# US 2019/0318247 A1 · Data storage using peptides

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- Number: US 2019/0318247 A1
- Document ID: US20190318247A1
- Status: Published application
- Kind: A1
- Application number: 16/224,957
- Filed: 2018-12-19
- Published: 2019-10-17
- Earliest claimed: 2018-04-13
- Assignees: The Hong Kong Polytechnic University
- Applicants: The Hong Kong Polytechnic University
- Inventors: Zhongping YAO; Cheuk Chi Albert NG; Chung Ming LAU; Wai Man TAM
- Web page: https://patentgrep.com/patent/US20190318247A1

## CPC

- G06N 3/123: DNA computing
- C12N 15/00: Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor (mutants or genetically engineered microorganisms, per se C12N1/00, C12N5/00, C12N7/00; new plants per se A01H; plant reproduction by tissue culture techniques A01H4/00; new animals per se A01K67/00; use of medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases, gene therapy A61K48/00)
- G06F 11/10: Adding special bits or symbols to the coded information, e.g. parity check, casting out 9's or 11's
- G06F 11/1048: {using arrangements adapted for a specific error detection or correction feature}
- G11C 13/0016: {comprising polymers}
- G11C 13/0019: {comprising bio-molecules}
- G11C 13/02: using elements whose operation depends upon chemical change {(G11C13/0009 takes precedence)}
- G16B 99/00: Subject matter not provided for in other groups of this subclass
- G16B 50/00: ICT programming tools or database systems specially adapted for bioinformatics
- G06N: COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N)
- G11C: STATIC STORES (semiconductor memory devices H10B)
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

## Abstract

Methods and systems for storing digital data into peptide sequences and retrieving digital data from peptide sequences are disclosed. The method for storing digital data into peptide sequences may include: encoding the digital data into a digital code; translating the digital code into the peptide sequences; and synthesizing the translated peptide sequences. The method for retrieving digital data from peptide sequences may include: sequencing and determining an order of the peptide sequences; converting the peptide sequences with the determined order into a digital code; and decoding the digital data from the digital code. Codes with error-correction capability are developed for encoding digital data into peptide sequences, and a computational method implemented in a software is developed for sequencing the digital data bearing peptides.

## Claims

### Claim 1

A method of storing digital data into peptide sequences.

### Claim 2 (depends on 1)

The method of claim 1, wherein the storing digital data into peptide sequences comprises:
encoding the digital data into a digital code;
translating the digital code into the peptide sequences; and
synthesizing the translated peptide sequences.

### Claim 3 (depends on 2)

The method of claim 2; wherein the translating of the digital code into peptide sequences comprises:
mapping a bit pattern or a symbol pattern into one or more amino acids such that the digital code is represented by a sequence of amino acids in the peptide sequences.

### Claim 4 (depends on 2)

The method of claim 2, the method further comprising forming a mixture of peptides based on the translated peptide sequences.

### Claim 5 (depends on 2)

The method of claim 2, the method further comprising adding one or more order-checking bits into the digital code, wherein the one or more order-checking bits are related to the order of the bits or symbols in the digital code.

### Claim 6 (depends on 2)

The method of claim 2, the method further comprising adding one or more error-correction codes into the digital code, wherein the one or more error-correction codes comprise any one or combination of repetition code, convolutional code, turbo code, fountain code, low-density parity-check (LDPC) code, Reed-Solomon (RS) code, Hadamard code, and Hamming code.

### Claim 7 (depends on 6)

The method of claim 6, wherein the one or more error-correction codes are generated based on the digital code, or both the digital code and order-checking bits added into the digital code.

### Claim 8 (depends on 1)

The method of claim 1, wherein the peptide sequences comprise distinct functional groups, isotope labels or affinity labels.

### Claim 9 (depends on 1)

The method of claim 1, wherein the peptide sequences comprise digital data bearing amino acids and non-digital data bearing amino acids.

### Claim 10

A method of retrieving digital data from peptide sequences.

### Claim 11 (depends on 10)

The method of claim 10, wherein the retrieving digital data from peptide sequences comprises:
sequencing and determining an order of the peptide sequences;
converting the peptide sequences with the determined order into a digital code; and
decoding the digital data from the digital code.

### Claim 12 (depends on 11)

The method of claim 11, wherein the converting of the peptide sequences with the determined order into the digital code comprises:
mapping one or more amino acids in the peptide sequences into a bit pattern or a symbol pattern such that the digital code is obtained from a sequence of amino acids in the peptide sequences with the determined order.

### Claim 13 (depends on 11)

The method of claim 11, the method further comprising separating peptide sequences from a mixture of peptides.

### Claim 14 (depends on 11)

The method of claim 11, wherein the digital code comprises one or more order-checking bits, wherein the one or more order-checking bits are related to the order of the bits or symbols in the digital code.

### Claim 15 (depends on 11)

The method of claim 11, wherein the digital code comprises one or more error-correction codes, wherein the one or more error-correction codes comprise any one or combination of repetition code, convolutional code, turbo code, fountain code, LDPC code, RS code, Hadamard code, and Hamming code.

### Claim 16 (depends on 15)

The method of claim 15, wherein decoding the digital data from digital code uses algorithms comprising belief-propagation algorithm, message-passing algorithm, sum-product algorithm, and bit-flipping algorithm.

### Claim 17 (depends on 14)

The method of claim 14, the method further comprising:
encoding the orders of one or more bits or symbols in the digital code;
comparing the order-checking bits with the encoded orders of the one or more bits or symbols in the digital code; and
indicating a detected error if the order-checking bits do not match the encoded orders of the one or more bits or symbols in the digital code.

### Claim 18

A system for storing digital data into peptide sequences, the system comprising:
a synthesizer configured to synthesize peptide sequences;
at least one processor in communication with the synthesizer; and
at least one memory including computer program code, the at least one memory and the computer program code configured to, with the at least one processor, cause the system at least to:
encode the digital data into a digital code;
translate the digital code into peptide sequences; and
synthesize the translated peptide sequences using the synthesizer.

### Claim 19 (depends on 18)

The system of claim 18, wherein the system is caused to translate the digital code into peptide sequences, the at least one memory and the computer program code configured to, with the at least one processor, cause the system at least to:
map a bit pattern or a symbol pattern of the digital code into one or more amino acids such that the digital code is represented by a sequence of amino acids in the peptide sequences.

### Claim 20 (depends on 18)

The system of claim 18, wherein the synthesizer is further configured to:
form a mixture of peptides based on the translated peptide sequences.

### Claim 21 (depends on 18)

The system of claim 18, wherein the at least one memory and the computer program code configured to, with the at least one processor, cause the system further to:
add one or more order-checking bits into the digital code, wherein the one or more order-checking bits are related to the order of the bits or symbols in the digital code.

### Claim 22 (depends on 18)

The system of claim 18, wherein the at least one memory and the computer program code configured to, with the at least one processor, cause the system further to:
add one or more error-correction codes into the digital code, wherein the one or more error-correction codes comprise any one or combination of repetition code, convolutional code, turbo code, fountain code, LDPC code, RS code, Hadamard code, and Hamming code.

### Claim 23 (depends on 22)

The system of claim 22, wherein the one or more error-correction codes are generated based on the digital code, or both the digital code and order-checking bits added into the digital code.

### Claim 24 (depends on 18)

The system of claim 18, wherein the peptide sequences comprise distinctfunctional groups, isotope labels or affinity labels.

### Claim 25 (depends on 18)

The system of claim 18, wherein the peptide sequences comprise digital data bearing amino acids and non-digital data bearing amino acids.

### Claim 26

A system for retrieving digital data from peptide sequences, the system comprising:
a sequencer configured to sequence and determine an order of the peptide sequences;
at least one processor in communication with the sequencer; and
at least one memory including computer program code, the at least one memory and the computer program code configured to, with the at least one processor, cause the system at least to:
sequence and determine the order of the peptide sequences using the sequencer;
convert the peptide sequences with the determined order into a digital code; and
decode the digital data from the digital code.

### Claim 27 (depends on 26)

The system of claim 26, wherein the system is caused to convert the peptide sequences with the determined order into a digital code, the at least one memory and the computer program code configured to, with the at least one processor, cause the system at least to:
map one or more amino acids in the peptide sequences into a bit pattern or a symbol pattern such that the digital code is obtained from a sequence of amino acids in the peptide sequences with the determined order.

### Claim 28 (depends on 26)

The system of claim 26, wherein the sequencer is further configured to:
separate peptide sequences from a mixture of peptides.

### Claim 29 (depends on 26)

The system of claim 26, wherein the digital code comprises one or more order-checking bits, wherein the one or more order-checking bits are related to the order of the bits or symbols in the digital code.

### Claim 30 (depends on 26)

The system of claim 26, wherein the digital code comprises one or more error-correction codes, wherein the one or more error-correction codes comprise any one or combination of repetition code, convolutional code, turbo code, fountain code, LDPC code, RS code, Hadamard code, and Hamming code.

### Claim 31 (depends on 30)

The system of claim 30, wherein decoding the digital data from digital code uses algorithms comprising belief-propagation algorithm, message-passing algorithm, sum-product algorithm, and bit-flipping algorithm.

### Claim 32 (depends on 29)

The system of claim 29, wherein the at least one memory and the computer program code configured to, with the at least one processor, cause the system further to:
encode the orders of one or more bits or symbols in the digital code;
compare the order-checking bits with the encoded orders of the one or more bits or symbols in the digital code; and
indicate a detected error if the order-checking bits do not match the encoded orders of the one or more bits or symbols in the digital code.

### Claim 33

A computational method for assigning peptide sequences, wherein the method comprises an algorithm that recognizes and scores one or more features.

### Claim 34 (depends on 33)

The computational method of claim 33, wherein the one or more of the features comprises:
length of consecutive amino acids retrieved;
isotope labels;
number of amino acids retrieved;
match error;
intensity; and
number of occurrences for different ion types with different offsets.