Decoding approaches for protein identification
Methods and systems are provided for accurate and efficient identification and quantification of proteins. In an aspect, disclosed herein is a method for identifying a protein in a sample of unknown proteins, comprising receiving information of a plurality of empirical measurements performed on the unknown proteins; comparing the information of empirical measurements against a database comprising a plurality of protein sequences, each protein sequence corresponding to a candidate protein among a plurality of candidate proteins; and for each of one or more of the plurality of candidate proteins, generating a probability that the candidate protein generates the information of empirical measurements, a probability that the plurality of empirical measurements is not observed given that the candidate protein is present in the sample, or a probability that the candidate protein is present in the sample; based on the comparison of the information of empirical measurements against the database.
1. A method for identifying at least one candidate protein of a sample, the method comprising:
(a) obtaining a series of empirical measurements from a series of covalent amino acid modification reactions performed serially on each protein of a plurality of proteins from the sample, the series of empirical measurements performed while the plurality of proteins of the sample is attached to a substrate, the series of empirical measurements indicating an order of covalently modified amino acids in individual proteins from the plurality of proteins from the sample, wherein the obtaining of the series of empirical measurements comprises:
(i) for each protein of the plurality of proteins, performing a covalent amino acid modification in the series of covalent amino acid modification reactions on the protein, wherein the covalent amino acid modification selectively modifies a particular amino acid of the protein,
(ii) detecting the presence or absence of the selectively modified amino acid of the protein, and
(iii) repeating (i) and (ii) to perform at least one additional covalent amino acid modification in the series of covalent amino acid modification reactions on the protein and to detect the presence or absence of another selectively modified amino acid of the protein, wherein the at least one additional covalent amino acid modification reaction selectively modifies the particular amino acid of the protein;
(b) comparing, by a computer, the series of empirical measurements to measurement outcomes for a plurality of candidate proteins; and
(c) based at least in part on the comparing in (b), identifying, by the computer, the at least one candidate protein in the sample, at least in part by applying a trained algorithm to the series of empirical measurements to determine a probability that the at least one candidate protein of the sample generates the series of empirical measurements.
2. The method of claim 1 , wherein the detecting comprises detecting fluorescence produced by the covalent amino acid modification reactions.
3. The method of claim 1 , wherein (c) comprises identifying, by the computer, the at least one candidate protein in the sample based at least in part on:
(i) the probability that the at least one candidate protein of the sample generates the series of empirical measurements, and
(ii) a probability that the series of empirical measurements is not observed given that the at least one candidate protein of the sample is present in the sample.
4. The method of claim 1 , wherein the measurement outcomes are derived from a database of previous measurements of the plurality of candidate proteins.
5. The method of claim 1 , wherein the measurement outcomes are calculated completely in silico.
6. The method of claim 1 , wherein the measurement outcomes are derived from features of an amino acid sequence of the at least one candidate protein of the sample.
7. The method of claim 1 , wherein the series of empirical measurements comprise binding measurements of affinity reagent probes configured to bind the at least one candidate protein of the sample.
8. The method of claim 1 , further comprising generating, for the at least one candidate protein of the sample, a confidence level that the at least one candidate protein of the sample matches a protein from the plurality of proteins from the sample.
9. The method of claim 1 , wherein (c) further comprises determining the probability that the at least one candidate protein of the sample generates the series of empirical measurements at least in part according to:
Pr
(
measurement
outcome
❘
protein
)
=
Pr
(
aa
-
counts
❘
protein
)
*
NUMORDER
wherein NUMORDER is a number of ways the measurement outcomes can be generated, wherein
Pr
(
aa
-
counts
❘
protein
)
=
∏
i
=
1
i
=
1
(
R
eai
)
Mi
*
(
1
-
R
asi
)
Caai
-
Mi
wherein Raai is an efficiency for a selective amino acid modification reaction that selectively modifies an amino acid i, wherein Mi is a number of times the amino acid i is measured in the protein, and wherein Caai is a number of times the amino acid i occurs in a candidate protein.
10. The method of claim 9 , wherein (c) further comprises determining the probability that the at least one candidate protein of the sample generates the series of empirical measurements at least in part according to:
Pr
(
measurement
outcome
❘
candidate
protein
)
∑
i
=
1
P
Pr
(
measurement
outcome
❘
protein
i
)
wherein Σ i=1 P Pr(measurement outcome|protein i ) is a sum of probabilities of the measurement outcomes for a set of P proteins.
11. The method of claim 1 , wherein each protein of the plurality of proteins from the sample is associated with a unique spatial address.
12. The method of claim 11 , wherein each protein from the plurality of proteins from the sample is optically resolvable from each other protein from the plurality of proteins from the sample.
13. The method of claim 12 , wherein the plurality of proteins from the sample is conjugated to the substrate at a plurality of spatially separate locations.
14. The method of claim 1 , wherein the series of empirical measurements is obtained using an optical detector.
15. The method of claim 1 , wherein the series of empirical measurements is obtained using a magnetic detector.
16. The method of claim 1 , wherein the series of empirical measurements is obtained using an electrostatic detector or an electrochemical detector.
17. The method of claim 1 , wherein the probability that at least one candidate protein of the sample generates the series of empirical measurements is determined using a plurality of measurement outcomes.
18. The method of claim 1 , wherein the probability that at least one candidate protein of the sample generates the series of empirical measurements is determined using a product of probabilities for the measurement outcomes of the at least one candidate protein of the sample.
19. The method of claim 1 , wherein the at least one candidate protein of the sample comprises at least 10 different candidate proteins.
20. The method of claim 1 , wherein the trained algorithm comprises a probabilistic model that is iteratively improved by performing an expectation maximization algorithm on the series of empirical measurements.
21. The method of claim 1 , wherein the series of empirical measurements from the series of covalent amino acid modification reactions comprise selective modification and detection of lysine amino acids.
22. The method of claim 1 , wherein the series of empirical measurements from the series of covalent amino acid modification reactions comprise selective modification and detection of cysteine amino acids.
23. The method of claim 1 , wherein the plurality of proteins comprises at least 1,000 proteins from a human protein sample.
24. The method of claim 1 , wherein the series of covalent amino acid modification reactions comprise modification reactions performed on 25 N-terminal amino acids of each protein of the plurality of proteins from the sample.
25. The method of claim 1 , wherein performing the series of covalent amino acid modification reactions on the protein of the plurality of proteins from the sample is by way of direct functionalization of amino acids, wherein each of the series of covalent amino acid modification reactions selectively and covalently modifies a particular amino acid in the protein of the plurality of proteins from the sample.
26. The method of claim 1 , further comprising, prior to (ii), attaching the plurality of proteins to the substrate.