 65 # 10 CART 2 030 60 MIX CART 3 031 98 BEGIN LOOP 2 032 24 CART TO AC 4 033 1 WAIT 4 034 99 END LOOP 1 035 111 end loop 1 036 62 DRAIN CART 4 037 67 #10 SML N 2 038 62 DRAIN CART 4 039 65 # 10 CART 4 040 13 #10 T VB 3 041 14 #10 BVB 3 042 9 GAS T VB 2 0

Applied Biosystems


Module A – Activation (continued)


43 10 GAS B VB 2 044 3 VORTEX OFF 1 0

Module A – Conditional: Activation

This module is found in the following Chemistry files:

• FastMoc 1.0 MonPrevPeak

• FastMoc 1.0 CondMonPrevPeak


1 36 #10 B ACT 22 20 MIX ACT 53 22 DRAIN ACT 54 98 BEGIN LOOP 25 21 VENT ACT 26 30 #10 A-DRN 57 22 DRAIN ACT 58 99 END LOOP 19 22 DRAIN ACT 1010 110 Begin loop 311 4 SAVE CART 1012 6 NEEDLE UP 1013 7 EJECT CART 1014 8 ADVAN CART 1015 5 NEEDLE DWN 1016 14 #10 B VB 117 9 GAS T VB 218 65 #10 CART 519 60 MIX CART 520 78 PRESS #M 1021 18 #5 B VB 122 94 #5 TO CART 823 60 MIX CART 33024 98 BEGIN LOOP 525 24 CART TO AC 426 1 WAIT 427 99 END LOOP 128 65 #10 CART 229 60 MIX CART 330 98 BEGIN LOOP 231 24 CART TO AC 432 1 WAIT 433 99 END LOOP 134 111 End loop 135 62 DRAIN CART 4

Applied Biosystems


Module A – Conditional: Activation (continued)


36 67 #10 SML N 237 62 DRAIN CART 438 65 #10 CART 439 13 #10 T VB 340 14 #10 B VB 341 9 GAS T VB 342 10 GAS B VB 3

Applied Biosystems


Module B – Deprotection


1 56 #10 B RV 20 52 2 VORTEX ON 1 03 56 #10 B RV 10 0 NMP wash4 88 RS TO RV 1 05 91 #10 TO RS 10 06 89 RS TO FC 1 07 40 MIX RV 5 08 1 WAIT 5 09 3 VORTEX OFF 1 010 42 DRAIN RV 40 511 50 #10 RV-DRN 5 012 42 DRAIN RV 10 513 56 #10 B RV 20 2 NMP14 79 PRS #1 10 015 51 #1 B RV 22 4 Piperidine16 56 #10 B RV 8 0 NMP17 40 MIX RV 3 018 2 VORTEX ON 5 019 40 MIX RV 3 020 13 #10 T VB 1 021 14 #10 B VB 1 022 9 GAS T VB 3 023 10 GAS B VB 3 024 1 WAIT 100 025 3 VORTEX OFF 1 026 42 DRAIN RV 40 527 56 #10 B RV 20 2 NMP28 79 PRS #1 5 029 51 #1 B RV 22 4 Piperidine30 56 #10 B RV 8 0 NMP31 40 MIX RV 3 032 41 VENT RV 2 033 88 RS TO RV 1 034 93 GAS TO RS 5 035 91 #10 TO RS 5 036 89 RS TO FC 1 037 2 VORTEX ON 5 038 40 MIX RV 3 039 98 BEGIN LOOP 2 0 Clean valve blocks40 13 #10 T VB 1 041 14 #10 B VB 3 0

Applied Biosystems


Module B – Deprotection


42 9 GAS T VB 3 043 10 GAS B VB 5 044 99 END LOOP 1 0

Applied Biosystems


Module B – Conditional: Deprotection/MonPrevPk





1 1 WAIT 12 58 INTERRUPT 3 135 Mon Reset 14 110 Begin loop 25 42 DRAIN RV 406 98 BEGIN LOOP 37 56 #10 B RV 20 58 2 VORTEX ON 19 56 #10 B RV 1010 88 RS TO RV 111 91 #10 TO RS 1012 89 RS TO FC 113 40 MIX RV 514 1 WAIT 515 3 VORTEX OFF 116 42 DRAIN RV 40 517 50 #10 RV-DRN 518 42 DRAIN RV 10 519 99 END LOOP 120 56 #10 B RV 20 221 79 PRS #1 1022 51 #1 B RV 22 423 56 #10 B RV 824 40 MIX RV 325 2 VORTEX ON 126 40 MIX RV 327 13 #10 T VB 128 14 #10 B VB 129 9 GAS T VB 330 10 GAS B VB 331 1 WAIT 9032 3 VORTEX OFF 133 1 WAIT 234 130 MonPrevPk 135 42 DRAIN RV 336 1 WAIT 337 131 Mon Stop 138 132 Save MonPk 139 42 DRAIN RV 40 5

Applied Biosystems


Module B – Conditional: Deprotection/MonPrevPk (continued)


40 111 End loop 141 133 MonBegLoop 342 98 BEGIN LOOP 3 143 56 #10 B RV 20 544 2 VORTEX ON 145 56 #10 B RV 846 40 MIX RV 447 88 RS TO RV 148 93 GAS TO RS 649 91 #10 TO RS 1050 89 RS TO FC 151 40 MIX RV 452 1 WAIT 353 3 VORTEX OFF 154 42 DRAIN RV 35 555 41 VENT RV 256 50 #10 RV-DRN 557 42 DRAIN RV 10 558 99 END LOOP 159 56 #10 B RV 20 260 79 PRS #1 561 51 #1 B RV 22 462 56 #10 B RV 863 40 MIX RV 364 2 VORTEX ON 165 40 MIX RV 366 41 VENT RV 267 88 RS TO RV 168 93 GAS TO RS 569 91 #10 TO RS 570 89 RS TO FC 171 13 #10 T VB 172 14 #10 B VB 173 9 GAS T VB 374 10 GAS B VB 375 98 BEGIN LOOP 676 2 VORTEX ON 1077 3 VORTEX OFF 578 99 END LOOP 179 1 WAIT 280 130 MonPrevPk 181 42 DRAIN RV 382 1 WAIT 383 131 Mon Stop 184 132 Save Mon Pk 1

Applied Biosystems


Module B – Conditional: Deprotection/MonPrevPk (continued)


85 42 DRAIN RV 40 586 134 MonEndLoop 10087 98 BEGIN LOOP 288 13 #10 T VB 189 14 #10 B VB 390 9 GAS T VB 391 10 GAS B VB 592 99 END LOOP 1

Applied Biosystems


Module b – Conditional: MonDoMod(deprot/MonPrevPk)


1 137 Do Mod Mon 12 42 DRAIN RV 40 23 56 #10 B RV 20 24 79 PRS #1 105 51 #1 B RV 22 46 56 #10 B RV 87 40 MIX RV 38 13 #10 T VB 29 14 #10 B VB 210 9 GAS T VB 511 10 GAS B VB 512 98 BEGIN LOOP 313 2 VORTEX ON 60014 3 VORTEX OFF 115 99 END LOOP 116 42 DRAIN RV 317 130 MonPrevPk 118 1 WAIT 319 131 Mon Stop 120 132 Save MonPk 1

Applied Biosystems


Module C – Capping with Ac2O Solution


• FastMoc 1.0 mmol




1 77 PRS #4 10 02 10 GAS B VB 2 03 52 #4 B RV 45 24 40 MIX RV 2 05 41 VENT RV 2 06 88 RS TO RV 1 07 93 GAS TO RS 3 08 89 RS TO FC 1 09 2 VORTEX ON 450 010 3 VORTEX OFF 1 011 88 RS TO RV 1 012 91 #10 TO RS 3 013 89 RS TO FC 1 014 42 DRAIN RV 25 2

Applied Biosystems


Module c – DCM Washes






1 11 # 9 T VB 1 02 12 # 9 B VB 2 03 9 GAS T VB 2 04 10 GAS B VB 2 05 98 BEGIN LOOP 6 0 Wash resin with DCM (6 times)6 55 # 9 B RV 20 57 2 VORTEX ON 1 08 40 MIX RV 2 09 41 VENT RV 1 010 88 RS TO RV 1 011 90 #9 TO RS 5 012 93 GAS TO RS 10 013 90 #9 TO RS 10 014 89 RS TO FC 1 015 40 MIX RV 2 016 1 WAIT 10 017 3 VORTEX OFF 1 018 42 DRAIN RV 15 519 49 #9 RV-DRN 10 020 42 DRAIN RV 10 521 99 END LOOP 1 022 10 GAS B VB 3 023 41 VENT RV 2 024 88 RS TO RV 1 025 93 GAS TO RS 5 026 41 VENT RV 2 027 89 RS TO FC 1 028 42 DRAIN RV 30 529 10 GAS B VB 10 030 9 GAS T VB 10 0

Applied Biosystems


Module D –NMP Washes






1 3 VORTEX OFF 1 02 41 VENT RV 1 03 88 RS TO RV 1 04 93 GAS TO RS 5 05 91 #10 TO RS 10 06 89 RS TO FC 1 07 40 MIX RV 2 08 42 DRAIN RV 45 59 98 BEGIN LOOP 6 1 Wash resin with NMP (6 times)10 56 #10 B RV 20 5 with Add Time of 1 to the loop.11 2 VORTEX ON 1 012 56 #10 B RV 8 013 40 MIX RV 4 014 88 RS TO RV 1 015 93 GAS TO RS 6 016 91 #10 TO RS 10 017 89 RS TO FC 1 018 40 MIX RV 4 019 1 WAIT 3 020 3 VORTEX OFF 1 021 42 DRAIN RV 35 522 41 VENT RV 2 023 50 #10 RV-DRN 5 024 42 DRAIN RV 10 525 99 END LOOP 1 0

Applied Biosystems


Module d – Conditional: MonDoMod (capping/wash)


1 137 Do Mod Mon 12 77 Pressurize #4 103 10 GAS B VB 24 52 #4 B RV 45 25 40 MIX RV 26 41 VENT RV 27 88 RS TO RV 18 93 GAS TO RS 39 89 RS TO FC 110 2 VORTEX ON 45011 3 VORTEX OFF 112 88 RS TO RV 113 91 #10 TO RS 314 89 RS TO FC 115 42 DRAIN RV 25 216 98 BEGIN LOOP 3 117 56 #10 B RV 20 518 2 VORTEX ON 119 56 #10 B RV 810 40 MIX RV 421 88 RS TO RV 122 93 GAS TO RS 623 91 #10 TO RS 1024 89 RS TO FC 125 40 MIX RV 426 1 WAIT 327 3 VORTEX OFF 128 42 DRAIN RV 35 529 41 VENT RV 230 50 #10 RV-DRN 531 42 DRAIN RV 10 532 99 END LOOP 1

Applied Biosystems


Module E –Transfer






1 10 GAS B VB 2 02 5 NEEDLE DWN 10 03 78 PRS #M 5 04 70 PURGE ML 2 05 98 BEGIN LOOP 6 0 Add 3 mL 2.0 M DIEA6 68 MEAS #7 2 07 23 ML TO ACT 2 08 99 END LOOP 1 09 1 WAIT 2 010 20 MIX ACT 1 011 98 BEGIN LOOP 4 0 Transfer to RV12 41 VENT RV 2 013 37 ACT TO RVc 8 014 2 VORTEX ON 5 015 3 VORTEX OFF 1 016 99 END LOOP 1 017 40 MIX RV 1 018 36 #10 B ACT 3 019 20 MIX ACT 4 020 98 BEGIN LOOP 2 021 41 VENT RV 2 022 37 ACT TO RVc 5 023 2 VORTEX ON 5 024 3 VORTEX OFF 1 025 99 END LOOP 1 026 41 VENT RV 2 027 88 RS TO RV 1 028 93 GAS TO RS 5 029 91 #10 TO RS 5 030 89 RS TO FC 1 031 2 VORTEX ON 5 032 40 MIX RV 2 033 21 VENT ACT 2 034 30 #10 A-DRN 5 035 22 DRAIN ACT 5 036 13 #10 T VB 1 037 14 #10 B VB 1 0

Applied Biosystems



38 9 GAS T VB 3 039 10 GAS B VB 3 0

Applied Biosystems


Module F – Clean cartridge, coupling, drain, and NMP washes


1 2 VORTEX ON 1 02 5 NEEDLE DWN 10 03 62 DRAIN CART 10 04 98 BEGIN LOOP 2 05 67 #10 SML N 2 06 62 DRAIN CART 10 07 99 END LOOP 1 08 98 BEGIN LOOP 4 0 Clean cartridge9 65 # 10 CART 24 010 60 MIX CART 10 011 24 CART TO AC 22 012 99 END LOOP 1 013 65 #10 CART 20 014 10 GAS B VB 2 015 98 BEGIN LOOP 40 2 Couple16 2 VORTEX ON 25 017 3 VORTEX OFF 1 018 99 END LOOP 1 019 3 VORTEX OFF 1 020 88 RS TO RV 1 021 91 #10 TO RS 10 022 89 RS TO FC 1 023 42 DRAIN RV 20 5 Drain24 98 BEGIN LOOP 2 025 3 VORTEX OFF 1 026 42 DRAIN RV 35 527 41 VENT RV 3 028 37 ACT TO RVc 25 0 Wash resin with NMP (2 times)29 40 MIX RV 1 030 2 VORTEX ON 1 031 40 MIX RV 5 032 1 WAIT 5 033 99 END LOOP 1 034 22 DRAIN ACT 5 035 24 CART TO AC 22 036 65 # 10 CART 20 037 60 MiX CART 5 038 24 CART TO AC 22 039 3 VORTEX OFF 1 040 42 DRAIN RV 30 541 41 VENT RV 3 042 37 ACT TO RVc 25 0 Wash resin with NMP (1 time)43 40 MIX RV 2 0

Applied Biosystems


Module F – Clean cartridge, coupling, drain, and NMP washes (continued)


44 2 VORTEX ON 1 045 40 MIX RV 3 046 62 DRAIN CART 5 047 60 MIX CART 2 048 61 VENT CART 2 049 22 DRAIN ACT 5 050 98 BEGIN LOOP 2 051 21 VENT ACT 2 052 30 #10 A-DRN 5 053 22 DRAIN ACT 5 054 99 END LOOP 1 055 22 DRAIN ACT 10 056 3 VORTEX OFF 1 057 42 DRAIN RV 40 5

Applied Biosystems


Module F – CondMonPrevPeak: Coupling etc/SkipMod


1 136 SkipModMon 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 26 67 #10 SML N 27 62 DRAIN CART 108 99 END LOOP 19 98 BEGIN LOOP 410 65 #10 CART 2411 60 MIX CART 1012 24 TRANSFER CART 2213 99 END LOOP 114 65 #10 CART 2015 10 GAS B VB 216 133 MonBegLoop 17 98 BEGIN LOOP 40 218 2 VORTEX ON 2519 3 VORTEX OFF 520 99 END LOOP 121 134 MonEndLoop 122 3 VORTEX OFF 123 88 RS TO RV 124 91 #10 TO RS 1025 89 RS TO FC 126 42 DRAIN RV 20 527 98 BEGIN LOOP 228 3 VORTEX OFF 129 42 DRAIN RV 35 530 41 VENT RV 331 37 ACT TO RVc 2532 40 MIX RV 133 2 VORTEX ON 134 40 END LOOP 535 1 WAIT 536 99 END LOOP 137 22 DRAIN ACT 538 24 TRANSFER CART 2239 65 #10 CART 2040 60 VORTEX OFF 541 24 TRANSFER CART 2242 3 VORTEX OFF 143 42 DRAIN RV 30 5

Applied Biosystems


Module F – CondMonPrevPeak: Coupling etc/SkipMod (continued)


44 41 VENT RV 345 37 ACT TO RVc 2546 40 MIX RV 247 2 VORTEX ON 148 40 MIX RV 349 62 DRAIN CART 550 60 MIX CART 251 61 VENT CART 252 22 DRAIN ACT 553 98 BEGIN LOOP 254 21 VENT ACT 255 30 #10 A-DRN 556 22 DRAIN ACT 557 99 END LOOP 158 22 DRAIN ACT 1059 3 VORTEX OFF 160 42 DRAIN RV 40 5

Applied Biosystems


Module f – CondMonPrevPeak: MonDoMod (coupling)


1 137 Do Mod Mon 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 180 26 2 VORTEX ON 257 3 VORTEX OFF 58 99 END LOOP 19 3 VORTEX OFF 110 88 RS TO RV 111 91 #10 TO RS 1012 89 RS TO FC 113 42 DRAIN RV 20 514 98 BEGIN LOOP 215 3 VORTEX OFF 116 42 DRAIN RV 35 517 41 VENT RV 318 37 ACT TO RVc 2519 40 MIX RV 120 2 VORTEX ON 121 40 MIX RV 522 1 WAIT 523 99 END LOOP 124 22 DRAIN ACT 525 24 CART TO ACT 2226 65 #10 CART 2027 60 MIX CART 528 24 CART TO ACT 2229 3 VORTEX OFF 130 42 DRAIN RV 30 531 41 VENT RV 332 37 ACT TO RVc 2533 40 MIX RV 234 2 VORTEX ON 135 40 MIX RV 336 62 DRAIN CART 537 60 MIX CART 238 61 VENT CART 239 22 DRAIN ACT 540 98 BEGIN LOOP 241 21 VENT ACT 242 30 #10 A-DRN 543 22 DRAIN ACT 5

Applied Biosystems


Module f – Conditional: MonDoMod coupling (continued)


44 99 END LOOP 145 22 DRAIN ACT 1046 3 VORTEX OFF 147 42 DRAIN RV 40 5

Applied Biosystems


Module G – Resin Sampling






1 14 #10 B VB 1 02 56 #10 B RV 25 5 Add NMP3 2 VORTEX ON 1 04 40 MIX RV 3 05 91 #10 TO RS 2 06 93 GAS TO RS 2 07 91 #10 TO RS 2 08 93 GAS TO RS 1 09 91 #10 TO RS 4 010 41 VENT RV 1 011 98 BEGIN LOOP 1 012 39 RELAY 0 1 013 88 RS TO RV 1 014 93 GAS TO RS 2 015 91 #10 TO RS 4 016 9 GAS T VB 3 017 13 #10 T VB 1 018 41 VENT RV 2 019 91 #10 TO RS 1 020 48 GAS T RV 2 021 87 TAKE SAMPL 2 0 Resin sample22 89 RS TO FC 1 023 91 #10 TO RS 2 024 93 GAS TO RS 2 025 91 #10 TO RS 2 026 93 GAS TO RS 2 027 91 #10 TO RS 4 028 93 GAS TO RS 4 029 41 VENT RV 2 030 88 RS TO RV 1 031 91 #10 TO RS 10 032 93 GAS TO RS 5 033 91 #10 TO RS 10 034 89 RS TO FC 1 035 39 RELAY 0 1 036 99 END LOOP 1 037 3 VORTEX OFF 1 038 42 DRAIN RV 40 3

Applied Biosystems


Module g – CondMonPrevPeak: MonDoMod (resin sampling)


1 137 Do Mod Mon 12 14 #10 B VB 13 56 #10 B RV 25 54 2 VORTEX ON 15 40 MIX RV 36 91 #10 TO RS 27 93 GAS TO RS 28 91 #10 TO RS 29 93 GAS TO RS 110 91 #10 TO RS 411 41 VENT RV 112 98 BEGIN LOOP 113 39 RELAY 0 114 88 RS TO RV 115 93 GAS TO RS 216 91 #10 TO RS 417 9 GAS T VB 318 13 #10 T VB 119 41 VENT RV 220 91 #10 TO RS 121 48 PRES RV 222 87 TAKE SAMPL 223 89 RS TO FC 124 91 #10 TO RS 225 93 GAS TO RS 226 91 #10 TO RS 227 93 GAS TO RS 228 91 #10 TO RS 429 93 GAS TO RS 430 41 VENT RV 231 88 RS TO RV 132 91 #10 TO RS 1033 93 GAS TO RS 534 91 #10 TO RS 1035 89 RS TO FC 136 39 RELAY 0 137 99 END LOOP 138 3 VORTEX RV 139 42 DRAIN RV 40 3

Applied Biosystems


Module H – Load and Cap


1 55 # 9 B RV 30 0 Add DCM to resin2 88 RS TO RV 1 03 90 #9 TO RS 10 04 89 RS TO FC 1 05 40 MIX RV 3 06 2 VORTEX ON 20 07 3 VORTEX OFF 1 08 42 DRAIN RV 25 09 110 begin loop 3 0 3 Amino Acid cartridges10 4 PRINT CART 10 011 6 NEEDLE UP 10 012 7 EJECT CART 10 013 8 ADVAN CART 10 014 5 NEEDLE DWN 10 015 10 GAS B VB 2 016 64 #9 CART 4 017 65 #10 CART 3 018 60 MIX CART 300 019 98 BEGIN LOOP 5 0 Transfer to RV20 41 VENT RV 4 021 96 CRT TO RVc 8 022 99 END LOOP 1 023 64 # 9 CART 8 024 60 MIX CART 4 025 78 PRS #M 10 026 98 BEGIN LOOP 2 0 Add DCC27 69 MEAS #8 3 028 43 ML TO RV 4 029 99 END LOOP 1 030 77 PRS #4 10 031 17 #4 B VB 1 032 10 GAS B VB 3 033 52 #4 B RV 1 0 Add DMAP34 44 CART TO RV 8 035 2 VORTEX ON 20 036 3 VORTEX OFF 1 037 111 end loop 1 038 67 #10 SML N 10 039 62 DRAIN CART 10 040 98 BEGIN LOOP 4 041 88 RS TO RV 1 042 93 GAS TO RS 3 0

Applied Biosystems


Module H – Load and Cap (continued)Step# Fxn# Function Name Time Add Key Events

43 89 RS TO FC 1 044 2 VORTEX ON 600 045 3 VORTEX OFF 1 046 99 END LOOP 1 047 6 NEEDLE UP 10 048 7 EJECT CART 10 049 8 ADVAN CART 10 050 5 NEEDLE DWN 10 051 64 # 9 CART 8 052 60 MIX CART 180 0 Dissolve benzoic anhydride53 88 RS TO RV 1 054 90 #9 TO RS 10 055 89 RS TO FC 1 056 42 DRAIN RV 60 0 Drain57 98 BEGIN LOOP 2 058 55 #9 B RV 20 0 DCM and59 54 #6 B RV 20 0 MeOH wash60 40 MIX RV 10 061 2 VORTEX ON 20 062 3 VORTEX OFF 10 063 42 DRAIN RV 3 0 Drain64 99 END LOOP 1 065 98 BEGIN LOOP 3 066 55 #9 B RV 35 0 DCM wash67 88 RS TO RV 1 068 90 #9 TO RS 10 069 89 RS TO FC 1 070 40 MIX RV 3 071 2 VORTEX O 15 072 3 VORTEX OFF 1 073 42 DRAIN RV 45 074 99 END LOOP 1 075 98 BEGIN LOOP 4 076 41 VENT RV 4 077 96 CRT TO RVc 8 0 Transfer benzoic anhydride to RV78 99 END LOOP 1 079 64 # 9 CART 6 080 60 MIX CART 5 081 77 PRS #4 10 082 52 #4 B RV 4 0 Add DMAP83 44 CART TO RV 8 084 55 #9 B RV 5 085 40 MIX RV 3 086 88 RS TO RV 1 0

Applied Biosystems


Module H – Load and Cap (continued)


87 93 GAS TO RS 4 088 89 RS TO FC 1 089 2 VORTEX ON 1 090 98 BEGIN LOOP 4 091 67 #10 SML N 3 092 62 DRAIN CART 10 093 99 END LOOP 1 094 65 #10 CART 5 095 10 GAS B VB 5 096 1 WAIT 300 0

Applied Biosystems


Module H – Conditional: Load and Cap





1 135 Mon Reset 12 55 # 9 B RV 30 0 Add DCM to resin3 88 RS TO RV 1 04 90 #9 TO RS 10 05 89 RS TO FC 1 06 40 MIX RV 3 07 2 VORTEX ON 20 08 3 VORTEX OFF 1 09 42 DRAIN RV 25 010 110 begin loop 3 0 3 Amino Acid cartridges11 4 PRINT CART 10 012 6 NEEDLE UP 10 013 7 EJECT CART 10 014 8 ADVAN CART 10 015 5 NEEDLE DWN 10 016 10 GAS B VB 2 017 64 #9 CART 4 018 65 #10 CART 3 019 60 MIX CART 300 020 98 BEGIN LOOP 5 0 Transfer to RV21 41 VENT RV 4 022 96 CRT TO RVc 8 023 99 END LOOP 1 024 64 # 9 CART 8 025 60 MIX CART 4 026 78 PRS #M 10 027 98 BEGIN LOOP 2 0 Add DCC28 69 MEAS #8 3 029 43 ML TO RV 4 030 99 END LOOP 1 031 77 PRS #4 10 032 17 #4 B VB 1 033 10 GAS B VB 3 034 52 #4 B RV 1 0 Add DMAP35 44 CART TO RV 8 036 2 VORTEX ON 20 037 3 VORTEX OFF 1 038 111 end loop 1 039 67 #10 SML N 10 0

Applied Biosystems


Module H – Conditional: Load and Cap (continued)


40 62 DRAIN CART 10 041 98 BEGIN LOOP 4 042 88 RS TO RV 1 043 93 GAS TO RS 3 044 89 RS TO FC 1 045 2 VORTEX ON 600 046 3 VORTEX OFF 1 047 99 END LOOP 1 048 6 NEEDLE UP 10 049 7 EJECT CART 10 050 8 ADVAN CART 10 051 5 NEEDLE DWN 10 052 64 # 9 CART 8 053 60 MIX CART 180 0 Dissolve benzoic anhydride54 88 RS TO RV 1 055 90 #9 TO RS 10 056 89 RS TO FC 1 057 42 DRAIN RV 60 0 Drain58 98 BEGIN LOOP 2 059 55 #9 B RV 20 0 DCM and60 54 #6 B RV 20 0 MeOH wash61 40 MIX RV 10 062 2 VORTEX ON 20 063 3 VORTEX OFF 10 064 42 DRAIN RV 3 0 Drain65 99 END LOOP 1 066 98 BEGIN LOOP 3 067 55 #9 B RV 35 0 DCM wash68 88 RS TO RV 1 069 90 #9 TO RS 10 070 89 RS TO FC 1 071 40 MIX RV 3 072 2 VORTEX O 15 073 3 VORTEX OFF 1 074 42 DRAIN RV 45 075 99 END LOOP 1 076 98 BEGIN LOOP 4 077 41 VENT RV 4 078 96 CRT TO RVc 8 0 Transfer benzoic anhydride to RV79 99 END LOOP 1 080 64 # 9 CART 6 081 60 MIX CART 5 082 77 PRS #4 10 083 52 #4 B RV 4 0 Add DMAP

Applied Biosystems


Module H – Conditional: Load and Cap (continued)


84 44 CART TO RV 8 085 55 #9 B RV 5 086 40 MIX RV 3 087 88 RS TO RV 1 088 93 GAS TO RS 4 089 89 RS TO FC 1 090 2 VORTEX ON 1 091 98 BEGIN LOOP 4 092 67 #10 SML N 3 093 62 DRAIN CART 10 094 99 END LOOP 1 095 65 #10 CART 5 096 10 GAS B VB 5 097 1 WAIT 300 0

Module I – Fifteen-minute wait


1 1 WAIT 900 0

Applied Biosystems


FastMoc 0.25 mmol Chemistry

Module A – Activation


1 1 WAIT 1 02 4 PRINT CART 10 03 6 NEEDLE UP 10 04 7 EJECT CART 10 05 8 ADVAN CART 10 06 5 NEEDLE DWN 10 07 14 #10 B VB 1 08 9 GAS T VB 2 09 65 #10 CART 5 010 60 MIX CART 5 011 78 PRS #M 10 012 18 #5 B VB 1 013 94 #5 TO CART 8 014 98 BEGIN LOOP 6 015 2 VORTEX ON 1 016 60 MIX CART 30 017 3 VORTEX OFF 1 018 60 MIX CART 30 019 99 END LOOP 1 0

Applied Biosystems




• FastMoc 0.25 CondMonPrevPk

• FastMoc 0.25 CondMon1-X


1 1 WAIT 1 02 98 BEGIN LOOP 23 13 #10 T VB 14 14 #10 B VB 35 9 GAS T VB 26 10 GAS B VB 57 99 END LOOP 18 4 PRINT CART 10 09 6 NEEDLE UP 10 010 7 EJECT CART 10 011 8 ADVAN CART 10 012 5 NEEDLE DWN 10 013 78 PRS #M 10 014 65 #10 CART 5 015 60 MIX CART 5 016 18 #5 B VB 1 017 94 #5 TO CART 8 018 98 BEGIN LOOP 6 019 2 VORTEX ON 1 020 60 MIX CART 30 021 3 VORTEX OFF 1 022 60 MIX CART 30 023 99 END LOOP 1 024 13 #10 T VB 125 14 #10 B VB 326 9 GAS T VB 227 10 GAS B VB 5

Applied Biosystems


Module A – Monitoring: Activation


• FastMoc 0.25 MonPrevPk

• FastMoc 0.25 Mon1st-X


1 1 WAIT 12 4 PRINT CART 103 6 NEEDLE UP 104 7 EJECT CART 105 8 ADVAN CART 106 5 NEEDLE DWN 107 14 #10 B VB 18 9 GAS T VB 29 65 #10 CART 510 60 MIX CART 511 78 PRES #M 1012 18 #5 B VB 113 94 #5 TO CART 814 98 BEGIN LOOP 615 2 VORTEX ON 116 60 MIX CART 3017 3 VORTEX OFF 118 60 MIX CART 3019 99 END LOOP 120 13 #10 T VB 121 14 #10 B VB 322 9 GAS T VB 223 10 GAS B VB 5

Applied Biosystems


Module a – Conditional: MonDoMod (activation/transfer)





1 137 DoModMon 12 1 WAIT 13 98 BEGIN LOOP 24 13 #10 T VB 15 14 #10 B VB 36 9 GAS T VB 27 10 GAS B VB 58 99 END LOOP 19 150 MATCH CART 1010 6 NEEDLE UP 1011 7 EJECT CART 1012 8 ADVAN CART 1013 5 NEEDLE DWN 1014 78 PRS #M 1015 65 #10 CART 516 60 MIX CART 517 18 #5 B VB 118 94 #5 TO CART 819 98 BEGIN LOOP 620 2 VORTEX ON 121 60 MIX CART 3022 3 VORTEX OFF 123 60 MIX CART 3024 99 END LOOP 125 1 WAIT 126 78 PRS #M 1027 10 GAS B VB 228 5 NEEDLE DWN 1029 70 PURGE ML 230 98 BEGIN LOOP 231 68 MEAS #7 232 63 ML TO CART 433 99 END LOOP 134 60 MIX CART 535 98 BEGIN LOOP 436 41 VENT RV 237 96 CRT TO RVc 638 2 VORTEX ON 3

Applied Biosystems


Module a – Conditional: MonDoMod (activation/transfer) continued...


39 3 VORTEX OFF 140 99 END LOOP 141 65 #10 CART 342 60 MIX CART 343 98 BEGIN LOOP 344 41 VENT RV 245 96 CRT TO RVc 546 99 END LOOP 147 40 MIX RV 248 93 GAS TO RS 249 41 VENT RV 250 88 RS TO RV 151 93 GAS TO RS 352 41 VENT RV 253 89 RS TO FC 154 2 VORTEX ON 155 62 DRAIN CART 556 40 MIX RV 1

Applied Biosystems


Module B – Piperidine deprotection


1 1 WAIT 1 02 58 INTERRUPT 0 03 56 #10 B RV 13 14 88 RS TO RV 1 05 91 #10 TO RS 4 06 89 RS TO FC 1 07 40 MIX RV 2 08 2 VORTEX ON 3 09 40 MIX RV 2 010 3 VORTEX OFF 1 011 42 DRAIN RV 15 112 56 #10 B RV 11 213 79 PRS #1 10 014 51 #1 B RV 8 115 56 #10 B RV 4 016 40 MIX RV 2 017 98 BEGIN LOOP 6 018 2 VORTEX ON 15 019 3 VORTEX OFF 15 020 99 END LOOP 1 021 42 DRAIN RV 18 122 56 #10 B RV 12 223 79 PRS #1 5 024 51 #1 B RV 10 125 56 #10 B RV 4 026 40 MIX RV 2 027 88 RS TO RV 1 028 93 GAS TO RS 3 029 89 RS TO FC 1 030 41 VENT RV 2 031 2 VORTEX ON 1 032 98 BEGIN LOOP 2 033 13 #10 T VB 1 034 14 #10 B VB 3 035 9 GAS T VB 5 036 10 GAS B VB 5 037 99 END LOOP 1 038 1 WAIT 180 0

Applied Biosystems


Module B – Deprotection/Mon 1st-X


1 1 WAIT 12 58 INTERRUPT 03 135 Mon Reset 14 42 DRAIN RV 185 98 BEGIN LOOP 36 56 #10 B RV 13 17 88 RS TO RV 18 91 #10 TO RS 49 89 RS TO FC 110 93 GAS TO RS 211 2 VORTEX ON 512 40 MIX RV 213 3 VORTEX OFF 114 42 DRAIN RV 15 115 99 END LOOP 116 56 #10 B RV 11 217 79 PRS #1 1018 51 #1 B RV 8 119 56 #10 B RV 420 40 MIX RV 221 2 VORTEX ON 15022 3 VORTEX OFF 123 42 DRAIN RV 324 13 #10 T VB 225 128 Mon1stPk- X 4526 1 WAIT 327 131 Mon Stop 128 132 Save MonPk 129 133 MonBegLoop 430 42 DRAIN RV 18 131 98 BEGIN LOOP 332 56 #10 B RV 13 133 88 RS TO RV 134 91 #10 TO RS 435 89 RS TO FC 136 40 MIX RV 237 2 VORTEX ON 538 40 MIX RV 239 3 VORTEX OFF 140 42 DRAIN RV 18 141 50 #10 RV-DRN 542 42 DRAIN RV 10 143 99 END LOOP 1

Applied Biosystems


Module B – Deprotection/ Mon 1st-X (continued)


44 56 #10 B RV 12 245 79 PRS #1 546 51 #1 B RV 10 147 56 #10 B RV 448 40 MIX RV 249 2 VORTEX ON 15050 3 VORTEX OFF 151 42 DRAIN RV 352 128 Mon1stPk - X 4553 1 WAIT 354 131 Mon Stop 155 132 Save Mon 156 134 MonEndLoop 10057 42 DRAIN RV 1858 10 GAS B VB 359 40 MIX RV 260 41 VENT RV 261 88 RS TO RV 162 93 GAS TO RS 363 41 VENT RV 164 89 RS TO FC 165 98 BEGIN LOOP 266 13 #10 T VB 367 14 #10 B VB 368 9 GAS T VB 369 10 GAS B VB 370 99 END LOOP 1

Applied Biosystems


Module B – Deprotection/MonPrevPk


1 1 WAIT 12 58 INTERRUPT 03 135 Mon Reset 14 110 begin loop 25 42 DRAIN RV 18 16 98 BEGIN LOOP 37 56 #10 B RV 13 18 88 RS TO RV 19 91 #10 TO RS 410 89 RS TO FC 111 93 GAS TO RS 212 2 VORTEX ON 513 40 MIX RV 214 3 VORTEX OFF 115 42 DRAIN RV 18 116 50 #10 RV-DRN 517 42 DRAIN RV 10 118 99 END LOOP 119 56 #10 B RV 12 220 79 PRS #1 1021 51 #1 B RV 10 122 56 #10 B RV 423 40 MIX RV 224 2 VORTEX ON 15025 3 VORTEX OFF 126 40 MIX RV 127 130 MonPrevPk 128 42 DRAIN RV 329 1 WAIT 330 131 Mon Stop 131 132 Save Mon 132 111 end loop 133 133 MonBegLoop 334 42 DRAIN RV 18 135 98 BEGIN LOOP 336 56 #10 B RV 13 137 88 RS TO RV 138 91 #10 TO RS 439 89 RS TO FC 140 40 MIX RV 241 2 VORTEX ON 542 40 MIX RV 243 3 VORTEX OFF 144 42 DRAIN RV 18 1

Applied Biosystems


Module B – Deprotection/ MonPrevPk(continued)


45 50 #10 RV-DRN 546 42 DRAIN RV 10 147 99 END LOOP 148 56 #10 B RV 12 249 79 PRS #1 550 51 #1 B RV 10 151 56 #10 B RV 452 40 MIX RV 253 2 VORTEX ON 15054 3 VORTEX OFF 155 40 MIX RV 156 130 MonPrevPk 157 42 DRAIN RV 358 1 WAIT 359 131 Mon Stop 160 132 Save Mon 161 134 MonEndLoop 10062 42 DRAIN RV 1863 10 GAS B VB 364 40 MIX RV 265 41 VENT RV 266 88 RS TO RV 167 93 GAS TO RS 368 41 VENT RV 169 89 RS TO FC 170 98 BEGIN LOOP 271 13 #10 T VB 372 14 #10 B VB 373 9 GAS T VB 374 10 GAS B VB 375 99 END LOOP 1

Applied Biosystems


Module B – Conditional: Deprotection/Mon1st-X


1 1 WAIT 12 58 INTERRUPT 03 135 Mon Reset 14 42 DRAIN RV 105 98 BEGIN LOOP 36 56 #10 B RV 13 17 88 RS TO RV 18 91 #10 TO RS 49 89 RS TO FC 110 93 GAS TO RS 211 2 VORTEX ON 512 40 MIX RV 213 3 VORTEX OFF 114 42 DRAIN RV 18 115 99 END LOOP 116 56 #10 B RV 12 217 79 PRS #1 1018 51 #1 B RV 1019 56 #10 B RV 420 40 MIX RV 221 2 VORTEX ON 15022 3 VORTEX OFF 123 42 DRAIN RV 324 13 #10 T VB 225 128 Mon 1stPk - X 4526 1 WAIT 327 131 Mon Stop 128 132 Save Mon 129 133 MonBegLoop 330 42 DRAIN RV 18 131 98 BEGIN LOOP 332 56 #10 B RV 13 133 88 RS TO RV 134 91 #10 TO RS 435 89 RS TO FC 136 93 GAS TO RS 237 2 VORTEX ON 538 40 MIX RV 239 3 VORTEX OFF 140 42 DRAIN RV 18 141 50 #10 RV-DRN 542 42 DRAIN RV 10 143 99 END LOOP 1

Applied Biosystems


Module B – Conditional: Deprotection/ Mon1st-X


44 56 #10 B RV 12 245 79 PRS #1 546 51 #1 B RV 10 147 56 #10 B RV 448 40 MIX RV 249 2 VORTEX ON 15050 3 VORTEX OFF 151 42 DRAIN RV 352 128 Mon1stPk - X 4553 1 WAIT 354 131 Mon Stop 155 132 Save Mon 156 134 MonEndLoop 10057 42 DRAIN RV 1858 10 GAS B VB 359 40 MIX RV 260 41 VENT RV 261 88 RS TO RV 162 93 GAS TO RS 363 41 VENT RV 164 89 RS TO FC 165 98 BEGIN LOOP 266 13 #10 T VB 367 14 #10 B VB 368 9 GAS T VB 369 10 GAS B VB 370 99 END LOOP 1

Applied Biosystems


Module B – Conditional: Deprotection/ MonPrevPk


1 1 WAIT 1 02 58 INTERRUPT 0 03 135 Mon Reset 1 04 110 begin loop 2 05 42 DRAIN RV 18 16 98 BEGIN LOOP 3 07 56 #10 B RV 13 18 88 RS TO RV 1 09 91 #10 TO RS 4 010 89 RS TO FC 1 011 93 GAS TO RS 2 012 2 VORTEX ON 5 013 40 MIX RV 2 014 3 VORTEX OFF 1 015 42 DRAIN RV 15 116 50 #10 RV-DRN 5 017 42 DRAIN RV 10 118 99 END LOOP 1 019 56 #10 B RV 12 220 79 PRS #1 10 021 51 #1 B RV 10 122 56 #10 B RV 4 023 40 MIX RV 2 024 2 VORTEX ON 150 025 3 VORTEX OFF 1 026 40 MIX RV 2 027 130 MonPrevPk 1 028 42 DRAIN RV 3 029 1 WAIT 3 030 131 Mon Stop 1 031 132 Save MonPk 1 032 111 end loop 1 033 133 MonBegLoop 2 034 42 DRAIN RV 18 135 98 BEGIN LOOP 3 036 56 #10 B RV 13 137 88 RS TO RV 1 038 91 #10 TO RS 4 039 89 RS TO FC 1 040 93 GAS TO RS 2 041 2 VORTEX ON 5 042 40 MIX RV 2 043 3 VORTEX OFF 1 0

Applied Biosystems


Module B – Conditional: Deprotection/ MonPrevPk


44 42 DRAIN RV 18 145 50 #10 RV-DRN 5 046 42 DRAIN RV 10 147 99 END LOOP 1 048 56 #10 B RV 12 249 79 PRS #1 10 050 51 #1 B RV 10 151 56 #10 B RV 4 052 40 MIX RV 2 053 2 VORTEX ON 150 054 3 VORTEX OFF 1 055 40 MIX RV 1 056 130 Mon PrevPk 1 057 42 DRAIN RV 3 058 1 WAIT 3 059 131 Mon Stop 1 060 132 Save MonPk 1 061 134 MonEndLoop 100 062 42 DRAIN RV 18 063 10 GAS B VB 3 064 40 MIX RV 2 065 41 VENT RV 2 066 88 RS TO RV 1 067 93 GAS TO RS 3 068 41 VENT RV 1 069 89 RS TO FC 1 070 98 BEGIN LOOP 2 071 13 #10 T VB 3 072 14 #10 B VB 3 073 9 GAS T VB 3 074 10 GAS B VB 3 075 99 END LOOP 1 0

Applied Biosystems


Module b – Conditional: MonDoMod (deprotection/Mon1-X)


1 137 Do Mod Mon 12 42 DRAIN RV 18 23 56 #10 B RV 12 24 79 PRS #1 105 51 #1 B RV 10 16 56 #10 B RV 47 40 MIX RV 28 13 #10 T VB 29 14 #10 B VB 210 9 GAS T VB 511 10 GAS B VB 512 98 BEGIN LOOP 313 2 VORTEX ON 60014 3 VORTEX OFF 115 99 END LOOP 116 42 DRAIN RV 217 128 Mon 1stPk-X 4518 1 WAIT 319 131 Mon Stop 120 132 Save MonPk 1

Applied Biosystems


Module b – Conditional: MonDoMod (deprotection/MonPrevPk)



Applied Biosystems


Module C –Acetic anhydride capping

This module is written with the acetic anhydride solution in Bottle 4. If loading with DMAP catalysis, remove the DMAP bottle after the loading steps, rinse out the lines, and put on a bottle of acetic anhydride solution. See Loading with HMP resin, followed by capping with acetic anhydride on page 7-16.








1 77 PRS #4 10 02 10 GAS B VB 2 03 52 #4 B RV 35 24 40 MIX RV 2 05 41 VENT RV 2 06 88 RS TO RV 1 07 93 GAS TO RS 3 08 91 #10 TO RS 29 93 GAS TO RS 3 010 89 RS TO FC 1 011 2 VORTEX ON 300 012 3 VORTEX OFF 1 013 88 RS TO RV 1 014 91 #10 TO RS 3 015 89 RS TO FC 1 016 93 GAS TO RS 3 017 42 DRAIN RV 20 2

Applied Biosystems


Module c – DCM washes








1 1 WAIT 12 12 #9 B VB 13 9 GAS T VB 24 10 GAS B VB 25 98 BEGIN LOOP 66 55 #9 B RV 12 17 40 MIX RV 28 2 VOTEX ON 19 41 VENT RV 110 88 RS TO RV 111 90 #9 TO RS 212 93 GAS TO RS 213 90 #9 TO RS 514 89 RS TO FC 115 40 MIX RV 216 1 WAIT 517 3 VORTEX OFF 118 42 DRAIN RV 10 119 41 VENT RV 220 49 #9 RV-DRN 521 42 DRAIN RV 15 122 99 END LOOP 123 10 GAS B VB 224 93 GAS TO RS 525 41 VENT RV 226 88 RS TO RV 127 93 GAS TO RS 528 41 VENT RV 229 89 RS TO FC 130 42 DRAIN RV 3031 29 #9 ACT-DRN 532 22 DRAIN ACT 3033 11 #9 T VB 134 12 #9 B VB 1

Applied Biosystems



35 10 GAS B VB 1036 9 GAS T VB 10

Module D – NMP washes








1 1 WAIT 12 3 VORTEX OFF 13 42 DRAIN RV 18 24 98 BEGIN LOOP 5 15 41 VENT RV 26 50 #10 RV-DRN 37 42 DRAIN RV 5 18 56 #10 B RV 13 19 2 VORTEX ON 510 40 MIX RV 511 88 RS TO RV 112 91 #10 TO RS 213 89 RS TO FC 114 93 GAS TO RS 215 1 WAIT 1516 3 VORTEX OFF 117 42 DRAIN RV 15 118 99 END LOOP 1

Applied Biosystems







1 137 Do Mod Mon 12 77 PRS #4 103 10 GAS B VB 24 52 #4 B RV 35 25 40 MIX RV 26 41 VENT RV 27 88 RS TO RV 18 93 GAS TO RS 39 91 #10 TO RS 210 93 GAS TO RS 211 89 RS TO FC 112 2 VORTEX ON 30013 3 VORTEX OFF 114 88 RS TO RV 115 91 #10 TO RS 316 89 RS TO FC 117 42 DRAIN RV 20 118 98 BEGIN LOOP 3 119 41 VENT RV 220 50 #10 RV-DRN 221 42 DRAIN RV 5 122 56 #10 B RV 13 123 40 MIX RV 224 2 VORTEX ON 1025 88 RS TO RV 126 91 #10 TO RS 227 89 RS TO FC 128 93 GAS TO RS 229 3 VORTEX OFF 130 42 DRAIN RV 15 131 99 END LOOP 1

Applied Biosystems


Module E – Transfer








1 1 WAIT 12 78 PRS #M 103 10 GAS B VB 24 5 NEEDLE DWN 105 70 PURGE ML 26 98 BEGIN LOOP 27 68 MEAS #7) 28 63 ML TO CART 49 99 END LOOP 110 60 MIX CART 511 98 BEGIN LOOP 412 41 VENT RV 213 96 CRT TO RVc 614 2 VORTEX ON 315 3 VORTEX OFF 116 99 END LOOP 117 65 #10 CART 318 60 MIX CART 319 98 BEGIN LOOP 320 41 VENT RV 221 96 CRT TO RVc 522 99 END LOOP 123 40 MIX RV 224 93 GAS TO RS 225 41 VENT RV 226 88 RS TO RV 127 93 GAS TO RS 328 41 VENT RV 229 89 RS TO FC 130 2 VORTEX ON 131 62 DRAIN CART 532 40 MIX RV 1

Applied Biosystems


Module F – Clean, couple, drain, and wash


1 1 WAIT 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 36 67 #10 SML N 27 62 DRAIN CART 58 99 END LOOP 19 98 BEGIN LOOP 310 65 #10 CART 2411 60 MIX CART 1012 24 CART TO AC 2013 62 DRAIN CART 1014 99 End Loop UPPER 115 98 BEGIN LOOP 216 67 #10 SML N 217 62 DRAIN CART 1018 99 End Loop UPPER 119 62 DRAIN CART 1020 60 MIX CART 521 61 VENT CART 222 98 BEGIN LOOP 30 223 2 VORTEX ON 1524 3 VORTEX OFF 1325 41 VENT RV 226 99 End Loop UPPER 127 88 RS TO RV 128 91 #10 TO RS 529 89 RS TO FC 130 98 BEGIN LOOP 431 3 VORTEX OFF 132 28 GAS T ACT 433 42 DRAIN RV 15 134 38 ACT TO RVo 1035 40 MIX RV 136 2 VORTEX ON 337 40 MIX RV 238 99 END LOOP 139 22 DRAIN ACT 540 3 VORTEX OFF 141 42 DRAIN RV 15 1

Applied Biosystems


Module F – Clean, couple, drain, and wash, with feedback





1 1 WAIT 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 36 67 #10 SML N 27 62 DRAIN CART 58 99 END LOOP 19 98 BEGIN LOOP 310 65 #10 CART 2411 60 MIX CART 1012 24 CART TO AC 2013 62 DRAIN CART 1014 99 END LOOP 115 98 BEGIN LOOP 216 67 #10 SML N 217 62 DRAIN CART 1018 99 END LOOP 119 62 DRAIN CART 1020 60 MIX CART 521 61 VENT CART 222 133 MonBegLoop23 98 BEGIN LOOP 30 224 2 VORTEX ON 1525 3 VORTEX OFF 1326 41 VENT RV 227 99 END LOOP 128 134 MonEndLoop 129 88 RS TO RV 130 91 #10 TO RS 531 89 RS TO FC 132 98 BEGIN LOOP 433 3 VORTEX OFF 134 28 GAS T ACT 435 42 DRAIN RV 15 136 38 ACT TO RVo 1037 40 MIX RV 138 2 VORTEX ON 339 40 MIX RV 240 99 END LOOP 141 22 DRAIN ACT 542 3 VORTEX OFF 143 42 DRAIN RV 15 1

Applied Biosystems


Module F – Conditional: Coupling etc/SkipMod





1 136 SkipModMon 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 36 67 #10 SML N 27 62 DRAIN CART 58 99 END LOOP 19 98 BEGIN LOOP 310 65 #10 CART 2411 60 MIX CART 1012 24 CART TO AC 2013 62 DRAIN CART 1014 99 End Loop UPPER 115 98 BEGIN LOOP 216 67 #10 SML N 217 62 DRAIN CART 1018 99 End Loop UPPER 119 62 DRAIN CART 1020 60 MIX CART 521 61 VENT CART 222 98 BEGIN LOOP 30 223 2 VORTEX ON 1524 3 VORTEX OFF 1325 41 VENT RV 226 99 End Loop UPPER 127 88 RS TO RV 128 91 #10 TO RS 529 89 RS TO FC 130 93 GAS TO RS 231 98 BEGIN LOOP 432 3 VORTEX OFF 133 28 GAS T ACT 434 42 DRAIN RV 15 135 38 ACT TO RVo 1036 40 MIX RV 137 2 VORTEX ON 338 40 MIX RV 239 99 END LOOP 1

Applied Biosystems


Module F – Conditional: Coupling etc/SkipMod (continued)


40 22 DRAIN ACT 541 3 VORTEX OFF 142 42 DRAIN RV 15 1

Applied Biosystems


Module f – Conditional: MonDoMod (Coupling)





1 137 Do ModMon 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 36 67 #10 SML N 27 62 DRAIN CART 58 99 END LOOP 19 98 BEGIN LOOP 310 65 #10 CART 2411 60 MIX CART 1012 24 CART TO AC 2013 62 DRAIN CART 1014 99 END LOOP 115 98 BEGIN LOOP 216 67 #10 SML N 217 62 DRAIN CART 1018 99 END LOOP 119 62 DRAIN CART 1020 60 MIX CART 521 61 VENT CART 222 98 BEGIN LOOP 100 223 2 VORTEX ON 1524 3 VORTEX OFF 1325 41 VENT RV 226 99 END LOOP 127 88 RS TO RV 128 91 #10 TO RS 529 89 RS TO FC 130 93 GAS TO RS 231 98 BEGIN LOOP 432 3 VORTEX OFF 133 28 GAS T ACT 434 42 DRAIN RV 15 135 38 ACT TO RVo 1036 40 MIX RV 137 2 VORTEX ON 338 40 MIX RV 239 99 END LOOP 140 22 DRAIN ACT 541 3 VORTEX OFF 142 42 DRAIN RV 15 1

Applied Biosystems


Module G – Resin sampling








1 1 WAIT 12 14 #10 B VB 13 56 #10 B RV 13 14 2 VORTEX ON 15 40 MIX RV 26 91 #10 TO RS 27 93 GAS TO RS 28 91 #10 TO RS 29 93 GAS TO RS 110 91 #10 TO RS 411 41 VENT RV 112 98 Loop UPPER 113 39 RELAY 0 114 88 RS TO RV 115 93 GAS TO RS 216 91 #10 TO RS 417 9 GAS T VB 318 13 #10 T VB 119 41 VENT RV 220 91 #10 TO RS 121 48 GAS T RV 222 87 TAKE SAMPL 223 89 RS TO FC 124 91 #10 TO RS 225 93 GAS TO RS 226 91 #10 TO RS 227 93 GAS TO RS 228 91 #10 TO RS 429 93 GAS TO RS 430 41 VENT RV 231 88 RS TO RV 132 91 #10 TO RS 333 93 GAS TO RS 334 91 #10 TO RS 535 89 RS TO FC 136 39 RELAY 0 137 99 END LOOP 1


Applied Biosystems


38 3 VORTEX OFF 139 42 DRAIN RV 18 1

Applied Biosystems


Module g – Conditional: MonDoMod (resin sampling)





1 137 Do ModMon 12 1 WAIT 13 14 #10 B VB 14 56 #10 B RV 13 15 2 VORTEX ON 16 40 MIX RV 27 91 #10 TO RS 28 93 GAS TO RS 29 91 #10 TO RS 210 93 GAS TO RS 111 91 #10 TO RS 412 41 VENT RV 113 98 Loop UPPER 114 39 RELAY 0 115 88 RS TO RV 116 93 GAS TO RS 217 91 #10 TO RS 418 9 GAS T VB 319 13 #10 T VB 120 41 VENT RV 221 91 #10 TO RS 122 48 GAS T RV 223 87 TAKE SAMPL 224 89 RS TO FC 125 91 #10 TO RS 226 93 GAS TO RS 227 91 #10 TO RS 228 93 GAS TO RS 229 91 #10 TO RS 430 93 GAS TO RS 431 41 VENT RV 232 88 RS TO RV 133 91 #10 TO RS 334 93 GAS TO RS 335 91 #10 TO RS 536 89 RS TO FC 137 93 GAS TO RS 238 39 RELAY 0 139 99 END LOOP 140 3 VORTEX OFF 141 42 DRAIN RV 18 1

Applied Biosystems


Module H – Load and cap







Step# Fxn# Function Name Time Add

1 1 WAIT 12 55 #9 B RV 203 88 RS TO RV 14 90 #9 TO RS 65 89 RS TO FC 16 40 MIX RV 27 2 VORTEX ON 18 4 SAVE CART 109 6 NEEDLE UP 1010 7 EJECT CART 1011 8 ADVAN CART 1012 5 NEEDLE DWN 1013 10 GAS B VB 214 64 #9 CART 415 65 #10 CART 316 60 MIX CART 30017 3 VORTEX OFF 118 42 DRAIN RV 2019 98 BEGIN LOOP 520 41 VENT RV 221 96 CRT TO RVc 822 99 END LOOP 123 64 #9 CART 824 60 MIX CART 425 78 PRS #M 1026 98 BEGIN LOOP 227 69 MEAS #8 328 43 ML TO RV 429 99 END LOOP 130 77 PRS #4 1031 17 #4 B VB 132 10 GAS B VB 233 52 #4 B RV 134 44 CART TO RV 1035 55 #9 B RV 2

Applied Biosystems


Module H – Load and cap (continued)


36 40 MIX RV 237 67 #10 SML N 538 62 DRAIN CART 1039 98 BEGIN LOOP 340 41 VENT RV 241 88 RS TO RV 142 93 GAS TO RS 343 89 RS TO FC 144 2 VORTEX ON 60045 3 VORTEX OFF 146 99 END LOOP 147 6 NEEDLE UP 1048 7 EJECT CART 1049 8 ADVAN CART 1050 5 NEEDLE DWN 1051 64 #9 CART 552 60 MIX CART 18053 41 VENT RV 254 88 RS TO RV 155 90 #9 TO RS 656 89 RS TO FC 157 42 DRAIN RV 3058 98 Loop UPPER 259 55 #9 B RV 1260 54 #6 B RV 1261 40 MIX RV 1062 2 VORTEX ON 1063 3 VORTEX OFF 164 42 DRAIN RV 2565 99 END LOOP 166 98 BEGIN LOOP 567 55 #9 B RV 1568 88 RS TO RV 169 90 #9 TO RS 670 89 RS TO FC 171 40 MIX RV 272 2 VORTEX ON 1073 3 VORTEX OFF 174 42 DRAIN RV 2075 99 END LOOP 176 98 BEGIN LOOP 477 41 VENT RV 278 96 CRT TO RVc) 679 99 END LOOP 180 64 #9 CART 6

Applied Biosystems




81 60 MIX CART 582 77 PRS #4 1083 17 #4 B VB 184 10 GAS B VB 285 52 #4 B RV 286 44 CART TO RV 887 55 #9 B RV 288 40 MIX RV 289 88 RS TO RV 190 93 GAS TO RS 491 89 RS TO FC 192 2 VORTEX ON 193 98 BEGIN LOOP 394 67 #10 SML N 395 62 DRAIN CART 1096 99 END LOOP 197 65 #10 CART 598 10 GAS B VB 299 1 WAIT 60

Applied Biosystems


Module I –Ten-minute wait








1 1 WAIT 600 0

Module i – Cart (eject/advance)/SkipMod





1 136 Skip ModMon 12 6 NEEDLE UP 103 7 EJECT CART 104 8 ADVAN CART 10

Applied Biosystems


FastMoc 0.10 mmol Chemistry

Module A – Dissolving amino acid

This module is found in the following SynthAssist files:


• FastMoc 0.10 Mon 1st-X



1 1 WAIT 1 02 4 PRINT CART 10 03 6 NEEDLE UP 10 04 7 EJECT CART 10 05 8 ADVAN CART 10 06 5 NEEDLE DWN 10 07 14 #10 B VB 1 08 9 GAS T VB 2 09 65 #10 CART 5 010 60 MIX CART 5 011 78 PRS #M 10 012 18 #5 B VB 1 013 94 #5 TO CART 8 014 98 BEGIN LOOP 6 015 2 VORTEX ON 1 016 60 MIX CART 30 017 3 VORTEX OFF 1 018 60 MIX CART 30 019 99 END LOOP 1 0

Applied Biosystems







1 1 WAIT 1 02 4 PRINT CART 10 03 6 NEEDLE UP 10 04 7 EJECT CART 10 05 8 ADVAN CART 10 06 5 NEEDLE DWN 10 07 14 #10 B VB 1 08 9 GAS T VB 2 09 65 #10 CART 5 010 60 MIX CART 5 011 78 PRS #M 10 012 18 #5 B VB 1 013 94 #5 TO CART 8 014 98 BEGIN LOOP 6 015 2 VORTEX ON 1 016 60 MIX CART 30 017 3 VORTEX OFF 1 018 60 MIX CART 30 019 99 END LOOP 1 020 13 #10 TVB 1 021 14 #10 B VB 3 022 9 GAS T VB 2 023 10 GAS B VB 5 0

Applied Biosystems


Module a – Conditional: MonDoMod (activation/transfer)





1 137 DoModMon 12 1 WAIT 13 98 BEGIN LOOP 24 13 #10 T VB 15 14 #10 B VB 36 9 GAS T VB 27 10 GAS B VB 58 99 END LOOP 19 150 MATCH CART 1010 6 NEEDLE UP 1011 7 EJECT CART 1012 8 ADVAN CART 1013 5 NEEDLE DWN 1014 78 PRS #M 1015 65 #10 CART 516 60 MIX CART 517 18 #5 B VB 118 94 #5 TO CART 819 98 BEGIN LOOP 620 2 VORTEX ON 121 60 MIX CART 3022 3 VORTEX OFF 123 60 MIX CART 3024 99 END LOOP 125 1 WAIT 126 78 PRS #M 1027 10 GAS B VB 228 5 NEEDLE DWN 1029 70 PURGE ML 230 98 BEGIN LOOP 231 68 MEAS #7) 232 63 ML TO CART 433 99 END LOOP 134 60 MIX CART 535 98 BEGIN LOOP 436 41 VENT RV 237 96 CRT TO RVc 638 2 VORTEX ON 3

Applied Biosystems


Module a – – Conditional: MonDoMod (activation/transfer continued)


39 3 VORTEX OFF 140 99 END LOOP 141 65 #10 CART 342 60 MIX CART 343 98 BEGIN LOOP 344 41 VENT RV 245 96 CRT TO RVc 546 99 END LOOP 147 40 MIX RV 248 93 GAS TO RS 249 41 VENT RV 250 88 RS TO RV 151 93 GAS TO RS 352 41 VENT RV 253 89 RS TO FC 154 2 VORTEX ON 155 62 DRAIN CART 556 40 MIX RV 1

Applied Biosystems


Module B – Piperidine deprotection


1 1 WAIT 1 02 58 INTERRUPT 0 03 56 #10 B RV 3 14 88 RS TO RV 1 05 91 #10 TO RS 4 06 89 RS TO FC 1 07 40 MIX RV 2 08 2 VORTEX ON 3 09 40 MIX RV 2 010 3 VORTEX OFF 1 011 42 DRAIN RV 8 112 56 #10 B RV 3 013 79 PRS #1 10 014 51 #1 B RV 5 015 56 #10 B RV 4 016 40 MIX RV 2 017 98 BEGIN LOOP 2 018 2 VORTEX ON 15 016 3 VORTEX OFF 15 020 99 END LOOP 1 021 42 DRAIN RV 10 122 56 #10 B RV 3 023 79 PRS #1 5 024 51 #1 B RV 5 025 56 #10 B RV 4 026 40 MIX RV 2 027 88 RS TO RV 1 028 93 GAS TO S 3 029 89 RS TO FC 1 030 41 VENT RV 2 031 2 VORTEX ON 1 032 98 BEGIN LOOP 2 033 13 #10 T VB 1 034 14 #10 B VB 3 035 9 GAS T VB 5 036 10 GAS B VB 5 037 99 END LOOP 1 038 1 WAIT 1 0

Applied Biosystems


Module B – Deprotection/Mon1st-X


1 1 WAIT 12 58 INTERRUPT 03 135 Mon Reset 14 42 DRAIN RV 105 98 BEGIN LOOP 36 56 #10 B RV 3 17 88 RS TO RV 18 91 #10 TO RS 49 89 RS TO FC 110 40 MIX RV 211 2 VORTEX ON 512 40 MIX RV 213 3 VORTEX OFF 114 42 DRAIN RV 8 115 99 END LOOP 116 56 #10 B RV 317 79 PRS #1 1018 51 #1 B RV 519 56 #10 B RV 420 40 MIX RV 221 2 VORTEX ON 12022 3 VORTEX OFF 123 42 DRAIN RV 224 13 #10 T VB 225 128 Mon 1stPk - X 4526 1 WAIT 327 131 Mon Stop 128 132 Save Mon 129 133 MonBegLoop 330 42 DRAIN RV 8 131 98 BEGIN LOOP 332 56 #10 B RV 3 133 88 RS TO RV 134 91 #10 TO RS 435 89 RS TO FC 136 40 MIX RV 237 2 VORTEX ON 538 40 MIX RV 239 3 VORTEX OFFf 140 42 DRAIN RV 10 141 50 #10 RV-DRN 342 42 DRAIN RV 5 143 99 END LOOP 1

Applied Biosystems


Module B – Deprotection/Mon1stPk-X (continued)


44 56 #10 B RV 345 79 PRS #1 546 51 #1 B RV 547 56 #10 B RV 448 40 MIX RV 249 2 VORTEX ON 12050 3 VORTEX OFF 151 42 DRAIN RV 252 128 Mon1stPk - X 4553 1 WAIT 354 131 Mon Stop 155 132 Save Mon 156 134 MonEndLoop 10057 10 GAS B VB 358 40 MIX RV 259 41 VENT RV 260 88 RS TO RV 161 93 GAS TO RS 362 41 VENT RV 163 89 RS TO FC 164 2 VORTEX ON 165 98 BEGIN LOOP 266 13 #10 T VB 167 14 #10 B VB 368 9 GAS T VB 569 10 GAS B VB 570 99 END LOOP 1

Applied Biosystems


Module B – Deprotection/MonPrevPk


1 1 WAIT 12 58 INTERRUPT 03 135 Mon Reset 14 110 begin loop 25 42 DRAIN RV 10 16 98 BEGIN LOOP 37 56 #10 B RV 4 18 88 RS TO RV 19 91 #10 TO RS 410 89 RS TO FC 111 40 MIX RV 212 2 VORTEX ON 513 40 MIX RV 214 3 VORTEX OFF 115 42 DRAIN RV 10 116 50 #10 RV-DRN 317 42 DRAIN RV 5 118 99 END LOOP 119 56 #10 B RV 320 79 PRS #1 1021 51 #1 B RV 522 56 #10 B RV 423 40 MIX RV 224 2 VORTEX ON 12025 3 VORTEX OFF 126 40 MIX RV 127 130 MonPrevPk 128 42 DRAIN RV 329 1 WAIT 330 131 Mon Stop 131 132 Save Mon 132 111 end loop 133 133 MonBegLoop 334 42 DRAIN RV 8 135 98 BEGIN LOOP 336 56 #10 B RV 4 137 88 RS TO RV 138 91 #10 TO RS 439 89 RS TO FC 140 40 MIX RV 241 2 VORTEX ON 542 40 MIX RV 243 3 VORTEX OFF 1

Applied Biosystems


Module B – Deprotection/MonPrevPk (continued)


44 42 DRAIN RV 10 145 50 #10 RV-DRN 346 42 DRAIN RV 5 147 99 END LOOP 148 56 #10 B RV 349 79 PRS #1 550 51 #1 B RV 551 56 #10 B RV 452 40 MIX RV 253 2 VORTEX ON 12054 3 VORTEX OFF 155 40 MIX RV 156 130 MonPrevPk 157 42 DRAIN RV 358 1 WAIT 359 131 Mon Stop 160 132 Save Mon 161 134 MonEndLoop 10062 10 GAS B VB 363 40 MIX RV 264 41 VENT RV 265 88 RS TO RV 166 93 GAS TO RS 367 41 VENT RV 168 89 RS TO FC 169 2 VORTEX ON 170 98 BEGIN LOOP 271 13 #10 T VB 172 14 #10 B VB 373 9 GAS T VB 574 10 GAS B VB 575 99 END LOOP 1

Applied Biosystems


Module B – Conditional: Deprotection/ Mon1stPeak-X


1 1 WAIT 12 58 INTERRUPT 03 135 Mon Reset 14 42 DRAIN RV 105 98 BEGIN LOOP 36 56 #10 B RV 3 17 88 RS TO RV 18 91 #10 TO RS 49 89 RS TO FC 110 93 GAS B VB 211 2 VORTEX ON 512 40 MIX RV 213 3 VORTEX OFF 114 42 DRAIN RV 10 115 99 END LOOP 116 56 #10 B RV 317 79 PRS #1 1018 51 #1 B RV 519 56 #10 B RV 420 40 MIX RV 221 2 VORTEX ON 12022 3 VORTEX OFF 123 42 DRAIN RV 224 13 #10 T VB 225 128 Mon 1stPk - X 4526 1 WAIT 327 131 Mon Stop 128 132 Save Mon 129 133 MonBegLoop 230 42 DRAIN RV 8 131 98 BEGIN LOOP 332 56 #10 B RV 3 133 88 RS TO RV 134 91 #10 TO RS 435 89 RS TO FC 136 93 GAS TO RS 237 2 VORTEX ON 538 40 MIX RV 239 3 VORTEX OFFf 140 42 DRAIN RV 8 141 50 #10 RV-DRN 342 42 DRAIN RV 5 143 99 END LOOP 1

Applied Biosystems


Module B – FastMoc 0.10 Conditional: Deprotection/ Mon1stPeak-X (continued)


44 56 #10 B RV 345 79 PRS #1 546 51 #1 B RV 547 56 #10 B RV 448 40 MIX RV 249 2 VORTEX ON 12050 3 VORTEX OFF 151 42 DRAIN RV 252 128 Mon1stPk - X 4553 1 WAIT 354 131 Mon Stop 155 132 Save Mon 156 134 MonEndLoop 10057 42 DRAIN RV 1058 10 GAS B VB 359 40 MIX RV 260 41 VENT RV 261 88 RS TO RV 162 93 GAS TO RS 363 41 VENT RV 164 89 RS TO FC 165 98 BEGIN LOOP 266 13 #10 T VB 367 14 #11 B VB 368 9 GAS T VB 369 10 GAS B VB 370 99 END LOOP 1

Applied Biosystems


Module B – Conditional: Deprotection/ MonPrevPeak


1 1 WAIT 12 58 INTERRUPT 03 135 Mon Reset 14 110 begin loop 25 42 DRAIN RV 10 16 98 BEGIN LOOP 37 56 #10 B RV 4 18 88 RS TO RV 19 91 #10 TO RS 410 89 RS TO FC 111 93 GAS TO RS 212 2 VORTEX ON 513 40 MIX RV 214 3 VORTEX OFF 115 42 DRAIN RV 10 116 50 #10 RV-DRN 317 42 DRAIN RV 5 118 99 END LOOP 119 56 #10 B RV 320 79 PRS #1 1021 51 #1 B RV 522 56 #10 B RV 423 40 MIX RV 224 2 VORTEX ON 12025 3 VORTEX OFF 126 40 MIX RV 127 130 MonPrevPk 128 42 DRAIN RV 329 1 WAIT 330 131 Mon Stop 131 132 Save Mon 132 111 end loop 133 133 MonBegLoop 234 42 DRAIN RV 8 135 98 BEGIN LOOP 336 56 #10 B RV 4 137 88 RS TO RV 138 91 #10 TO RS 439 89 RS TO FC 140 93 GAS TO RS 241 2 VORTEX ON 542 40 MIX RV 2 543 3 VORTEX OFF 1

Applied Biosystems


Module B – Conditional: Deprotection/ MonPrevPeak (continued)


44 42 DRAIN RV 10 145 50 #10 RV-DRN 346 42 DRAIN RV 5 147 99 END LOOP 148 56 #10 B RV 349 79 PRS #1 1050 51 #1 B RV 551 56 #10 B RV 452 40 MIX RV 253 2 VORTEX ON 12054 3 VORTEX OFF 155 40 MIX RV 156 130 MonPrevPk 157 42 DRAIN RV 358 1 WAIT 359 131 Mon Stop 160 132 Save Mon 161 134 MonEndLoop 10062 42 DRAIN RV 863 10 GAS B VB 364 40 MIX RV 265 41 VENT RV 266 88 RS TO RV 167 93 GAS TO RS 368 41 VENT RV 169 89 RS TO FC 170 98 BEGIN LOOP 271 13 #10 T VB 372 14 #10 B VB 373 9 GAS T VB 374 10 GAS B VB 375 99 END LOOP 1

Applied Biosystems


Module b – Conditional: MonDoMod (deprot/Mon1stPk-X)


1 137 Do Mod Mon 12 42 DRAIN RV 10 13 56 #10 B RV 3 24 79 PRS #1 105 51 #1 B RV 5 16 56 #10 B RV 47 40 MIX RV 28 13 #10 T VB 29 14 #10 B VB 210 9 GAS T VB 511 10 GAS B VB 512 98 BEGIN LOOP 313 2 VORTEX ON 60014 3 VORTEX OFF 115 99 END LOOP 116 42 DRAIN RV 217 128 Mon 1stPk-X 4518 1 WAIT 319 131 Mon Stop 120 132 Save MonPk 1

Applied Biosystems


Module b – Conditional: MonDoMod (deprot/MonPrevPeak)



Applied Biosystems


Module C – Capping with Ac2O

This module is written with the acetic anhydride solution in Bottle 4. If loading with DMAP catalysis, remove the DMAP bottle after the loading steps, rinse out the lines, and put on a bottle of acetic anhydride solution. See ABI 433A Peptide Synthesizer User Guide , Volume 1, Loading with HMP resin, followed by capping with acetic anhydride on page 7-16.








1 77 PRS #4 10 02 10 GAS B VB 2 03 52 #4 B RV 15 14 40 MIX RV 2 05 41 VENT RV 2 06 88 RS TO RV 1 07 93 GAS TO RS 3 08 91 #10 TO RS 29 93 GAS TO RS 310 89 RS TO FC 1 011 2 VORTEX ON 300 012 3 VORTEX OFF 1 013 88 RS TO RV 1 014 91 #10 TO RS 3 015 89 RS TO FC 1 016 93 GAS TO RS 317 42 DRAIN RV 10 1

Applied Biosystems


Module c – DCM washes








1 1 WAIT 12 12 #9 B VB 13 9 GAS T VB 24 10 GAS B VB 25 98 BEGIN LOOP 66 55 #9 B RV 5 17 40 MIX RV 28 2 VORTEX ON 19 41 VENT RV 110 88 RS TO RV 111 90 #9 TO RS 212 93 GAS TO RS 213 90 #9 TO RS 514 89 RS TO FC 115 40 MIX RV 216 1 WAIT 517 3 VORTEX OFF 118 42 DRAIN RV 5 119 41 VENT RV 220 49 #9 RV-DRN 321 42 DRAIN RV 10 122 99 END LOOP 123 10 GAS B VB 224 93 GAS TO RS 525 41 VENT RV 226 88 RS TO RV 127 93 GAS TO RS 528 41 VENT RV 229 89 RS TO FC 130 42 DRAIN RV 3031 29 #9 ACT-DRN 532 22 DRAIN ACT 3033 11 #9 T VB 134 12 #9 B VB 1

Applied Biosystems


35 10 GAS B VB 1036 9 GAS T VB 10

Module D – NMP washes








1 1 WAIT 12 3 VORTEX OFF 13 42 DRAIN RV 10 14 98 BEGIN LOOP 4 15 41 VENT RV 26 50 #10 RV-DRN 27 42 DRAIN RV 5 18 56 #10 B RV 4 19 2 VORTEX ON 310 40 MIX RV 211 88 RS TO RV 112 91 #10 TO RS 213 89 RS TO FC 114 93 GAS TO RS 215 1 WAIT 1515 3 VORTEX OFF 116 42 DRAIN RV 10 117 99 END LOOP 1

Applied Biosystems







1 137 Do Mod Mon 12 77 PRS #4 103 10 GAS B VB 24 52 #4 B RV 15 15 40 MIX RV 26 41 VENT RV 27 88 RS TO RV 18 93 GAS TO RS 39 91 #10 TO RS 210 93 GAS TO RS 211 89 RS TO FC 112 2 VORTEX ON 30013 3 VORTEX OFF 114 88 RS TO RV 115 91 #10 TO RS 316 89 RS TO FC 117 42 DRAIN RV 10 118 98 BEGIN LOOP 3 119 41 VENT RV 220 50 #10 RV-DRN 221 42 DRAIN RV 5 122 56 #10 B RV 4 123 40 MIX RV 224 2 VORTEX ON 825 88 RS TO RV 126 91 #10 TO RS 227 89 RS TO FC 128 93 GAS TO RS 229 3 VORTEX OFF 130 42 DRAIN RV 10 131 99 END LOOP 1

Applied Biosystems


Module E – Transfer








1 1 WAIT 12 78 PRS #M 103 10 GAS B VB 24 5 NEEDLE DWN 105 70 PURGE ML 26 98 BEGIN LOOP 27 68 MEAS #7) 28 63 ML TO CART 49 99 END LOOP 110 60 MIX CART 511 98 BEGIN LOOP 412 41 VENT RV 213 96 CRT TO RVc 614 2 VORTEX ON 315 3 VORTEX OFF 116 99 END LOOP 117 98 BEGIN LOOP 318 41 VENT RV 219 96 CRT TO RVc 520 99 END LOOP 121 40 MIX RV 122 93 GAS TO RS 223 41 VENT RV 224 88 RS TO RV 125 93 GAS TO RS 326 41 VENT RV 227 89 RS TO FC 128 2 VORTEX ON 129 62 DRAIN CART 530 40 MIX RV 1

Applied Biosystems


Module F – Clean, couple, drain, and wash


1 1 WAIT 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 36 67 #10 SML N 27 62 DRAIN CART 58 99 END LOOP 19 98 BEGIN LOOP 210 65 #10 CART 1811 60 MIX CART 1012 24 CART TO AC 2013 62 DRAIN CART 1014 99 End Loop UPPER 115 98 BEGIN LOOP 216 67 #10 SML N 217 62 DRAIN CART 1018 99 End Loop UPPER 119 62 DRAIN CART 1020 60 MIX CART 521 61 VENT CART 222 98 BEGIN LOOP 9 123 2 VORTEX ON 1524 3 VORTEX OFF 1325 41 VENT RV 226 99 End Loop UPPER 127 88 RS TO RV 128 91 #10 TO RS 529 89 RS TO FC 130 98 BEGIN LOOP 331 3 VORTEX OFF 132 28 GAS T ACT 433 42 DRAIN RV 7 134 38 ACT TO RVo 635 40 MIX RV 136 2 VORTEX ON 337 40 MIX RV 238 99 END LOOP 139 22 DRAIN ACT 540 3 VORTEX OFF 141 42 DRAIN RV 7 1

Applied Biosystems


Module F – Clean, couple, drain, and wash, with feedback





1 1 WAIT 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 36 67 #10 SML N 27 62 DRAIN CART 58 99 END LOOP 19 98 BEGIN LOOP 310 65 #10 CART 1811 60 MIX CART 1012 24 CART TO AC 2013 62 DRAIN CART 1014 99 END LOOP 115 98 BEGIN LOOP 216 67 #10 SML N 217 62 DRAIN CART 1018 99 END LOOP 119 62 DRAIN CART 1020 60 MIX CART 521 61 VENT CART 222 133 MonBegLoop23 98 BEGIN LOOP 9 124 2 VORTEX ON 1525 3 VORTEX OFF 1326 41 VENT RV 227 99 END LOOP 128 134 MonEndLoop 129 88 RS TO RV 130 91 #10 TO RS 531 89 RS TO FC 132 98 BEGIN LOOP 333 3 VORTEX OFF 134 28 GAS T ACT 435 42 DRAIN RV 7 136 38 ACT TO RVo 637 40 MIX RV 138 2 VORTEX ON 339 40 MIX RV 240 99 END LOOP 141 22 DRAIN ACT 542 3 VORTEX OFF 143 42 DRAIN RV 7 1

Applied Biosystems


Module F – Conditional: Coupling etc./SkipMod





1 136 SkipModMon 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 36 67 #10 SML N 27 62 DRAIN CART 58 99 END LOOP 19 98 BEGIN LOOP 210 65 #10 CART 1811 60 MIX CART 1012 24 CART TO AC 2013 62 DRAIN CART 1014 99 END LOOP 115 98 BEGIN LOOP 216 67 #10 SML N 217 62 DRAIN CART 1018 99 END LOOP 119 62 DRAIN CART 1020 60 MIX CART 521 61 VENT CART 222 98 BEGIN LOOP 923 2 VORTEX ON 1524 3 VORTEX OFF 1325 41 VENT RV 226 99 END LOOP 127 88 RS TO RV 128 91 #10 TO RS 529 89 RS TO FC 130 93 GAS TO RS 231 98 BEGIN LOOP 332 3 VORTEX OFF 133 28 GAS T ACT 434 42 DRAIN RV 7 135 38 ACT TO RVo 636 40 MIX RV 137 2 VORTEX ON 338 40 MIX RV 239 99 END LOOP 1

Applied Biosystems


Module F – Conditional: Coupling etc./SkipMod, continued


40 22 DRAIN ACT 541 3 VORTEX OFF 142 42 DRAIN RV 7 1

Applied Biosystems


Module f – Conditional: MonDoMod (coupling)





1 137 Do ModMon 12 2 VORTEX ON 13 5 NEEDLE DWN 104 62 DRAIN CART 105 98 BEGIN LOOP 36 67 #10 SML N 27 62 DRAIN CART 58 99 END LOOP 19 98 BEGIN LOOP 210 65 #10 CART 1811 60 MIX CART 1012 24 CART TO AC 2013 62 DRAIN CART 1014 99 END LOOP 115 98 BEGIN LOOP 216 67 #10 SML N 217 62 DRAIN CART 1018 99 END LOOP 119 62 DRAIN CART 1020 60 MIX CART 521 61 VENT CART 222 98 BEGIN LOOP 10023 2 VORTEX ON 1524 3 VORTEX OFF 1325 41 VENT RV 226 99 END LOOP 127 88 RS TO RV 128 91 #10 TO RS 529 89 RS TO FC 130 93 GAS TO RS 231 98 BEGIN LOOP 332 3 VORTEX OFF 133 28 GAS T ACT 434 42 DRAIN RV 7 135 38 ACT TO RVo 636 40 MIX RV 137 2 VORTEX ON 338 40 MIX RV 239 99 END LOOP 140 22 DRAIN ACT 541 3 VORTEX OFF 142 42 DRAIN RV 7 1

Applied Biosystems


Module G – Resin sampling


• FastMoc 0.10 mmol• FastMoc 0.10 Mon 1st-X• FastMoc 0.10 MonPrevPk




1 1 WAIT 12 14 #10 B VB 13 56 #10 B RV 5 14 2 VORTEX ON 15 40 MIX RV 26 91 #10 TO RS 27 93 GAS TO RS 28 91 #10 TO RS 29 93 GAS TO RS 110 91 #10 TO RS 411 41 VENT RV 112 98 Loop UPPER 113 39 RELAY 0 114 88 RS TO RV 115 93 GAS TO RS 216 91 #10 TO RS 417 9 GAS T VB 318 13 #10 T VB 119 41 VENT RV 220 91 #10 TO RS 121 48 GAS T RV 222 87 TAKE SAMPL 223 89 RS TO FC 124 91 #10 TO RS 225 93 GAS TO RS 226 91 #10 TO RS 227 93 GAS TO RS 228 91 #10 TO RS 429 93 GAS TO RS 430 41 VENT RV 231 88 RS TO RV 132 91 #10 TO RS 333 93 GAS TO RS 334 91 #10 TO RS 535 89 RS TO FC 1

Applied Biosystems


Module G – FastMoc 0.10: Resin sampling (continued)


36 39 RELAY 0 137 99 END LOOP 138 3 VORTEX OFF 139 42 DRAIN RV 10 1

Applied Biosystems


Module g – Conditional: MonDoMod (resin sampling)





1 137 Do ModMon 12 1 WAIT 13 14 #10 B VB 14 56 #10 B RV 5 15 2 VORTEX ON 16 40 MIX RV 27 91 #10 TO RS 28 93 GAS TO RS 29 91 #10 TO RS 210 93 GAS TO RS 111 91 #10 TO RS 412 41 VENT RV 113 98 Loop UPPER 114 39 RELAY 0 115 88 RS TO RV 116 93 GAS TO RS 217 91 #10 TO RS 418 9 GAS T VB 319 13 #10 T VB 120 41 VENT RV 221 91 #10 TO RS 122 48 GAS T RV 223 87 TAKE SAMPL 224 89 RS TO FC 125 91 #10 TO RS 226 93 GAS TO RS 227 91 #10 TO RS 228 93 GAS TO RS 229 91 #10 TO RS 430 93 GAS TO RS 431 41 VENT RV 232 88 RS TO RV 133 91 #10 TO RS 334 93 GAS TO RS 335 91 #10 TO RS 536 89 RS TO FC 137 93 GAS TO RS 238 39 RELAY 0 139 99 END LOOP 140 3 VORTEX OFF 141 42 DRAIN RV 10 1

Applied Biosystems


Module H – Load and cap

This module is found in the following SynthAssist files:• FastMoc 0.10 mmol• FastMoc 0.10 Mon 1st-X• FastMoc 0.10 MonPrevPk




1 1 WAIT 12 55 #9 B RV 103 88 RS TO RV 14 90 #9 TO RS 65 89 RS TO FC 16 40 MIX RV 27 2 VORTEX ON 18 4 SAVE CART 109 6 NEEDLE UP 1010 7 EJECT CART 1011 8 ADVAN CART 1012 5 NEEDLE DWN 1013 10 GAS B VB 214 64 #9 CART 415 65 #10 CART 316 60 MIX CART 30017 3 VORTEX OFF 118 42 DRAIN RV 1019 98 BEGIN LOOP 520 41 VENT RV 221 96 CRT TO RVc 822 99 END LOOP 123 64 #9 CART 524 60 MIX CART 425 78 PRS #M 1026 98 BEGIN LOOP 227 69 MEAS #8 328 43 ML TO RV 429 99 END LOOP 130 77 PRS #4 1031 17 #4 B VB 132 10 GAS B VB 233 52 #4 B RV 134 44 CART TO RV 8

Applied Biosystems




35 55 #9 B RV 136 40 MIX RV 137 67 #10 SML N 538 62 DRAIN CART 1039 98 BEGIN LOOP 340 41 VENT RV 241 88 RS TO RV 142 93 GAS TO RS 343 89 RS TO FC 144 2 VORTEX ON 60045 3 VORTEX OFF 146 99 END LOOP 147 6 NEEDLE UP 1048 7 EJECT CART 1049 8 ADVAN CART 1050 5 NEEDLE DWN 1051 64 #9 CART 552 60 MIX CART 18053 41 VENT RV 254 88 RS TO RV 155 90 #9 TO RS 656 89 RS TO FC 157 42 DRAIN RV 2058 98 Loop UPPER 259 55 #9 B RV 560 54 #6 B RV 561 40 MIX RV 1062 2 VORTEX ON 1063 3 VORTEX OFF 164 42 DRAIN RV 1565 99 END LOOP 166 98 BEGIN LOOP 567 55 #9 B RV 868 88 RS TO RV 169 90 #9 TO RS 670 89 RS TO FC 171 40 MIX RV 272 2 VORTEX ON 1073 3 VORTEX OFF 174 42 DRAIN RV 1075 99 END LOOP 176 98 BEGIN LOOP 477 41 VENT RV 278 96 CRT TO RVc) 679 99 END LOOP 180 64 #9 CART 381 60 MIX CART 5

Applied Biosystems




82 77 PRS #4 1083 17 #4 B VB 184 10 GAS B VB 285 52 #4 B RV 286 44 CART TO RV 887 55 #9 B RV 188 40 MIX RV 289 88 RS TO RV 190 93 GAS TO RS 491 89 RS TO FC 192 2 VORTEX ON 193 98 BEGIN LOOP 394 67 #10 SML N 395 62 DRAIN CART 1096 99 END LOOP 197 65 #10 CART 598 10 GAS B VB 299 1 WAIT 60

Applied Biosystems


Module I – Ten-minute wait

This module is found in the following SynthAssist files:• FastMoc 0.10 mmol• FastMoc 0.10 Mon 1st-X• FastMoc 0.10 MonPrevPk




1 1 WAIT 600 0

Module i – Cart(eject/advance)/SkipMod





1 136 Do ModMon 12 6 NEEDLE UP 103 7 EJECT CART 104 8 ADVAN CART 10

Applied Biosystems


Fmoc/HOBt/DCC 0.25 mmol Chemistry

Module a – Activation


1 1 WAIT 12 58 INTERRUPT 0 0 (for power failure feature)3 61 VENT CART 10 04 4 SAVE CART 10 0 Print AA Name5 6 NEEDLE UP 10 06 7 EJECT CART 10 0 Eject old cart.7 8 ADVAN CART 10 0 Advance new cart.8 5 NEEDLE DWN 10 09 14 #10 B VB 1 010 9 GAS T VB 2 011 20 MIX ACT 2 012 78 PRS #M 10 013 65 #10 CART 5 0 Add 2.1 mL NMP14 60 MIX CART 5 0 to cartridge15 98 BEGIN LOOP 2 016 68 MEAS #7 3 017 36 #10 B ACT 1 018 20 MIX ACT 5 0 Add 1.0 mL HOBt19 63 ML TO CART 3 0 to cartridge20 1 WAIT 2 021 63 ML TO CART 3 022 99 END LOOP 1 023 98 BEGIN LOOP 5 024 60 MIX CART 60 025 2 VORTEX ON 15 026 3 VORTEX OFF 1 027 20 MIX ACT 2 028 1 WAIT 50 0 Dissolve amino acid29 60 MIX CART 60 030 99 END LOOP 1 031 98 BEGIN LOOP 5 032 60 MIX CART 10 033 2 VORTEX ON 10 034 3 VORTEX OFF 1 035 1 WAIT 10 036 99 END LOOP 1 0\37 20 MIX ACT 5 038 22 DRAIN ACT 10 039 11 #9 T VB 1 040 29 #9 ACT-DRN 4 041 22 DRAIN ACT 40 0

Applied Biosystems


Module a – Activation (continued)


42 14 #10 B VB 1 043 10 GAS B VB 6 044 60 MIX CART 10 045 24 CART TO AC 24 046 98 BEGIN LOOP 4 047 24 CART TO AC 3 048 1 WAIT 5 049 99 END LOOP 1 050 65 #10 CART 1 051 60 MIX CART 5 052 78 PRS #M 5 053 98 BEGIN LOOP 2 054 69 MEAS #8 3 055 23 ML TO ACT 3 0 Add 1.0 mL DCC to 56 1 WAIT 5 0 Activator57 23 ML TO ACT 3 058 99 END LOOP 1 059 60 MIX CART 3 060 24 CART TO AC 4 061 65 #10 CART 2 0 Clean needle with NMP62 10 GAS B VB 6 063 20 MIX ACT 1 064 14 #10 B VB 1 065 2 VORTEX ON 10 066 3 VORTEX OFF 1 067 10 GAS B VB 3 068 14 #10 B VB 1 069 1 WAIT 5 070 10 GAS B VB 6 071 20 MIX ACT 1 072 12 #9 B VB 1 073 1 WAIT 5 074 10 GAS B VB 2 075 14 #10 B VB 1 076 9 GAS T VB 10 077 10 GAS B VB 10 0

Applied Biosystems


Module b – Piperidine Deprotection


1 14 #10 B VB 1 02 56 #10 B RV 15 13 88 RS TO RV 1 04 91 #10 TO RS 5 05 41 VENT RV 2 0 Wash with NMP6 89 RS TO FC 1 07 2 VORTEX ON 5 08 40 MIX RV 3 09 10 GAS B VB 6 010 20 MIX ACT 1 011 3 VORTEX OFF 1 012 42 DRAIN RV 15 113 56 #10 B RV 13 214 79 PRS #1 10 015 51 #1 B RV 8 116 56 #10 B RV 2 017 40 MIX RV 3 018 98 BEGIN LOOP 6 019 2 VORTEX ON 15 0 3-minute deprotection20 3 VORTEX OFF 15 0 with 20% Piperidine in NMP21 99 END LOOP 1 022 79 PRS #1 5 023 41 VENT RV 3 024 42 DRAIN RV 25 125 56 #10 B RV 8 126 51 #1 B RV 10 127 56 #10 B RV 8 128 40 MIX RV 3 029 41 VENT RV 2 030 93 GAS TO RS 3 031 88 RS TO RV 1 032 93 GAS TO RS 3 033 41 VENT RV 2 034 89 RS TO FC 1 035 9 GAS T VB 3 036 10 GAS B VB 3 0 15-minute deprotection 37 98 BEGIN LOOP 14 0 with 20% Piperidine in NMP38 2 VORTEX ON 15 039 3 VORTEX OFF 15 040 99 END LOOP 1 041 41 VENT RV 2 042 88 RS TO RV 1 043 93 GAS TO RS 3 0

Applied Biosystems


Module b – Piperidine Deprotection (continued)


44 41 VENT RV 2 045 89 RS TO FC 1 046 98 BEGIN LOOP 14 047 2 VORTEX ON 15 048 3 VORTEX OFF 15 049 99 END LOOP 1 050 41 VENT RV 2 051 88 RS TO RV 1 052 91 #10 TO RS 5 053 89 RS TO FC 1 054 50 #10 RV-DRN 5 055 42 DRAIN RV 20 156 56 #10 B RV 27 157 40 MIX RV 2 058 2 VORTEX ON 5 059 3 VORTEX OFF 2 060 42 DRAIN RV 20 1 Wash with NMP61 50 #10 RV-DRN 5 062 42 DRAIN RV 10 0

Applied Biosystems




1 10 GAS B VB 2 02 9 GAS T VB 2 03 12 #9 B VB 1 04 11 #9 T VB 1 05 55 #9 B RV 10 16 2 VORTEX ON 1 07 40 MIX RV 2 08 90 #9 TO RS 1 09 93 GAS TO RS 3 0

10 41 VENT RV 2 0 Wash the resin and 11 88 RS TO RV 1 0 resin-sampling line with12 90 #9 TO RS 2 0 DCM, once13 93 GAS TO RS 2 014 90 #9 TO RS 5 015 89 RS TO FC 1 016 40 MIX RV 2 017 3 VORTEX OFF 1 018 42 DRAIN RV 10 019 49 #9 RV-DRN 5 020 42 DRAIN RV 8 121 98 BEGIN LOOP 6 022 55 #9 B RV 8 123 2 VORTEX ON 1 0 wash the resin with DCM,24 55 #9 B RV 4 0 six times25 40 MIX RV 4 026 3 VORTEX OFF 1 027 42 DRAIN RV 10 028 49 #9 RV-DRN 4 029 42 DRAIN RV 10 130 99 END LOOP 1 031 55 #9 B RV 10 132 2 VORTEX ON 1 033 40 MIX RV 2 034 41 VENT RV 2 035 88 RS TO RV 1 0 wash the resin and 36 90 #9 TO RS 2 0 resin-sample line with37 93 GAS TO RS 2 0 DCM, once38 90 #9 TO RS 5 039 89 RS TO FC 1 040 40 MIX RV 2 041 3 VORTEX OFF 1 042 42 DRAIN RV 10 043 49 #9 RV-DRN 5 0

Applied Biosystems


Module c – DCM Washes (continued)


44 42 DRAIN RV 20 145 41 VENT RV 2 046 12 #9 B VB 1 047 10 GAS B VB 10 048 93 GAS TO RS 10 049 9 GAS T VB 10 0

Applied Biosystems


Module d – NMP Washes


1 14 #10 B VB 1 02 56 #10 B RV 12 13 2 VORTEX ON 1 04 40 MIX RV 2 05 41 VENT RV 1 06 88 RS TO RV 1 0 Wash the resin and resin-7 93 GAS TO RS 3 0 sample line with NMP, once8 91 #10 TO RS 5 09 89 RS TO FC 1 010 40 MIX RV 2 011 10 GAS B VB 6 012 20 MIX ACT 1 013 3 VORTEX OFF 1 014 42 DRAIN RV 10 115 50 #10 RV-DRN 5 016 42 DRAIN RV 10 017 98 BEGIN LOOP 4 018 56 #10 B RV 13 119 2 VORTEX ON 1 020 40 MIX RV 3 021 10 GAS B VB 6 022 20 MIX ACT 1 0 Wash the resin with NMP,23 3 VORTEX OFF 1 0 four times24 42 DRAIN RV 10 125 50 #10 RV-DRN 5 026 42 DRAIN RV 10 027 99 END LOOP 1 028 56 #10 B RV 12 129 2 VORTEX ON 1 030 41 VENT RV 1 031 88 RS TO RV 1 032 93 GAS TO RS 3 033 91 #10 TO RS 5 034 89 RS TO FC 1 0 Wash the resin and resin-35 40 MIX RV 2 0 sample line with NMP, once36 10 GAS B VB 6 037 98 BEGIN LOOP 3 038 20 MIX ACT 1 039 1 WAIT 2 040 99 END LOOP 1 041 3 VORTEX OFF 1 042 42 DRAIN RV 10 143 50 #10 RV-DRN 5 0

Applied Biosystems


Module d – NMP Washes (continued)


44 42 DRAIN RV 15 045 9 GAS T VB 3 046 10 GAS B VB 3 047 93 GAS TO RS 2 0

Applied Biosystems


Module e – Transfer


1 14 #10 B VB 1 02 5 NEEDLE DWN 10 03 60 MIX CART 2 04 10 GAS B VB 3 05 20 MIX ACT 1 06 2 VORTEX ON 1 07 98 BEGIN LOOP 2 08 28 GAS T ACT 3 09 38 ACT TO RVo 4 010 99 END LOOP 1 011 3 VORTEX OFF 1 012 98 BEGIN LOOP 3 013 28 GAS T ACT 2 0 Transfer activated amino 14 38 ACT TO RVo 3 0 acid from the Activator15 99 END LOOP 1 0 to the Reaction Vessel16 21 VENT ACT 2 017 26 #10 T ACT 2 018 28 GAS T ACT 3 019 21 VENT ACT 2 020 36 #10 B ACT 2 021 20 MIX ACT 5 022 28 GAS T ACT 3 023 38 ACT TO RVo 6 024 40 MIX RV 2 025 93 GAS TO RS 2 026 41 VENT RV 2 027 88 RS TO RV 1 028 93 GAS TO RS 3 029 41 VENT RV 2 030 89 RS TO FC 1 031 2 VORTEX ON 1 032 11 #9 T VB 1 033 21 VENT ACT 2 034 29 #9 ACT-DRN 5 035 62 DRAIN CART 5 036 3 VORTEX OFF 1 0 Clean the empty Cartridge37 34 #6 B ACT 16 0 and Activator38 20 MIX ACT 3 039 67 #10 SML N 2 040 66 #9 SML N 2 041 62 drain cart 15 042 12 #9 B VB 1 043 98 BEGIN LOOP 2 0

Applied Biosystems


Module e – Transfer (continued)


44 64 #9 CART 20 045 2 VORTEX ON 1 046 1 WAIT 3 047 60 MIX CART 5 048 3 VORTEX OFF 1 049 24 CART TO AC 20 050 99 END LOOP 1 051 2 VORTEX ON 1 052 62 DRAIN CART 10 053 60 MIX CART 15 054 61 VENT CART 5 055 3 VORTEX OFF 1 056 98 BEGIN LOOP 7 057 20 MIX ACT 5 058 1 WAIT 5 059 99 END LOOP 1 060 22 DRAIN ACT 20 061 2 VORTEX ON 1 062 22 DRAIN ACT 10 063 3 VORTEX OFF 1 064 98 BEGIN LOOP 3 065 29 #9 ACT-DRN 3 066 22 DRAIN ACT 5 067 99 END LOOP 1 068 2 VORTEX ON 1 069 12 #9 B VB 1 070 35 #9 B ACT 2 071 20 MIX ACT 3 072 3 VORTEX OFF 1 073 22 DRAIN ACT 30 074 9 GAS T VB 5 075 10 GAS B VB 5 0

Applied Biosystems


Module f – Coupling


1 14 #10 B VB 1 02 13 #10 T VB 1 03 10 GAS B VB 5 04 9 GAS T VB 5 05 98 BEGIN LOOP 18 06 2 VORTEX ON 13 07 10 GAS B VB 3 08 20 MIX ACT 1 0

9 3 VORTEX OFF 15 0 20 minutes of Coupling

10 99 END LOOP 1 0 with one cleaning of

11 91 #10 TO RS 1 0 the resin-sample line 12 93 GAS TO RS 2 013 41 VENT RV 2 014 88 RS TO RV 1 015 93 GAS TO RS 2 016 41 VENT RV 1 017 89 RS TO FC 1 018 98 BEGIN LOOP 18 019 2 VORTEX ON 13 020 10 GAS B VB 3 021 20 MIX ACT 1 022 3 VORTEX OFF 15 023 99 END LOOP 1 024 9 GAS T VB 2 025 13 #10 T VB 1 026 9 GAS T VB 5 027 14 #10 B VB 1 028 10 GAS B VB 5 0

Applied Biosystems


Module g – NMP Washes and Resin Sampling


1 13 #10 T VB 1 02 91 #10 TO RS 2 03 41 VENT RV 2 04 88 RS TO RV 1 05 93 GAS TO RS 3 06 91 #10 TO RS 5 0

7 89 RS TO FC 1 0 Drain Reaction Vessel8 98 BEGIN LOOP 3 09 14 #10 B VB 1 010 40 MIX RV 4 011 99 END LOOP 1 012 2 VORTEX ON 5 013 40 MIX RV 4 014 3 VORTEX OFF 1 015 40 MIX RV 4 016 10 GAS B VB 6 017 20 MIX ACT 1 018 42 DRAIN RV 20 219 56 #10 B RV 14 120 41 VENT RV 1 021 88 RS TO RV 1 022 91 #10 TO RS 5 0

23 89 RS TO FC 1 0 Wash the resin and resin-

24 2 VORTEX ON 3 0 sample line with NMP,

25 40 MIX RV 3 0 one time26 3 VORTEX OFF 1 027 42 DRAIN RV 15 128 50 #10 rv-DRN 4 029 42 DRAIN RV 10 030 98 BEGIN LOOP 4 031 56 #10 B RV 14 132 2 VORTEX ON 1 0

33 40 MIX RV 3 0 Wash the resin with

34 3 VORTEX OFF 1 0 NMP, four times35 42 DRAIN RV 10 136 50 #10 RV-DRN 4 037 42 DRAIN RV 10 038 99 END LOOP 1 039 56 #10 B RV 14 140 41 VENT RV 1 041 88 RS TO RV 1 0

42 91 #10 TO RS 5 0 Wash the resin and

43 89 RS TO FC 1 0 resin-sample line with

Applied Biosystems


Module g – NMP Washes and Resin Sampling (continued)


44 2 VORTEX ON 1 0 NMP, one time45 40 MIX RV 3 046 10 GAS B VB 6 047 20 MIX ACT 1 048 3 VORTEX OFF 1 049 42 DRAIN RV 15 150 14 #10 B VB 1 051 56 #10 B RV 14 152 2 VORTEX ON 1 053 40 MIX RV 1 054 91 #10 TO RS 2 055 93 GAS TO RS 2 056 90 #9 TO RS 2 057 93 GAS TO RS 1 058 91 #10 TO RS 4 059 41 VENT RV 1 060 98 BEGIN LOOP 1 061 39 RELAY 0 1 062 88 RS TO RV 1 063 93 GAS TO RS 2 064 91 #10 TO RS 4 065 9 GAS T VB 3 066 13 #10 T VB 1 067 41 VENT RV 2 0 Taking resin sample68 91 #10 TO RS 1 069 48 GAS T RV 2 070 87 TAKE SAMPL 2 071 89 RS TO FC 1 072 90 #9 TO RS 2 073 93 GAS TO RS 2 074 90 #9 TO RS 2 075 93 GAS TO RS 2 076 90 #9 TO RS 4 077 93 GAS TO RS 4 078 41 VENT RV 2 079 88 RS TO RV 1 080 91 #10 TO RS 3 081 93 GAS TO RS 3 082 91 #10 TO RS 5 083 89 RS TO FC 1 084 39 RELAY 0 1 085 99 END LOOP 1 086 3 VORTEX OFF 1 087 42 DRAIN RV 20 2

Applied Biosystems


Module h – Loading


1 61 VENT CART 10 0

2 4 PRINT CART 10 0 Print the amino acid name3 6 NEEDLE UP 10 0

4 7 EJECT CART 10 0 Eject the blank cartridge

5 8 ADVAN CART 10 0 Advance the new cartridge6 5 NEEDLE DWN 10 07 14 #10 B VB 1 08 10 GAS B VB 2 09 36 #10 B ACT 3 010 20 MIX ACT 10 0

11 65 #10 CART 2 0 Add 0.8 mL NMP to cartridge

12 64 #9 CART 3 0 Add 1.8 mL DCM to cartridge13 60 MIX CART 30 014 91 #10 TO RS 1 015 93 GAS TO RS 5 016 55 #9 B RV 10 017 88 RS TO RV 1 018 93 GAS TO RS 5 0 Dissolve amino acid19 90 #9 TO RS 5 020 89 RS TO FC 1 021 93 GAS TO RS 5 022 56 #10 B RV 6 023 40 MIX RV 2 024 2 VORTEX ON 10 025 3 VORTEX OFF 1 026 98 BEGIN LOOP 3 027 60 MIX CART 60 028 1 WAIT 15 029 99 END LOOP 1 030 22 DRAIN ACT 15 031 30 #10 A-DRN 2 032 22 DRAIN ACT 5 033 29 #9 ACT-DRN 4 034 22 DRAIN ACT 20 035 10 GAS B VB 5 036 60 MIX CART 30 037 98 BEGIN LOOP 3 0

38 24 CART TO AC 4 0 Transfer amino acid to

39 1 WAIT 4 0 activator40 99 END LOOP 1 041 64 #9 cart 2 0

Applied Biosystems


Module h – Loading (continued)


42 60 MIX CART 3 043 78 PRS #M 10 044 98 BEGIN LOOP 1 045 69 MEAS #8 3 046 23 ML TO ACT 3 0

47 1 WAIT 3 0 Add 0.5 mL DCC to the

48 23 ML TO ACT 3 0 activator49 1 WAIT 3 050 99 END LOOP 1 051 24 CART TO AC 6 052 1 WAIT 3 053 35 #9 B ACT 1 054 20 MIX ACT 2 055 65 #10 CART 1 056 60 MIX CART 2 057 65 #10 CART 2 058 10 GAS B VB 6 059 98 BEGIN LOOP 50 060 20 MIX ACT 1 0

61 1 WAIT 15 0 13 minutes of activation62 99 END LOOP 1 063 77 PRS #4 10 064 42 DRAIN RV 15 065 49 #9 RV-DRN 3 066 42 DRAIN RV 10 067 17 #4 B VB 1 068 10 GAS B VB 1 069 52 #4 B RV 1 0

70 55 #9 B RV 1 0 Add 0.36 mL of

71 40 MIX RV 2 0 0.1M DMAP to resin72 10 GAS B VB 2 073 9 GAS T VB 2 074 20 MIX ACT 1 075 10 GAS B VB 1 0

Module i – Waiting


1 1 WAIT 900 0 Wait for 15 minutes

Applied Biosystems


Fmoc/HOBt/DCC 0.10 mmol Chemistry


Step# Fxn# Function Name Tme Add Key Events

1 1 WAIT 12 58 INTERRUPT 0 0 (for power failure feature)3 61 VENT CART 10 0

4 4 PRINT CART 10 0 Print amino acid name5 6 NEEDLE UP 10 0

6 7 EJECT CART 10 0 Eject old cartridge

7 8 ADVAN CART 10 0 Advance new cartridge8 5 NEEDLE DWN 10 09 14 #10 B VB 1 010 9 GAS T VB 2 011 20 MIX ACT 4 0 12 78 PRS #M 10 013 10 GAS B VB 2 014 98 BEGIN LOOP 2 015 68 MEAS #7 3 016 20 MIX ACT 2 0

17 63 ML TO CART 6 0 Add 1.0 mL HOBT to cartridge18 99 END LOOP 1 0

19 65 #10 CART 5 0 Add 2.1 mL NMP to cartridge20 60 MIX CART 10 021 9 GAS T VB 5 022 10 GAS B VB 5 023 98 BEGIN LOOP 10 024 60 MIX CART 60 025 2 VORTEX ON 10 0

26 20 MIX ACT 2 0 Dissolve amino acid27 3 VORTEX OFF 5 028 99 END LOOP 1 029 98 BEGIN LOOP 4 030 60 MIX CART 10 031 2 VORTEX ON 10 032 3 VORTEX OFF 8 033 20 MIX ACT 2 034 99 END LOOP 1 035 22 DRAIN ACT 10 036 35 #9 B ACT 2 037 20 MIX ACT 4 038 98 BEGIN LOOP 2 039 22 DRAIN ACT 5 040 21 VENT ACT 2 0

Applied Biosystems




41 25 #9 T ACT 2 042 99 END LOOP 1 043 22 DRAIN ACT 2 044 2 VORTEX ON 1 045 10 GAS B VB 6 046 60 MIX CART 10 047 3 VORTEX OFF 1 048 22 DRAIN ACT 35 049 2 VORTEX ON 1 050 10 GAS B VB 4 051 24 CART TO AC 24 0

52 3 VORTEX OFF 1 0 Transfer amino acid to activator53 98 BEGIN LOOP 4 054 24 CART TO AC 3 055 1 WAIT 4 056 99 END LOOP 1 057 65 #10 CART 1 058 60 MIX CART 3 059 78 PRS #M 5 060 98 BEGIN LOOP 2 061 69 Meas #8 3 062 23 ML TO ACT 3 0 Add 1.0 mL DCC to activator63 1 WAIT 4 064 23 ML TO ACT 3 065 99 END LOOP 1 066 65 #10 CART 2 067 10 GAS B VB 6 068 20 MIX ACT 1 069 14 #10 B VB 1 070 2 VORTEX ON 1 071 10 GAS B VB 6 072 20 MIX ACT 1 073 11 #9 T VB 1 074 12 #9 B VB 1 075 9 GAS T VB 15 076 10 GAS B VB 15 077 3 VORTEX OFF 1 0

Applied Biosystems


Module b – Piperidine Deprotection


1 14 #10 B VB 1 02 9 GAS T VB 2 03 93 GAS TO RS 3 04 56 #10 B RV 3 15 88 RS TO RV 1 06 93 GAS TO RS 2 07 91 #10 TO RS 5 08 89 RS TO FC 1 09 40 MIX RV 2 010 2 VORTEX ON 1 0

11 10 GAS B VB 6 0 Wash with NMP12 20 MIX ACT 1 013 3 VORTEX OFF 1 014 79 PRS #1 10 015 42 DRAIN RV 5 016 50 #10 RV-DRN 2 017 42 DRAIN RV 5 018 50 #10 RV-DRN 2 019 42 DRAIN RV 10 120 56 #10 B RV 2 021 51 #1 B RV 4 022 56 #10 B RV 3 023 40 MIX RV 2 024 9 GAS T VB 5 025 10 GAS B VB 5 0

26 98 BEGIN LOOP 6 0 3-minute deprotection with

27 2 VORTEX ON 15 0 20% Piperidine in NMP28 3 VORTEX OFF 14 029 41 VENT RV 1 030 99 END LOOP 1 031 79 PRS #1 5 032 42 DRAIN RV 12 133 56 #10 B RV 2 034 51 #1 B RV 4 035 56 #10 B RV 3 0

36 40 MIX RV 2 0 11-minute deprotection

37 93 GAS TO RS 3 0 with 20% Piperidine

38 41 VENT RV 1 0 in NMP39 88 RS TO RV 1 040 93 GAS TO RS 2 041 89 RS TO FC 1 042 9 GAS T VB 5 043 10 GAS B VB 5 0

Applied Biosystems


Module b – Piperidine Deprotection (continued)


44 98 BEGIN LOOP 10 045 2 VORTEX ON 15 046 3 VORTEX OFF 15 047 99 END LOOP 1 048 41 VENT RV 1 049 10 GAS B VB 2 050 93 GAS TO RS 2 051 88 RS TO RV 1 052 93 GAS TO RS 1 053 89 RS TO FC 1 054 98 BEGIN LOOP 10 055 2 VORTEX ON 15 056 3 VORTEX OFF 15 057 99 END LOOP 1 058 41 VENT RV 1 059 10 GAS B VB 2 060 88 RS TO RV 1 061 91 #10 TO RS 1 062 93 GAS TO RS 3 063 91 #10 TO RS 5 064 89 RS TO FC 1 065 93 GAS TO RS 2 066 42 DRAIN RV 12 167 13 #10 T VB 1 068 50 #10 RV-DRN 2 069 42 DRAIN RV 10 170 56 #10 B RV 4 171 40 MIX RV 2 072 2 VORTEX ON 1 073 9 GAS T VB 4 074 10 GAS B VB 4 075 3 VORTEX OFF 1 0

76 40 MIX RV 2 0 Wash with NMP77 9 GAS T VB 2 078 42 DRAIN RV 5 079 50 #10 RV-DRN 2 080 42 DRAIN RV 5 081 50 #10 RV-DRN 2 082 42 DRAIN RV 10 183 10 GAS B VB 2 0

Applied Biosystems




1 12 #9 B VB 1 02 55 #9 B RV 4 13 40 MIX RV 2 04 2 VORTEX ON 1 0

5 41 VENT RV 2 0 Wash the resin and

6 88 RS TO RV 1 0 resin-sample line with

7 93 GAS TO RS 2 0 DCM, one time 8 90 #9 TO RS 5 09 89 RS TO FC 1 010 40 MIX RV 3 011 3 VORTEX OFF 1 012 42 DRAIN RV 5 013 49 #9 RV-DRN 2 014 42 DRAIN RV 5 015 49 #9 RV-DRN 2 016 42 DRAIN RV 10 117 98 BEGIN LOOP 6 018 55 #9 B RV 4 119 40 MIX RV 2 0

20 2 VORTEX ON 3 0 Wash the resin with

21 40 MIX RV 3 0 DCM six times22 3 VORTEX OFF 1 023 42 DRAIN RV 5 024 49 #9 RV-DRN 2 025 42 DRAIN RV 5 026 49 #9 RV-DRN 2 027 42 DRAIN RV 10 128 99 END LOOP 1 029 55 #9 B RV 4 130 40 MIX RV 2 031 41 VENT RV 2 032 88 RS TO RV 1 0

33 93 GAS TO RS 2 0 Wash the resin and

34 90 #9 TO RS 5 0 resin-sample line

35 89 RS TO FC 1 0 with DCM one time36 2 VORTEX ON 3 037 40 MIX RV 2 038 93 GAS TO RS 8 039 3 VORTEX OFF 1 040 42 DRAIN RV 5 041 49 #9 RV-DRN 2 042 42 DRAIN RV 5 0

Applied Biosystems


Module c – DCM Washes (continued)


43 49 #9 RV-DRN 2 044 42 DRAIN RV 10 145 41 VENT RV 2 0

46 88 RS TO RV 1 0 Remove DCM from

47 93 GAS TO RS 8 0 resin-sample line 48 89 RS TO FC 1 049 42 DRAIN RV 20 050 41 VENT RV 5 051 11 #9 T VB 1 052 12 #9 B VB 1 053 9 GAS T VB 15 054 10 GAS B VB 15 0

Applied Biosystems


Module d – NMP Washes


1 14 #10 B VB 1 02 98 BEGIN LOOP 2 03 56 #10 B RV 3 14 40 MIX RV 1 05 88 RS TO RV 1 06 93 GAS TO RS 4 07 91 #10 TO RS 5 08 89 RS TO FC 1 09 40 MIX RV 2 0

10 2 VORTEX ON 1 0 Wash the resin and

11 10 GAS B VB 6 0 resin-sample line with

12 20 MIX ACT 1 0 NMP, twice13 9 GAS T VB 2 014 40 MIX RV 2 015 3 VORTEX OFF 1 016 42 DRAIN RV 5 017 50 #10 RV-DRN 2 018 42 DRAIN RV 10 119 99 END LOOP 1 020 98 BEGIN LOOP 2 021 56 #10 B RV 3 1

22 40 MIX RV 2 0 Wash the resin with

23 2 VORTEX ON 1 0 NMP, twice24 10 GAS B VB 6 025 20 MIX ACT 1 026 40 MIX RV 2 027 3 VORTEX OFF 1 028 42 DRAIN RV 5 029 50 #10 RV-DRN 2 030 42 DRAIN RV 10 131 99 END LOOP 1 032 56 #10 B RV 3 133 40 MIX RV 1 0

34 88 RS TO RV 1 0 Wash the resin and

35 93 GAS TO RS 5 0 resin-sample line

36 91 #10 TO RS 6 0 with NMP, once37 89 RS TO FC 1 038 40 MIX RV 2 039 2 VORTEX ON 1 040 93 GAS TO RS 2 041 10 GAS B VB 6 042 20 MIX ACT 1 0

Applied Biosystems


Module d – NMP Washes (continued)


43 3 VORTEX OFF 1 044 42 DRAIN RV 4 045 50 #10 RV-DRN 2 046 42 DRAIN RV 4 047 50 #10 RV-DRN 2 048 42 DRAIN RV 12 1

Applied Biosystems




1 14 #10 B VB 1 02 5 NEEDLE DWN 10 03 60 MIX CART 2 04 10 GAS B VB 3 05 20 MIX ACT 1 06 9 GAS T VB 2 07 28 GAS T ACT 2 0

8 38 ACT TO RVo 4 0 Transfer activated amino

9 98 BEGIN LOOP 4 0 acid from the activator

10 37 ACT TO RVc 4 0 to the reaction vessel11 41 VENT RV 1 012 99 END LOOP 1 013 14 #10 B VB 1 014 40 MIX RV 1 015 93 GAS TO RS 3 016 41 VENT RV 1 017 88 RS TO RV 1 018 93 GAS TO RS 1 019 89 RS TO FC 1 020 2 VORTEX ON 1 021 21 VENT ACT 1 022 29 #9 ACT-DRN 2 023 22 DRAIN ACT 1 024 60 MIX CART 5 025 34 #6 B ACT 10 026 3 VORTEX OFF 1 027 20 MIX ACT 3 028 62 DRAIN CART 15 029 67 #10 SML N 1 030 66 #9 SML N 1 031 62 DRAIN CART 15 032 64 #9 CART 2 033 2 VORTEX ON 5 034 60 MIX CART 5 035 24 CART TO AC 10 0

36 62 DRAIN CART 10 0 Clean the empty cartridge

37 64 #9 CART 18 0 and activator38 60 MIX CART 5 039 3 VORTEX OFF 1 040 24 CART TO AC 20 041 62 DRAIN CART 10 042 2 VORTEX ON 1 043 64 #9 CART 2 0

Applied Biosystems




44 60 MIX CART 2 045 24 CART TO AC 10 046 62 DRAIN CART 10 047 60 MIX CART 15 048 61 VENT CART 5 049 3 VORTEX OFF 1 050 98 BEGIN LOOP 5 051 20 MIX ACT 6 052 1 WAIT 4 053 99 END LOOP 1 054 2 VORTEX ON 1 055 22 DRAIN ACT 25 056 98 BEGIN LOOP 3 057 29 #9 ACT-DRN 2 058 22 DRAIN ACT 10 059 99 END LOOP 1 060 35 #9 B ACT 2 061 20 MIX ACT 3 062 22 DRAIN ACT 20 063 3 VORTEX OFF 1 064 9 GAS T VB 10 065 10 GAS B VB 10 0

Applied Biosystems


Module f – Coupling


1 14 #10 B VB 1 02 9 GAS T VB 3 03 93 GAS TO RS 3 04 10 GAS B VB 6 05 20 MIX ACT 1 06 41 VENT RV 1 07 88 RS TO RV 1 08 93 GAS TO RS 1 09 89 RS TO FC 1 0

10 98 BEGIN LOOP 8 0 8.5 minutes of coupling

11 2 VORTEX ON 15 0 with one rinse of

12 3 VORTEX OFF 15 0 the resin-sample line13 99 END LOOP 1 014 10 GAS B VB 6 015 20 MIX ACT 1 016 9 GAS T VB 3 017 98 BEGIN LOOP 8 018 2 VORTEX ON 15 019 3 VORTEX OFF 15 020 99 END LOOP 1 021 9 GAS T VB 3 022 10 GAS B VB 6 023 20 MIX ACT 1 024 9 GAS T VB 3 0

Applied Biosystems


Module g – NMP Washes


1 91 #10 TO RS 1 02 93 GAS TO RS 5 03 41 VENT RV 1 04 88 RS TO RV 1 05 93 GAS TO RS 3 06 91 #10 TO RS 5 07 89 RS TO FC 1 08 98 BEGIN LOOP 3 09 14 #10 B VB 1 010 40 MIX RV 8 011 99 END LOOP 1 0

12 42 DRAIN RV 20 1 Drain reaction vessel

13 14 #10 b vb 1 014 56 #10 B RV 6 115 40 MIX RV 2 016 2 VORTEX ON 1 017 93 GAS TO RS 2 018 90 #9 TO RS 1 019 93 GAS TO RS 3 020 90 #9 TO RS 1 021 93 GAS TO RS 3 022 98 BEGIN LOOP 1 023 39 RELAY 0 1 024 41 VENT RV 1 025 88 RS TO RV 1 026 91 #10 TO RS 1 027 93 GAS TO RS 1 028 48 GAS T RV 1 0

29 87 TAKE SAMPL 1 0 Take resin sample30 89 RS TO FC 1 031 90 #9 TO RS 1 032 93 GAS TO RS 3 033 90 #9 TO RS 1 034 93 GAS TO RS 3 035 90 #9 TO RS 2 036 93 GAS TO RS 3 037 41 VENT RV 1 038 88 RS TO RV 1 039 91 #10 TO RS 1 040 93 GAS TO RS 2 041 91 #10 TO RS 5 042 89 RS TO FC 1 0

Applied Biosystems


Module g – NMP Washes (continued)


43 39 RELAY 0 1 044 99 END LOOP 1 045 3 VORTEX OFF 1 046 42 DRAIN RV 5 047 50 #10 RV-DRN 2 048 42 DRAIN RV 5 049 50 #10 RV-DRN 2 050 42 DRAIN RV 10 151 56 #10 B RV 3 152 40 MIX RV 2 053 93 GAS TO RS 3 054 88 RS TO RV 1 055 93 GAS TO RS 3 056 91 #10 TO RS 5 057 89 RS TO FC 1 058 40 MIX RV 2 059 2 VORTEX ON 5 0

60 40 MIX RV 2 0 Wash the resin and

61 3 VORTEX OFF 1 0 resin-sample line with

62 42 DRAIN RV 5 0 NMP, once63 50 #10 RV-DRN 2 064 42 DRAIN RV 10 165 98 BEGIN LOOP 3 066 56 #10 B RV 3 167 40 MIX RV 2 068 2 VORTEX ON 1 0

69 10 GAS B VB 6 0 Wash the Resin with

70 20 MIX ACT 1 0 NMP, three times71 40 MIX RV 2 072 3 VORTEX OFF 1 073 42 DRAIN RV 5 074 50 #10 RV-DRN 2 075 42 DRAIN RV 10 176 99 END LOOP 1 077 11 #9 T VB 1 078 12 #9 B VB 1 079 9 GAS T VB 5 080 10 GAS B VB 5 0

Applied Biosystems


Module h – Loading


1 61 VENT CART 10 0


4 7 EJECT CART 10 0 Eject the blank cartridge

5 8 ADVAN CART 10 0 Advance the new cartridge6 5 NEEDLE DWN 10 07 14 #10 B VB 1 08 10 GAS B VB 2 09 36 #10 B ACT 3 0

10 20 MIX ACT 10 0 Add 0.8 mL NMP to cartridge

11 65 #10 CART 2 0 Add 1.8 mL DCM to cartridge12 64 #9 CART 3 013 60 MIX CART 30 014 91 #10 TO RS 1 015 93 GAS TO RS 5 016 55 #9 B RV 5 017 88 RS TO RV 1 0

18 93 GAS TO RS 5 0 Resin swelling in

19 90 #9 TO RS 5 0 DCM/NMP20 89 RS TO FC 1 021 93 GAS TO RS 5 022 56 #10 B RV 2 023 40 MIX RV 2 024 2 VORTEX ON 10 025 3 VORTEX OFF 1 026 98 BEGIN LOOP 3 0

27 60 MIX CART 60 0 Dissolve amino acid28 1 WAIT 15 029 99 END LOOP 1 030 22 DRAIN ACT 15 031 30 #10 A-DRN 2 032 22 DRAIN ACT 5 033 29 #9 ACT-DRN 4 034 22 DRAIN ACT 20 035 10 GAS B VB 5 036 60 MIX CART 30 037 98 BEGIN LOOP 3 0

38 24 CART TO AC 4 0 Transfer amino acid to activator39 1 WAIT 4 040 99 END LOOP 1 041 64 #9 CART 2 042 60 MIX CART 3 0

Applied Biosystems


Module h - Loading (continued)


43 78 PRS #M 10 044 98 BEGIN LOOP 1 0

45 69 MEAS #8 3 0 Add 0.5 mL DCC

46 23 ML TO ACT 3 0 to the activator47 1 WAIT 3 048 23 ML TO ACT 3 049 1 WAIT 3 050 99 END LOOP 1 051 24 CART TO AC 6 052 1 WAIT 3 053 35 #9 B ACT 1 054 20 MIX ACT 2 055 65 #10 CART 1 056 60 MIX CART 2 057 65 #10 CART 2 058 10 GAS B VB 6 059 98 BEGIN LOOP 50 060 20 MIX ACT 1 0

61 1 WAIT 15 0 13 minutes of activation62 99 END LOOP 1 063 77 PRS #4 10 064 42 DRAIN RV 10 065 49 #9 RV-DRN 2 066 42 DRAIN RV 8 067 17 #4 B VB 1 068 10 GAS B VB 1 0

69 52 #4 B RV 1 0 Add 0.36 mL of 0.1M DMAP

70 55 #9 B RV 1 0 Add 0.6 mL DCM to resin71 40 MIX RV 2 072 10 GAS B VB 2 073 9 GAS T VB 2 074 20 MIX ACT 1 0

Module i – Wait



Applied Biosystems


Boc/HOBt/DCC 0.50 mmol Chemistry



1 1 WAIT 1 02 58 INTERRUPT 0 0 (for power failure feature)3 12 #9 B VB 1 04 73 VENT #2 2 05 10 GAS B VB 3 06 74 FLUSH #2 2 0

7 73 VENT #2 2 0 Clean the valve blocks and

8 9 GAS T VB 1 0 vent the TFA bottle9 10 GAS B VB 2 010 14 #10 B VB 1 011 13 #10 T VB 1 012 61 VENT CART 10 0

13 4 PRINT CART 10 0 Print the amino acid name14 6 NEEDLE UP 10 015 7 EJECT CART 10 0

16 8 ADVAN CART 10 0 Advance the new cartridge17 5 NEEDLE DWN 10 018 9 GAS T VB 1 019 13 #10 T VB 1 020 10 GAS B VB 1 021 14 #10 B VB 1 022 20 MIX ACT 2 0

23 65 #10 CART 8 0 Add 3.4 mL NMP to cartridge24 60 MIX CART 120 025 98 BEGIN LOOP 8 0

26 20 MIX ACT 2 0 Dissolve amino acid27 60 MIX CART 15 028 2 VORTEX ON 5 029 3 VORTEX OFF 6 030 99 END LOOP 1 031 10 GAS B VB 2 032 14 #10 B VB 1 033 78 PRS #M 10 034 70 PURGE ML 2 035 14 #10 B VB 1 0

36 98 BEGIN LOOP 4 0 Add 2.0 mL 1M HOBT

37 68 MEAS #7 3 0 to the cartridge38 14 #10 B VB 1 039 20 MIX ACT 2 040 63 ML TO CART 5 0

Applied Biosystems




41 99 END LOOP 1 042 10 GAS B VB 1 043 14 #10 B VB 1 044 98 BEGIN LOOP 6 045 20 MIX ACT 2 0 Mix cartridge contents46 60 MIX CART 4 047 2 VORTEX ON 6 048 3 VORTEX OFF 12 049 99 END LOOP 1 050 20 MIX ACT 2 051 9 GAS T VB 1 052 11 #9 T VB 1 053 2 VORTEX ON 1 054 22 DRAIN ACT 10 055 29 #9 ACT-DRN 4 056 3 VORTEX OFF 1 057 22 DRAIN ACT 40 058 10 GAS B VB 1 059 14 #10 B VB 1 060 24 CART TO AC 26 061 98 BEGIN LOOP 5 062 24 CART TO AC 2 063 1 WAIT 5 064 99 END LOOP 1 0

65 10 GAS B VB 1 0 Transfer amino acid to activator66 14 #10 B VB 1 067 60 MIX CART 3 068 24 CART TO AC 2 069 1 WAIT 5 070 24 CART TO AC 2 071 78 PRS #M 5 072 24 CART TO AC 2 073 70 PURGE ML 2 074 14 #10 B VB 1 075 98 BEGIN LOOP 4 076 69 MEAS #8 3 077 14 #10 B VB 1 0

78 23 ML TO ACT 2 0 Add 2.0 mL 1M DCC

79 1 WAIT 5 0 to activator80 23 ML TO ACT 2 081 1 WAIT 5 082 23 ML TO ACT 2 083 1 WAIT 1 084 99 END LOOP 1 0

Applied Biosystems




85 14 #10 B VB 1 086 60 MIX CART 4 087 20 MIX ACT 1 088 65 #10 CART 3 0 Clean needle with NMP89 2 VORTEX ON 10 090 3 VORTEX OFF 1 091 11 #9 T VB 1 092 12 #9 B VB 1 093 9 GAS T VB 5 094 10 GAS B VB 5 0

Applied Biosystems


Module b – TFA Deprotection


1 12 #9 B VB 1 02 93 GAS TO RS 2 03 55 #9 B RV 10 14 88 RS TO RV 1 0

5 90 #9 TO RS 4 0 Wash with DCM6 89 RS TO FC 1 07 2 VORTEX ON 1 08 40 MIX RV 2 09 10 GAS B VB 6 010 20 MIX ACT 1 011 3 VORTEX OFF 1 012 73 VENT #2 2 013 75 GAS-VENT #2 2 014 76 PRS #2 15 015 42 DRAIN RV 14 116 41 VENT RV 2 017 88 RS TO RV 1 018 90 #9 TO RS 5 019 89 RS TO FC 1 020 93 GAS TO RS 3 021 42 DRAIN RV 10 122 41 VENT RV 2 023 72 #2 B RV 30 624 55 #9 B RV 12 125 40 MIX RV 1 026 2 VORTEX ON 1 027 10 GAS B VB 6 028 73 VENT #2 5 0

29 74 FLUSH #2 3 0 3-minute deprotection with

30 73 VENT #2 2 0 25% TFA in DCM31 3 VORTEX OFF 2 032 41 VENT RV 4 033 13 #10 T VB 2 034 14 #10 B VB 2 035 11 #9 T VB 3 036 12 #9 B VB 3 037 9 GAS T VB 8 038 10 GAS B VB 8 039 98 BEGIN LOOP 3 040 2 VORTEX ON 15 041 3 VORTEX OFF 20 042 99 END LOOP 1 043 76 PRS #2 20 0

Applied Biosystems


Module b – TFA Deprotection (continued)Step# Fxn# Function Name Time Add Key Events

44 41 VENT RV 8 045 11 #9 T VB 1 046 42 DRAIN RV 18 147 12 #9 B VB 2 048 10 GAS B VB 3 049 41 VENT RV 2 050 72 #2 B RV 48 1051 55 #9 B RV 4 052 40 MIX RV 2 053 2 VORTEX ON 1 054 9 GAS T VB 2 055 10 GAS B VB 6 056 73 VENT #2 5 057 74 FLUSH #2 6 058 73 VENT #2 2 059 75 GAS-VENT #2 4 060 74 FLUSH #2 4 061 73 VENT #2 3 062 3 VORTEX OFF 1 063 93 GAS TO RS 3 064 41 VENT RV 4 065 88 RS TO RV 1 066 93 GAS TO RS 2 0

67 41 VENT RV 2 0 16-minute deprotection

68 89 RS TO FC 1 0 with 50% TFA in DCM69 13 #10 T VB 2 070 14 #10 B VB 2 071 98 BEGIN LOOP 4 072 12 #9 B VB 2 073 11 #9 T VB 2 074 10 GAS B VB 3 075 9 GAS T VB 3 076 99 END LOOP 1 077 9 GAS T VB 10 078 10 GAS B VB 10 079 98 BEGIN LOOP 11 080 2 VORTEX ON 15 081 3 VORTEX OFF 15 082 99 END LOOP 1 083 41 VENT RV 5 084 12 #9 B VB 1 085 11 #9 T VB 1 086 9 GAS T VB 6 087 10 GAS B VB 6 0

Applied Biosystems


Module b – TFA Deprotection (continued)


88 98 BEGIN LOOP 11 089 2 VORTEX ON 15 090 3 VORTEX OFF 15 091 99 END LOOP 1 092 41 VENT RV 10 093 88 RS TO RV 1 094 90 #9 TO RS 5 095 89 RS TO FC 1 096 42 DRAIN RV 10 097 49 #9 RV-DRN 5 098 42 DRAIN RV 18 1

Applied Biosystems




1 10 GAS B VB 1 02 9 GAS T VB 1 03 12 #9 B VB 1 04 11 #9 T VB 1 05 55 #9 B RV 7 16 90 #9 TO RS 1 07 41 VENT RV 1 08 88 RS TO RV 1 09 2 VORTEX ON 1 0


11 90 #9 TO RS 4 0 resin-sampling line

12 89 RS TO FC 1 0 with DCM, once13 40 MIX RV 2 014 3 VORTEX OFF 1 015 40 MIX RV 3 016 9 GAS T VB 1 017 49 #9 RV-DRN 4 018 42 DRAIN RV 9 119 98 BEGIN LOOP 3 020 12 #9 B VB 1 021 9 GAS T VB 1 0

22 55 #9 B RV 6 1 Wash resin with DCM,

23 2 VORTEX ON 1 0 3 Times24 55 #9 B RV 3 025 40 MIX RV 3 026 3 VORTEX OFF 1 027 9 GAS T VB 1 028 49 #9 RV-DRN 4 029 42 DRAIN RV 9 130 99 END LOOP 1 031 12 #9 B VB 1 032 9 GAS T VB 1 033 55 #9 B RV 7 134 2 VORTEX ON 1 035 90 #9 TO RS 1 036 88 RS TO RV 1 0


38 90 #9 to RS 4 0 resin-sample line

39 89 RS TO FC 1 0 with DMC, once40 40 MIX RV 2 041 3 VORTEX OFF 1 042 40 MIX RV 3 0

Applied Biosystems


Module c – Boc/HOBt/DCC 0.25 mmol: DCM Washes


43 9 GAS T VB 1 044 49 #9 RV-DRN 4 045 42 DRAIN RV 4 046 49 #9 RV-DRN 5 047 42 DRAIN RV 12 148 41 VENT RV 3 049 10 GAS B VB 5 050 9 GAS T VB 5 0

Applied Biosystems


Module d – DIEA Neutralization and NMP Washes


1 12 #9 B VB 1 02 11 #9 T VB 1 03 55 #9 B RV 12 14 79 PRS #1 10 05 98 BEGIN LOOP 2 06 3 VORTEX OFF 1 07 51 #1 B RV 4 08 56 #10 B RV 8 09 40 MIX RV 4 010 2 VORTEX ON 3 011 13 #10 T VB 1 012 41 VENT RV 2 013 88 RS TO RV 1 014 93 GAS TO RS 2 015 92 #1 TO RS 1 0

16 91 #10 TO RS 5 0 DIEA neutralization:

17 89 RS TO FC 1 0 First in DCM/NMP, then in

18 40 MIX RV 5 0 NMP19 9 GAS T VB 2 020 3 VORTEX OFF 1 021 13 #10 T VB 1 022 41 VENT RV 2 023 47 #1 T RV 2 024 50 #10 RV-DRN 6 025 42 DRAIN RV 15 126 14 #10 B VB 1 027 56 #10 B RV 20 128 2 VORTEX ON 1 029 40 MIX RV 2 030 10 GAS B VB 6 031 20 MIX ACT 1 0

32 99 END LOOP 1 0 Wash the resin with

33 91 #10 TO RS 4 0 NMP, once34 9 GAS T VB 2 035 3 VORTEX OFF 1 036 50 #10 RV-DRN 3 037 42 DRAIN RV 15 138 98 BEGIN LOOP 1 039 14 #10 B VB 1 040 9 GAS T VB 1 041 56 #10 B RV 10 1

42 2 VORTEX ON 1 0 Wash the resin with NMP,

Applied Biosystems


Module d – DIEA Neutralization and NMP Washes (continued)


43 56 #10 B RV 3 0 once44 40 MIX RV 3 045 10 GAS B VB 6 046 20 MIX ACT 1 047 3 VORTEX OFF 1 048 50 #10 RV-DRN 4 049 42 DRAIN RV 15 150 99 END LOOP 1 051 14 #10 B VB 1 052 9 GAS T VB 1 053 56 #10 B RV 10 154 2 VORTEX ON 1 055 56 #10 B RV 2 0

56 91 #10 TO RS 1 0 Wash the resin and

57 88 RS TO RV 1 0 resin-sample line with

58 93 GAS TO RS 2 0 NMP, once59 91 #10 TO RS 4 060 89 RS TO FC 1 061 40 MIX RV 3 062 10 GAS B VB 6 063 20 MIX ACT 1 064 3 VORTEX OFF 1 065 50 #10 RV-DRN 4 066 42 DRAIN RV 15 167 98 BEGIN LOOP 2 068 14 #10 B VB 1 069 9 GAS T VB 1 070 56 #10 B RV 10 171 2 VORTEX ON 1 072 56 #10 B RV 3 0

73 40 MIX RV 3 0 Wash resin with

74 10 GAS B VB 6 0 NMP, 2 times75 20 MIX ACT 1 076 3 VORTEX OFF 1 077 50 #10 RV-DRN 4 078 42 DRAIN RV 15 179 99 END LOOP 1 080 14 #10 B VB 1 081 9 GAS T VB 1 082 56 #10 B RV 10 183 2 VORTEX ON 1 084 56 #10 B RV 2 0

Applied Biosystems




85 91 #10 TO RS 1 0

86 88 RS TO RV 1 0 Wash the resin and

87 93 GAS TO RS 2 0 resin-sample line

88 91 #10 TO RS 4 0 with NMP, once 89 89 RS TO FC 1 090 40 MIX RV 3 091 10 GAS B VB 6 092 20 MIX ACT 1 093 3 VORTEX OFF 1 094 50 #10 RV-DRN 4 095 42 DRAIN RV 15 196 13 #10 T VB 1 097 14 #10 B VB 1 098 93 GAS TO RS 2 0

Applied Biosystems




1 9 GAS T VB 1 02 5 NEEDLE DWN 10 03 60 MIX CART 3 04 10 GAS B VB 2 05 20 MIX ACT 1 06 9 GAS T VB 1 07 28 GAS T ACT 2 08 13 #10 T VB 1 09 38 ACT TO RVo 4 010 2 VORTEX ON 1 011 56 #10 B RV 1 012 9 GAS T VB 1 013 28 GAS T ACT 2 014 13 #10 T VB 1 015 38 ACT TO RVo 3 016 40 MIX RV 1 017 9 GAS T VB 1 018 28 GAS T ACT 2 019 13 #10 T VB 1 0

20 3 VORTEX OFF 1 0 Transfer activated amino

21 38 ACT TO RVo 4 0 acid from the activator to

22 40 MIX RV 1 0 the reaction vessel 23 2 VORTEX ON 1 024 9 GAS T VB 1 025 28 GAS T ACT 2 026 3 VORTEX OFF 1 027 38 ACT TO RVo 8 028 40 MIX RV 1 029 98 begin loop 2 030 13 #10 T VB 1 031 21 VENT ACT 2 032 26 #10 T ACT 1 033 28 GAS T ACT 3 034 13 #10 T VB 1 035 38 ACT TO RVo 6 036 99 END LOOP 1 037 40 MIX RV 2 038 93 GAS TO RS 2 039 41 VENT RV 2 040 88 RS TO RV 1 041 93 GAS TO RS 3 042 89 RS TO FC 1 043 2 VORTEX ON 1 0

Applied Biosystems




44 11 #9 T VB 1 045 29 #9 ACT-DRN 5 046 62 DRAIN CART 10 047 3 VORTEX OFF 1 048 34 #6 B ACT 16 049 20 MIX ACT 3 050 67 #10 SML N 2 051 66 #9 SML N 2 052 62 DRAIN CART 15 053 12 #9 B VB 1 054 98 BEGIN LOOP 2 055 64 #9 CART 20 056 2 VORTEX ON 1 057 1 WAIT 5 058 60 MIX CART 5 059 3 VORTEX OFF 1 060 24 CART TO AC 20 061 99 END LOOP 1 062 20 MIX ACT 5 063 62 DRAIN CART 5 064 66 #9 SML N 2 065 62 DRAIN CART 5 066 66 #9 SML N 2 067 62 DRAIN CART 15 068 20 MIX ACT 5 069 2 VORTEX ON 1 070 60 MIX CART 15 0

71 20 MIX ACT 5 0 Clean the empty cartridge

72 61 VENT CART 5 0 and activator 73 3 VORTEX OFF 1 074 98 BEGIN LOOP 8 075 20 MIX ACT 5 076 1 WAIT 5 077 99 END LOOP 1 078 11 #9 T VB 1 079 2 VORTEX ON 1 080 22 DRAIN ACT 30 081 3 VORTEX OFF 1 082 98 BEGIN LOOP 3 083 29 #9 ACT-DRN 2 084 22 DRAIN ACT 5 085 99 END LOOP 1 086 2 VORTEX ON 1 087 12 #9 B VB 1 0

Applied Biosystems




88 35 #9 B ACT 2 089 20 MIX ACT 3 090 11 #9 T VB 1 091 3 VORTEX OFF 1 092 22 DRAIN ACT 30 0

Applied Biosystems


Module f – Coupling in NMP and Adding DMSO


1 10 GAS B VB 2 02 12 #9 B VB 1 03 9 GAS T VB 2 04 11 #9 T VB 1 05 93 GAS TO RS 2 06 10 GAS B VB 2 07 14 #10 B VB 1 08 9 GAS T VB 2 09 13 #10 T VB 1 010 2 VORTEX ON 10 011 3 VORTEX OFF 1 012 10 GAS B VB 2 013 14 #10 B VB 1 014 9 GAS T VB 2 015 13 #10 T VB 1 016 91 #10 TO RS 1 017 93 GAS TO RS 3 018 41 VENT RV 1 019 88 RS TO RV 1 020 93 GAS TO RS 1 021 2 VORTEX ON 1 022 93 GAS TO RS 1 023 89 RS TO FC 1 024 13 #10 T VB 1 025 14 #10 B VB 1 026 9 GAS T VB 5 0

27 10 GAS B VB 5 0 Coupling in NMP28 98 BEGIN LOOP 26 029 2 VORTEX ON 12 030 3 VORTEX OFF 1 031 1 WAIT 17 032 99 END LOOP 1 033 10 GAS B VB 2 034 14 #10 B VB 1 035 9 GAS T VB 2 036 13 #10 T VB 1 037 91 #10 TO RS 1 038 93 GAS TO RS 3 039 41 VENT RV 1 040 88 RS TO RV 1 041 93 GAS TO RS 1 042 91 #10 TO RS 1 043 93 GAS TO RS 2 0

Applied Biosystems


Module f – Couple in NMP and Add DMSO (continued)


44 2 VORTEX ON 1 045 93 GAS TO RS 1 046 89 RS TO FC 1 047 13 #10 T VB 1 048 14 #10 B VB 1 049 9 GAS T VB 5 050 10 GAS B VB 5 051 98 BEGIN LOOP 26 052 2 VORTEX ON 12 053 3 VORTEX OFF 1 054 1 WAIT 17 055 99 END LOOP 1 056 10 GAS B VB 2 057 14 #10 B VB 1 058 9 GAS T VB 2 059 13 #10 T VB 1 060 10 GAS B VB 2 061 14 #10 B VB 1 062 9 GAS T VB 2 063 13 #10 T VB 1 064 10 GAS B VB 2 065 14 #10 B VB 1 066 79 PRS #1 10 067 16 #1 B VB 1 068 78 PRS #M 10 069 14 #10 B VB 1 070 10 GAS B VB 2 071 18 #5 B VB 3 072 41 VENT RV 1 073 53 #5 B RV 14 1 Adding DMSO74 40 MIX RV 3 075 13 #10 T VB 1 076 14 #10 B VB 1 077 91 #10 TO RS 1 078 93 GAS TO RS 3 079 41 VENT RV 1 080 88 RS TO RV 1 081 91 #10 TO RS 1 082 2 VORTEX ON 1 083 93 GAS TO RS 2 084 89 RS TO FC 1 085 9 GAS T VB 10 086 10 GAS B VB 10 087 3 VORTEX OFF 1 0

Applied Biosystems


Module g – DIEA addition, resin sampling and capping


1 79 PRS #1 10 02 16 #1 B VB 1 03 10 GAS B VB 2 0

4 51 #1 B RV 1 0 Adding DIEA5 56 #10 B RV 1 06 40 MIX RV 3 07 41 VENT RV 2 08 88 RS TO RV 1 09 93 GAS TO RS 2 010 89 RS TO FC 1 011 14 #10 B VB 1 012 9 GAS T VB 5 013 10 GAS B VB 5 014 98 BEGIN LOOP 8 015 2 VORTEX ON 12 016 3 VORTEX OFF 18 017 99 END LOOP 1 018 98 BEGIN LOOP 2 019 93 GAS TO RS 3 020 91 #10 TO RS 1 021 99 END LOOP 1 022 14 #10 B VB 1 023 88 RS TO RV 1 024 93 GAS TO RS 2 025 91 #10 TO RS 4 026 89 RS TO FC 1 027 56 #10 B RV 1 028 40 MIX RV 4 029 9 GAS T VB 2 030 15 #1 T VB 1 031 50 #10 RV-drn 4 0

32 42 DRAIN RV 35 1 Drain33 14 #10 B VB 1 034 13 #10 T VB 1 035 56 #10 B RV 14 136 2 VORTEX ON 1 037 40 MIX RV 2 038 98 BEGIN LOOP 1 039 93 GAS TO RS 2 040 39 RELAY 0 1 041 92 #1 TO RS 1 042 91 #10 TO RS 4 043 88 RS TO RV 1 0

Applied Biosystems


Module g – DIEA addition, resin sampling and capping (continued)


44 93 GAS TO RS 2 045 91 #10 TO RS 4 046 9 GAS T VB 3 047 13 #10 T VB 1 048 41 VENT RV 2 049 91 #10 TO RS 1 050 48 GAS T RV 2 0

51 87 TAKE SAMPL 2 0 Resin sample52 89 RS TO FC 1 053 90 #9 TO RS 2 054 93 GAS TO RS 2 055 90 #9 TO RS 2 056 93 GAS TO RS 2 057 91 #10 TO RS 3 058 41 VENT RV 1 059 88 RS TO RV 1 060 91 #10 TO RS 1 061 93 GAS TO RS 3 062 91 #10 TO RS 4 063 89 RS TO FC 1 064 39 RELAY 0 1 065 99 END LOOP 1 066 3 VORTEX OFF 1 067 79 PRS #1 5 068 51 #1 B RV 2 069 56 #10 B RV 1 070 40 MIX RV 3 071 2 VORTEX ON 1 072 77 PRS #4 10 073 17 #4 B VB 1 074 3 VORTEX OFF 1 075 52 #4 B RV 5 076 56 #10 B RV 2 077 40 MIX RV 3 0

78 93 GAS TO RS 3 0 Capping79 88 RS TO RV 1 080 93 GAS TO RS 2 081 89 RS TO FC 1 082 9 GAS T VB 5 083 10 GAS B VB 5 084 98 BEGIN LOOP 16 085 2 VORTEX ON 12 086 3 VORTEX OFF 18 0

Applied Biosystems


Module g – DIEA addition, resin sampling and capping (continued)


87 99 END LOOP 1 088 88 RS TO RV 1 089 90 #9 TO RS 4 090 89 RS TO FC 1 091 9 GAS T VB 2 092 42 DRAIN RV 18 1

Module h – Coupling


1 14 #10 B VB 1 02 93 GAS TO RS 3 03 9 GAS T VB 5 04 10 GAS B VB 5 05 41 VENT RV 2 06 88 RS TO RV 1 07 93 GAS TO RS 2 08 2 VORTEX ON 1 09 93 GAS TO RS 1 010 89 RS TO FC 1 011 10 GAS B VB 5 012 9 GAS T VB 5 0

13 98 BEGIN LOOP 40 0 Coupling14 2 VORTEX ON 12 015 3 VORTEX OFF 18 016 99 END LOOP 1 017 12 #9 B VB 1 018 11 #9 T VB 1 019 10 GAS B VB 10 020 9 GAS T VB 10 0

Module i – Wait



Applied Biosystems


Boc/HOBt/DCC 0.10 mmol



1 1 WAIT 1 02 58 INTERRUPT 0 0 (for power failure feature)3 61 VENT CART 10 0


6 7 EJECT CART 10 0 Advance the new cartridge7 8 ADVAN CART 10 08 5 NEEDLE DWN 10 09 2 VORTEX ON 1 010 14 #10 B VB 1 011 9 GAS T VB 2 012 20 MIX ACT 4 013 3 VORTEX OFF 1 014 65 #10 CART 4 0

15 60 MIX CART 60 0 Add 1.7 mL NMP to cartridge16 2 VORTEX ON 1 017 78 PRS #M 10 018 10 GAS B VB 2 019 3 VORTEX OFF 1 020 98 BEGIN LOOP 2 021 68 MEAS #7 3 0

22 20 MIX ACT 2 0 Add 1.0 mL 1M HOBT to

23 63 ML TO CART 6 0 cartridge24 99 END LOOP 1 025 9 GAS T VB 5 026 10 GAS B VB 5 027 98 BEGIN LOOP 8 028 60 MIX CART 60 029 2 VORTEX ON 8 030 20 MIX ACT 2 031 3 VORTEX OFF 1 0 Dissolve amino acid32 99 END LOOP 1 033 22 DRAIN ACT 10 034 35 #9 B ACT 2 035 20 MIX ACT 4 036 98 BEGIN LOOP 2 037 22 DRAIN ACT 5 038 21 VENT ACT 2 039 25 #9 T ACT 2 040 99 END LOOP 1 0

Applied Biosystems




41 22 DRAIN ACT 2 042 2 VORTEX ON 1 043 10 GAS B VB 6 044 60 MIX CART 30 045 3 VORTEX OFF 1 046 22 DRAIN ACT 30 047 10 GAS B VB 3 048 60 MIX CART 30 049 2 VORTEX ON 1 050 10 GAS B VB 3 051 24 CART TO AC 18 052 3 VORTEX OFF 1 053 98 BEGIN LOOP 4 0 Transfer amino acid to

54 24 CART TO AC 3 0 activator55 1 WAIT 4 056 99 END LOOP 1 057 65 #10 CART 1 058 60 MIX CART 3 059 78 PRS #M 5 060 98 BEGIN LOOP 2 061 69 MEAS #8 3 062 23 ML TO ACT 3 063 1 WAIT 3 0 Add 1.0 mL 1M DCC

64 23 ML TO ACT 3 0 to activator65 99 END LOOP 1 066 60 MIX CART 3 067 62 DRAIN CART 5 068 67 #10 SML N 1 069 62 DRAIN CART 5 0

70 67 #10 SML N 1 0 Clean needle with NMP71 62 DRAIN CART 10 072 64 #9 CART 9 0

73 60 MIX CART 5 0 Add DCM and NMP to

74 65 #10 CART 2 0 cartridge75 10 GAS B VB 6 076 20 MIX ACT 1 077 14 #10 B VB 1 078 2 VORTEX ON 1 079 10 GAS B VB 6 080 20 MIX ACT 1 081 11 #9 T VB 1 082 12 #9 B VB 1 083 9 GAS T VB 5 084 10 GAS B VB 5 085 3 VORTEX OFF 1 0

Applied Biosystems


Module b – TFA Deprotection


1 12 #9 B VB 1 02 93 GAS TO RS 2 03 55 #9 B RV 3 14 88 RS TO RV 1 05 90 #9 TO RS 4 06 89 RS TO FC 1 07 40 MIX RV 2 08 2 VORTEX ON 1 09 10 GAS B VB 6 010 20 MIX ACT 1 011 3 VORTEX OFF 1 012 73 VENT #2 2 0

13 75 GAS-VENT #2 2 0 Washing with DCM14 76 PRS #2 15 015 42 DRAIN RV 5 016 41 VENT RV 2 017 88 RS TO RV 1 018 90 #9 TO RS 4 019 89 RS TO FC 1 020 93 GAS TO RS 3 021 42 DRAIN RV 10 122 41 VENT RV 2 023 72 #2 B RV 11 124 40 MIX RV 1 025 55 #9 B RV 4 026 40 MIX RV 1 027 10 GAS B VB 6 028 73 VENT #2 5 029 74 FLUSH #2 3 030 73 VENT #2 2 031 41 VENT RV 2 0

32 13 #10 T VB 1 0 3-minute deprotection

33 14 #10 B VB 1 0 with 25% TFA in DCM34 11 #9 T VB 2 035 12 #9 B VB 2 036 9 GAS T VB 5 037 10 GAS B VB 5 038 98 BEGIN LOOP 3 039 2 VORTEX ON 15 040 3 VORTEX OFF 15 041 99 END LOOP 1 042 76 PRS #2 20 043 41 VENT RV 3 0

Applied Biosystems




44 42 DRAIN RV 12 145 12 #9 B VB 2 046 10 GAS B VB 3 047 41 VENT RV 2 048 72 #2 B RV 20 049 40 MIX RV 1 050 55 #9 B RV 2 051 40 MIX RV 1 052 2 VORTEX ON 1 053 9 GAS T VB 2 054 10 GAS B VB 6 055 73 VENT #2 5 056 74 FLUSH #2 6 057 73 VENT #2 2 958 75 GAS-VENT #2 4 059 74 FLUSH #2 4 060 73 VENT #2 3 061 3 VORTEX OFF 1 062 93 GAS TO RS 3 063 41 VENT RV 2 064 88 RS TO RV 1 065 93 GAS TO RS 2 0

66 41 VENT RV 2 0 11-minute deprotection

67 89 RS TO FC 1 0 with 50% TFA in DCM68 13 #10 T VB 1 069 14 #10 B VB 1 070 98 BEGIN LOOP 3 071 12 #9 B VB 2 072 11 #9 T VB 2 073 10 GAS B VB 2 074 9 GAS T VB 2 075 99 END LOOP 1 076 9 GAS T VB 6 077 10 GAS B VB 6 078 98 BEGIN LOOP 9 079 2 VORTEX ON 15 080 3 VORTEX OFF 15 081 99 END LOOP 1 082 41 VENT RV 2 083 12 #9 B VB 1 084 11 #9 T VB 1 085 9 GAS T VB 6 086 10 GAS B VB 6 087 98 BEGIN LOOP 9 0

Applied Biosystems




88 2 VORTEX ON 15 089 3 VORTEX OFF 15 090 99 END LOOP 1 091 41 VENT RV 2 092 88 RS TO RV 1 093 90 #9 TO RS 5 094 89 RS TO FC 1 095 42 DRAIN RV 5 096 49 #9 RV-DRN 5 097 42 DRAIN RV 12 1

Applied Biosystems




1 12 #9 B VB 1 02 55 #9 B RV 2 13 40 MIX RV 2 04 2 VORTEX ON 1 0


6 88 RS TO RV 1 0 resin-sampling line

7 93 GAS TO RS 2 0 with DCM, once8 90 #9 TO RS 4 09 89 RS TO FC 1 010 93 GAS TO RS 2 011 40 MIX RV 2 012 3 VORTEX OFF 1 013 49 #9 RV-DRN 1 014 42 DRAIN RV 3 015 49 #9 RV-DRN 1 016 42 DRAIN RV 5 117 98 BEGIN LOOP 3 018 55 #9 B RV 2 119 40 MIX RV 2 020 2 VORTEX ON 3 0

21 40 MIX RV 2 0 Wash resin with DCM,

22 3 VORTEX OFF 1 0 3 times23 49 #9 RV-DRN 1 024 42 DRAIN RV 3 025 49 #9 RV-DRN 1 026 42 DRAIN RV 5 127 99 END LOOP 1 0

Applied Biosystems


Module d – DIEA Neutralization and NMP Washes


1 79 PRS#1 5 02 14 #10 B VB 1 03 98 BEGIN LOOP 2 04 56 #10 B RV 4 05 51 #1 B RV 2 06 56 #10 B RV 3 07 40 MIX RV 2 08 41 VENT RV 2 09 88 RS TO RV 1 0

10 93 GAS TO RS 3 0 DIEA neutralization11 91 #10 TO RS 1 012 92 #1 TO RS 1 013 91 #10 TO RS 4 014 89 RS TO FC 1 015 40 MIX RV 2 016 2 VORTEX ON 1 017 79 PRS #1 5 018 40 MIX RV 2 019 9 GAS T VB 1 020 3 VORTEX OFF 1 021 50 #10 RV-DRN 2 022 42 DRAIN RV 2 023 41 VENT RV 2 024 13 #10 T VB 1 025 47 #1 T RV 1 026 50 #10 RV-DRN 4 027 42 DRAIN RV 10 128 99 END LOOP 1 029 98 BEGIN LOOP 2 030 56 #10 B RV 3 131 40 MIX RV 2 132 2 VORTEX ON 1 0

33 10 GAS B VB 6 1 Wash the resin with

34 20 MIX ACT 1 0 NMP, 2 times35 40 MIX RV 3 036 3 VORTEX OFF 1 037 50 #10 RV-DRN 2 038 42 DRAIN RV 5 139 99 END LOOP 1 040 56 #10 B RV 3 141 40 MIX RV 2 0


Applied Biosystems




43 88 RS TO RV 1 0 resin sample line with

44 93 GAS TO RS 3 0 NMP, once45 91 #10 TO RS 5 046 89 RS TO FC 1 047 40 MIX RV 2 048 2 VORTEX ON 1 049 10 GAS B VB 6 050 20 MIX ACT 1 051 40 MIX RV 3 052 3 VORTEX OFF 1 053 50 #10 RV-DRN 2 054 42 DRAIN RV 2 055 50 #10 RV-DRN 2 056 42 DRAIN RV 5 157 56 #10 B RV 3 058 40 MIX RV 2 0

59 2 VORTEX ON 1 0 Wash resin with

60 10 GAS B VB 6 0 NMP, once61 20 MIX ACT 1 062 40 MIX RV 3 063 3 VORTEX OFF 1 064 50 #10 RV-DRN 2 065 42 DRAIN RV 5 166 56 #10 B RV 3 167 40 MIX RV 2 068 41 VENT RV 2 069 88 RS TO RV 1 0


71 91 #10 TO RS 5 0 resin-sample line with

72 89 RS TO FC 1 0 NMP, once73 40 MIX RV 2 074 2 VORTEX ON 1 075 93 GAS TO RS 3 076 10 GAS B VB 6 077 20 MIX ACT 1 078 40 MIX RV 3 079 3 VORTEX OFF 1 080 50 #10 RV-DRN 2 081 42 DRAIN RV 2 082 50 #10 RV-DRN 2 083 42 DRAIN RV 12 1

Applied Biosystems




1 14 #10 B VB 1 02 5 NEEDLE DWN 10 03 60 MIX CART 2 04 10 GAS B VB 3 05 20 MIX ACT 1 06 9 GAS T VB 2 07 28 GAS T ACT 2 08 38 ACT TO RVo 4 09 98 BEGIN LOOP 4 0

10 37 ACT TO RVc 4 0 Transfer activated amino

11 41 VENT RV 1 0 acid from the activator

12 99 END LOOP 1 0 to the reaction vessel 13 36 #10 B ACT 1 014 20 MIX ACT 2 015 98 BEGIN LOOP 2 016 37 ACT TO RVc 4 017 41 VENT RV 1 018 99 END LOOP 1 019 93 GAS TO RS 3 020 41 VENT RV 1 021 88 RS TO RV 1 022 93 GAS TO RS 1 023 89 RS TO FC 1 024 2 VORTEX ON 1 025 21 VENT ACT 1 026 29 #9 ACT-DRN 2 027 22 DRAIN ACT 1 028 34 #6 B ACT 9 029 3 VORTEX OFF 1 030 20 MIX ACT 2 031 64 #9 CART 5 032 2 VORTEX ON 5 033 60 MIX CART 10 034 24 CART TO AC 15 035 66 #9 SML N 1 036 24 CART TO AC 4 037 66 #9 SML N 1 038 24 CART TO AC 10 039 3 VORTEX OFF 1 040 62 DRAIN CART 10 041 64 #9 CART 5 042 60 MIX CART 10 043 2 VORTEX ON 1 0

Applied Biosystems




44 24 CART TO AC 10 045 62 DRAIN CART 10 046 60 MIX CART 15 0 Clean the empty cartridge47 61 VENT CART 3 0 and activator48 3 VORTEX OFF 1 049 98 BEGIN LOOP 5 050 20 MIX ACT 6 051 1 WAIT 4 052 99 END LOOP 1 053 2 VORTEX ON 1 054 22 DRAIN ACT 20 055 98 BEGIN LOOP 2 056 29 #9 ACT-DRN 2 057 22 DRAIN ACT 5 058 99 END LOOP 1 059 35 #9 B ACT 1 060 20 MIX ACT 3 061 22 DRAIN ACT 20 062 3 VORTEX OFF 1 063 9 GAS T VB 3 064 10 GAS B VB 3 0

Applied Biosystems


Module F – DMSO, DIEA, & Drain


1 78 PRS #M 52 18 #5 B VB 13 10 GAS B VB 24 53 #5 B RV 65 40 MIX RV 16 1 WAIT 27 40 MIX RV 18 93 GAS TO RS 39 41 VENT RV 210 88 RS TO RV 111 93 GAS TO RS 112 89 RS TO FC 113 9 GAS T VB 514 10 GAS B VB 515 98 BEGIN LOOP 1516 2 VORTEX ON 1517 3 VORTEX OFF 1518 99 END LOOP 119 79 PRS #1 1520 10 GAS B VB 321 51 #1 B RV 122 56 #10 B RV 123 40 MIX RV 124 1 WAIT 225 40 MIX RV 126 9 GAS T VB 527 10 GAS B VB 528 98 BEGIN LOOP 729 2 VORTEX ON 1530 3 VORTEX OFF 1531 99 END LOOP 132 77 PRS #4 1533 41 VENT RV 234 88 RS TO RV 135 93 GAS TO RS 336 91 #10 TO RS 537 89 RS TO FC 138 14 #10 B VB 139 40 MIX RV 840 42 DRAIN RV 25 1

Applied Biosystems


Module f – Coupling in NMP


1 9 GAS T VB 3 02 10 GAS B VB 3 03 98 BEGIN LOOP 19 04 2 VORTEX ON 10 05 3 VORTEX OFF 20 06 99 END LOOP 1 0

7 9 GAS T VB 3 0 20 min. coupling in NMP8 10 GAS B VB 3 09 93 GAS TO RS 3 010 41 VENT RV 2 011 88 RS TO RV 1 012 93 GAS TO RS 1 013 89 RS TO FC 1 014 9 GAS T VB 3 015 10 GAS B VB 3 016 98 BEGIN LOOP 19 017 2 VORTEX ON 10 018 3 VORTEX OFF 20 019 99 END LOOP 1 020 9 GAS T VB 3 021 10 GAS B VB 3 0

Applied Biosystems


Module G – DMSO, DIEA, Drain & R.S.


1 78 PRS #M 52 18 #5 B VB 13 10 GAS B VB 24 53 #5 B RV 65 40 MIX RV 16 1 WAIT 27 40 MIX RV 18 93 GAS TO RS 39 41 VENT RV 210 88 RS TO RV 111 93 GAS TO RS 112 89 RS TO FC 113 9 GAS T VB 514 10 GAS B VB 515 98 BEGIN LOOP 1516 2 VORTEX ON 1517 3 VORTEX OFF 1518 99 END LOOP 119 79 PRS #1 1520 10 GAS B VB 321 51 #1 B RV 122 56 #10 B RV 123 40 MIX RV 124 1 WAIT 225 40 MIX RV 126 9 GAS T VB 527 10 GAS B VB 528 98 BEGIN LOOP 729 2 VORTEX ON 1530 3 VORTEX OFF 1531 99 END LOOP 132 77 PRS #4 1533 41 VENT RV 234 88 RS TO RV 135 93 GAS TO RS 336 91 #10 TO RS 537 89 RS TO FC 138 14 #10 B VB 139 40 MIX RV 840 42 DRAIN RV 25 141 56 #10 B RV 6 142 40 MIX RV 243 2 VORTEX ON 144 90 #5 B RV 1

Applied Biosystems


Module G – DMSO, DIEA, Drain & R.S. (continued)


45 93 GAS TO RS 346 90 #5 B RV 147 93 GAS TO RS 348 98 BEGIN LOOP 149 39 RELAY 0 150 92 #1 TO RS 151 91 #10 TO RS 152 93 GAS TO RS 253 41 VENT RV 154 88 RS TO RV 155 91 #10 TO RS 156 93 GAS TO RS 157 48 PRS RV 158 87 TAKE SMPL 159 89 RS TO FC 160 90 #5 B RV 161 93 GAS TO RS 362 90 #5 B RV 163 93 GAS TO RS 364 90 #5 B RV 265 93 GAS TO RS 366 41 VENT RV 267 88 RS TO RV 168 91 #10 TO RS 169 93 GAS TO RS 270 91 #10 TO RS 471 89 RS TO FC 172 39 RELAY 0 173 99 END LOOP 174 3 VORTEX ON 175 50 #10 RV-DRN 276 42 DRAIN RV 12 1

Applied Biosystems


Module g – DMSO and DIEA Addition, Resin Sampling, and Capping


1 78 PRS #M 5 02 18 #5 B VB 1 03 10 GAS B VB 2 04 53 #5 B RV 6 05 40 MIX RV 1 06 1 WAIT 2 07 40 MIX RV 1 0

8 93 GAS TO RS 3 0 Adding DMSO and

9 41 VENT RV 2 0 reacting 8 minutes10 88 RS TO RV 1 011 93 GAS TO RS 1 012 89 RS TO FC 1 013 9 GAS T VB 5 014 10 GAS B VB 5 015 98 BEGIN LOOP 15 016 2 VORTEX ON 15 017 3 VORTEX OFF 15 018 99 END LOOP 1 019 79 PRS #1 15 020 10 GAS B VB 3 021 51 #1 B RV 1 022 56 #10 B RV 1 0

23 40 MIX RV 1 0 Adding DIEA and

24 1 WAIT 2 0 reacting 4 minutes25 40 MIX RV 1 026 9 GAS T VB 5 027 10 GAS B VB 5 028 98 BEGIN LOOP 7 029 2 VORTEX ON 15 030 3 VORTEX OFF 15 031 99 END LOOP 1 032 77 PRS #4 15 033 41 VENT RV 2 034 88 RS TO RV 1 035 93 GAS TO RS 3 036 91 #10 TO RS 5 037 89 RS TO FC 1 038 14 #10 B VB 1 039 40 MIX RV 8 0

40 42 DRAIN RV 25 1 Drain41 56 #10 B RV 6 142 40 MIX RV 2 0

Applied Biosystems


Module g – DMSO and DIEA Addition, Resin Sampling, and Capping (continued)


43 2 VORTEX ON 1 044 90 #9 TO RS 1 045 93 GAS TO RS 3 046 90 #9 TO RS 1 047 93 GAS TO RS 3 048 98 BEGIN LOOP 1 049 39 RELAY 0 1 050 92 #1 TO RS 1 051 91 #10 TO RS 1 052 93 GAS TO RS 2 053 41 VENT RV 1 054 88 RS TO RV 1 055 91 #10 TO RS 1 056 93 GAS TO RS 1 057 48 GAS T RV 1 058 87 TAKE SAMPL 1 0

59 89 RS TO FC 1 0 Resin sample (optional)60 90 #9 TO RS 1 061 93 GAS TO RS 3 062 90 #9 TO RS 1 063 93 GAS TO RS 3 064 90 #9 TO RS 2 065 93 GAS TO RS 3 066 41 VENT RV 2 067 88 RS TO RV 1 068 91 #10 TO RS 1 069 93 GAS TO RS 2 070 91 #10 TO RS 4 071 89 RS TO FC 1 072 39 RELAY 0 1 073 99 END LOOP 1 074 3 VORTEX OFF 1 075 50 #10 RV-DRN 2 076 42 DRAIN RV 12 177 17 #4 B VB 1 078 10 GAS B VB 2 079 56 #10 B RV 2 080 51 #1 B RV 1 081 52 #4 B RV 2 082 56 #10 B RV 4 0

83 40 MIX RV 2 0 Capping for 5 minutes84 93 GAS TO RS 3 085 41 VENT RV 2 0

Applied Biosystems


Module g – DMSO and DIEA Addition, Resin Sampling, and Capping (continued)


86 88 RS TO RV 1 087 93 GAS TO RS 2 088 89 RS TO FC 1 089 9 GAS T VB 5 090 10 GAS B VB 5 091 98 BEGIN LOOP 8 092 2 VORTEX ON 15 093 3 VORTEX OFF 15 094 99 END LOOP 1 095 41 VENT RV 2 096 88 RS TO RV 1 097 90 #9 TO RS 3 098 89 RS TO FC 1 099 42 DRAIN RV 12 1

Module i – Wait


1 1 WAIT 900 O Wait for 15 minutes

Applied Biosystems


Applied Biosystems

March 2004 Appendix F: Parts List and Plumbing Schematic F-1

Appendix F: Parts List and Plumbing Schematic

Illustrated Parts List

IMPORTANT Not all parts on this list apply to ABI 431 units that have had 631 Monitoring Kits installed. Wherever this symbol (•) appears the correct part number may vary from the number shown. Contact Applied Biosystems for correct part numbers.

PhotoReference PartNumber Number Description

1 604061 Delivery valve assembly, 4 port2 604060 Delivery valve assembly, 8 port3 601374 Delivery valve assembly, 11 port4 •603209 Signal distribution printed circuit board

5 600344 Valve assembly, solenoid, Angar (7 valves)6 600640 Valve assembly, TFA pressure/vent (2 valves)7 600437 Activator vessel/holder assembly8 •603082 Reaction vessel holder assembly (RTF)9C •401571 RTF reaction vessel assembly (8 mL)

•401572 Resin-sampling RTF reaction vessel assy (8 mL)9A 401573 RTF reaction vessel assy (41 mL)9B 401574 Resin-sampling RTF reaction vessel assy (41 mL)

•401575 RTF reaction vessel assy (55 mL)•401576 Resin-sampling RTF reaction vessel assy (55 mL)

600626 Gasket, 0.500-in. o.d. x 0.062-in. i.d., Kalrez™401524 Filters, reaction vessel (tabbed)400256 Metering vessel

10 •603084 Vortexer assembly DC (Model 433)603092 Vortexer bearing

•004397 Vortexer belt•603211 Vortexer PCB

11 601317 Autosampler assembly 224009 Constant force spring 003969 Needle cover plate

12 601318 Autosampler ejector assembly601283T Autosampler PCB

13 602995 Needle assembly14 •603351 433 barcode reader assembly15 602576 Keyboard/display assembly

Valve Blocks

Assemblies

Applied Biosystems

F-2 Appendix F: Parts List and Plumbing Schematic March 2004


16 601377 Resin sampler assembly601591 Fraction collector line, 1/16 in. x 0.8 mm x 48 in.

17 004053 Valve assembly, 4-way pneumatic18 601313 Vacuum ballast assembly (not visible)19 130096 Vacuum pump assembly20 601310 Waste manifold assembly21 601311 Nitrogen inlet assembly22 002192 Manifold tube, input/output23 130042 Pressure/vent valve, 3-way toggle

24 001208 Housing, receptacle (7 positions) 003560 Lid, receptacle, ratchet (7 positions) 003558 Receptacle, ratchet, 8 oz (positions 1*, 7, 8) 003559 Receptacle, ratchet, 16 oz (positions 1*, 2, 4, 5, 6) 002571 Wave spring, nickle-plated (7 positions)

601338 Ratchet insert assembly, position 1 or603842 Ratchet insert assembly, position 1* (16 oz)

(* position 1 is 16 oz in monitoring systems) 601341 Ratchet insert assembly, position 2 601337 Ratchet insert assembly, position 4 602977 Ratchet insert assembly, position 5 + 6 601339 Ratchet insert assembly, positions 7 and 8 400790 Bottle seals, 200 mL (8 oz), 10/box 400501 Bottle seals, 450 mL (16 oz), 10/box 400790 Bottle seals, 450 mL (16 oz) position 2, 10/pkg

25 601309 Regulator assembly, upper26 601319 Regulator assembly, lower

27 •603927 Controller board28 •603409 Multifunction board29 4346754 Power supply

603615 Universal Voltage Kit31 •603153 Input/output signal cable32 •601054 20-pin jumper cable33 •603279 Vortexer motor cable assembly (not visible)34 •601379 Power switch assembly35 603544 Cartridge, version 1.0136 603073 Conductivity PC Board37 603083 Conductivity cell assembly38 603079 Light socket assembly, mini-bayonet

200591 Light bulb, 28V, bayonet

Bottle Cap Assemblies

Regulator Assemblies

Electronics

Applied Biosystems



39 401770 Disposable In-line filter (20/pkg; used in 5 places)40A 603132 Cap assembly, 1-gal reagent bottle40B 603133 Parallel cap assembly (dual bottles)

004498 Gasket200270 Inlet filter, 40 µm0392-0003 Ext. ret. ring pliers (tool for gasket replacement)

41 140041 Safety carrier (used in 2 places)42 002170 Rack, 1-gal bottle carrier (2 pieces)43 602544 Cap assembly, waste bottle44 140040 Jerrican, 2-1/2 gal, polyethylene45 110130 T-fitting, 1/4-28, Teflon46 000878 Manifold, 6-port

110019 Plug, 1/4-28, Teflon47 110131 Cross-fitting, 1/4-28, Teflon48 004864 Bulkhead fitting for resin sampler with safety cover49 110087 Plug, port, 1/8 T, brass50 225005 Parflex™ tubing, 1/8-in. o.d.51 002480 Cartridge bucket

Miscellaneous

Applied Biosystems


Figure F-1. Front view of the ABI 433A with bottles removed

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Applied Biosystems


Figure F-2. Rear view of the ABI 433A with panel removed

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Applied Biosystems


Figure F-3. Close-up of autosampler assembly

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Applied Biosystems


Figure F-4. Left side of the ABI 433A with the panel detached

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Applied Biosystems


Figure F-5. Left side panel electronics

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Applied Biosystems


Figure F-6. Conductivity flow cell close up

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Applied Biosystems


Figure F-7. Conductivity flow cell and valve blocks

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Applied Biosystems


Figure F-8. Close-up of rear of instrument, interior

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Applied Biosystems


Figure F-9. ABI 433A reagent bottles, tubing, and reaction vessels

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9B

9C9A

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Headquarters

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Printed in USA, 03/2004Part Number 904856 Rev. D

ABI 433A Peptide Synthesizertools.thermofisher.com/content/sfs/manuals/cms_041851.pdf · 4 DMAP...

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Transcript of ABI 433A Peptide Synthesizertools.thermofisher.com/content/sfs/manuals/cms_041851.pdf · 4 DMAP...