Patent Application
20220036973
The present invention is in the field of machine learning and nanopore-based protein sequencing.
Modern DNA sequencing techniques have revolutionized genomics, but extending these methods to routine proteome analysis, and specifically to single-cell proteomics, remains a global unmet challenge. This is attributed to the fundamental complexity of the proteome: protein expression level spans several orders of magnitude, from a single copy to tens of thousands of copies per cell; and the total number of proteins in each cell is staggering. Given the lack of in-vitro protein amplification assays the ability to accurately quantify both abundant and rare proteins hinges on the development of single-protein identification methods that also feature extraordinary-high sensing throughput. To date, however, protein sequencing techniques, such as mass-spectrometry, have not reached single-molecule resolution, and rely on bulk averaging from hundreds of cells or more. Affinity-based method can reach single protein sensitivity, but depend on limited repertoires of antibodies, thus severely hindering their applicability for proteome-wide analyses. Consequently, in the past few years single-molecule approaches for proteome analysis based on Edman degradation or FRET have been proposed. To date, however, profiling of the entire proteome of individual cells remains the ultimate challenge in proteomics.
Nanopores are single-molecule biosensors adapted for DNA sequencing, as well as other biosensing applications. Recent nanopore studies extended nucleic-acid detection to proteins, demonstrating that ion current traces contain information about protein size, charge and structure. However, to date, the challenge of deconvolving the electrical ion-current trace to determine the protein's amino-acid sequence from the time-dependent electrical signal has remained elusive. In an analogy to the field of transcriptomics, in many practical cases it is sufficient to identify and quantify each protein among the repertoire of known proteins, instead of re-sequencing it. It has been shown that theoretically most, but not all, proteins in the human proteome database can be uniquely identified by the order of appearance of just two amino-acids, lysine and cysteine (K and C, respectively). However, taking into account common experimental errors, for example due to false calling of an amino-acid, or an unlabeled amino-acid, sharply reduces the identification accuracy. A protein identification method that correctly identifies all proteins and remains robust against the expected experimental errors is greatly needed.
The present invention provides methods and systems for identifying a peptide by analyzing a linear readout representative of at least a portion of at least two amino acids along the peptide using a machine learning model, wherein the machine learning model is trained on linear readouts representative of a set of peptides of known sequence. Methods of training a machine learning model on linear readouts representative of a set of known peptides are also provided.
According to a first aspect, there is provided a method of identifying a peptide, comprising:
According to another aspect, there is provided a method comprising:
at a training stage, training a machine learning model on a training set comprising:
According to another aspect, there is provided a system comprising:
at least one hardware processor; and
a non-transitory computer-readable storage medium having stored thereon program instructions, the program instructions executable by the at least one hardware processor to:
train a machine learning model based, at least in part, on a training set comprising:
According to some embodiments, the portion is at least 60%. According to some embodiments, the portion of the first amino acid is at least 60%. According to some embodiments, the portion of the second amino acid is at least 60%. According to some embodiments, the portion is at least 80%. According to some embodiments, the portion of the first amino acid is at least 80%. According to some embodiments, the portion of the second amino acid is at least 90%.
According to some embodiments, the machine learning model is trained on linear readouts of a set of peptides, wherein each linear readout represents at least a portion of the first amino acid and at least a portion of the second amino acid along a peptide from the set of peptides.
According to some embodiments, the method of the invention further comprises labeling at least a portion of the first amino acid with a first label and at least a portion of the second amino acid with a second label along the peptide.
According to some embodiments, the method of the invention further comprises detecting the first and second label linearly along the peptide to produce the readout.
According to some embodiments, the detecting comprises passing the labeled peptide though a nanopore, wherein the first and second labels are uniquely detectable as each label passes through the nanopore.
According to some embodiments, the label comprises a fluorophore and an optical sensor at the nanopore is configured to detect fluorescence at the nanopore.
According to some embodiments, the label is a bulky group and an electrical sensor at the nanopore is configured to detect electrical current and/or voltage at the nanopore.
According to some embodiments, the nanopore contains a plasmonic nanostructure, wherein the plasmonic nanostructure is configures to localize electromagnetic excitation below a wavelength of light. According to some embodiments, the plasmonic nanostructure is configures to amplify localized fluorescence emission at the nanopore at a plurality of wavelengths.
According to some embodiments, the nanopore has a resolution of at least 100 nm.
According to some embodiments, the linear readout is a linear temporal trace of the peptide as it passes through a nanopore.
According to some embodiments, the peptide is an undigested or unfragmented protein.
According to some embodiments, the linear readout is further representative of a portion of at least a third amino acid along the peptide.
According to some embodiments, the first, second and third amino acids are lysine, cysteine and methionine.
According to some embodiments, the set of peptides is a set of peptides selected from:
According to some embodiments, the linear readouts of a set of peptides comprise at least 50 linear readouts representative of each peptide from the set.
According to some embodiments, the linear readouts of a set of peptides are simulated linear readouts based on a known sequence for each peptide wherein at least a portion of the first amino acid and a portion of the second amino acid are represented in the simulated readout.
According to some embodiments, the training set comprises linear readouts of a set of peptides expected to be in a sample and the target peptide is from the sample.
According to some embodiments, the training set comprises linear readouts of all proteins found in plasma, or all proteins found in a proteome.
According to some embodiments, the training set comprises linear readouts for at least 15 peptides and at least 50 readouts for each peptide.
According to some embodiments, the linear readouts are simulated linear readouts generated by selecting a known sequence of a peptide and generating a linear representation of at least a portion of the first amino acids and at least a portion of the second amino acids along the peptide.
According to some embodiments, the liner readouts further represent at least a portion of a third amino acid along the peptide.
According to some embodiments, the linear readouts comprise a linear temporal trace of a labeled peptide as it passes through a nanopore, wherein the peptide is labeled at least at a portion of the first amino acid and at least at a portion of the second amino acid along the peptide.
Further embodiments and the full scope of applicability of the present invention will become apparent from the detailed description given hereinafter. However, it should be understood that the detailed description and specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.
The present invention, in some embodiments, provides methods for identifying a peptide by analyzing a linear readout representative of at least a portion of at least two amino acids along the peptide using a machine learning model, wherein the machine learning model is trained on linear readouts representative of a set of peptides. Methods of training a machine learning model on linear readouts representative of a set of known peptides, as well as systems for performing the methods of the invention are also provided.
The present invention is based on the surprising finding that by using machine learning models trained on linear representations of only a portion of a few amino acids in a peptide, peptides with imperfect labeling and/or imperfect detection conditions can be accurately identified. Identifying proteins by perfectly labeling two amino acids throughout the protein chain and then generating the exact order and position of those two amino acids is known in the art. However, in practice 100% labeling is almost never achieved and thus a degenerate readout with only some of the amino acids accounted for is what needs to be analyzed. Further, detection apparatuses are not 100% accurate either, and often have suboptimal resolution. This can lead to missing of a labeled amino acid, or discrepancies in the order/position. Generally, the variation and lack of reproducibility from one experiment to the next and one laboratory to the next, makes analyzing peptides by labeling only two amino acids not currently feasible.
However, by using a machine learning model even very degenerate readouts for peptides can be correctly identified. In the instant invention, a machine learning model is trained on numerous readouts of peptides/proteins where conditions are not ideal, but when the input peptide/protein is known. Thus, when an unknown sample is analyzed by the model, even is the sample is also poorly labeled or scanned, the machine learning model is still able to identify the peptide/protein with very high accuracy. The feasibility of this approach has been confirmed with a training set of the full human proteome, and for analysis of not only the whole human proteome, but also the plasma proteome and a panel of cytokines.
By a first aspect, there is provided a method comprising, analyzing a readout representative of at least a portion of a first amino acid along a peptide with a machine learning model, wherein the machine learning model predicts the identity of the peptide.
According to another aspect, there is provided a method comprising:
According to another aspect, there is provided a method comprising:
at a training stage, training a machine learning model on a training set comprising:
at an inference stage, applying the trained machine learning model to a target linear readout representing at least a portion of the first amino acid along a target peptide, to identify the target peptide
According to another aspect, there is provided a system comprising:
According to another aspect, there is provided a system comprising:
at least one hardware processor; and
a non-transitory computer-readable storage medium having stored thereon program instructions, the program instructions executable by the at least one hardware processor to:
train a machine learning model based, at least in part, on a training set comprising:
In some embodiments, the method is for identifying a peptide. In some embodiments, the system is for use in identifying a peptide. As used herein, the term “identifying” does not require providing the full sequence of a peptide, but rather identifying it by name. Proteins often have multiple isoforms or point mutations and the method of the invention need not provide the full sequence of an analyzed peptide but rather merely identify the protein by name so as to distinguish it from other proteins. Similarly, a protein may be identified as being a protein in a group of proteins, such as the protein is either protein A or protein B. It is often useful to know the proteomic make up of a sample, even if the specific isoforms or sequences of the proteins in the sample do not need to be known. Thus, for example a protein being analyzed could be identified as “Albumen” even if the full sequence of albumen is not detected.
In some embodiments, the method is for sequencing a peptide. In some embodiments, the system is for identifying a peptide. In some embodiments, the method is for identifying a plurality of peptides in a sample. In some embodiments, the method if for identifying a purified peptide. In some embodiments, the method is for proteomic analysis. In some embodiments, the method is for proteomic analysis of a sample. In some embodiments, the method is for peptide quantification. In some embodiments, the method is for relative peptide quantification. In some embodiments, the method is for distinguishing a peptide from other peptides in a set of peptides.
As used herein, the terms “peptide”, “polypeptide” and “protein” are used interchangeably to refer to a polymer of amino acid residues. In another embodiment, the terms “peptide”, “polypeptide” and “protein” as used herein encompass native peptides, peptidomimetics (typically including non-peptide bonds or other synthetic modifications) and the peptide analogues peptoids and semipeptoids or any combination thereof. In another embodiment, the peptides polypeptides and proteins described have modifications rendering them more stable while in the body or more capable of penetrating into cells. In one embodiment, the terms “peptide”, “polypeptide” and “protein” apply to naturally occurring amino acid polymers. In another embodiment, the terms “peptide”, “polypeptide” and “protein” apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid.
As used herein, the term “isolated peptide” refers to a peptide that is essentially free from contaminating cellular components, such as carbohydrate, lipid, or other proteinaceous impurities associated with the peptide in nature. Typically, a preparation of isolated peptide contains the peptide in a highly purified form, i.e., at least about 80% pure, at least about 90% pure, at least about 95% pure, greater than 95% pure, or greater than 99% pure.
In some embodiments, the peptide is a protein. In some embodiments, the peptide is an isolated peptide. In some embodiments, the peptide is a peptide from a sample. In some embodiments, the peptide is a complete protein. In some embodiments, the peptide is an intact protein. In some embodiments, the peptide is an undigested protein. In some embodiments, the peptide is an unfragmented protein. In some embodiments, the peptide is a protein that has not been shortened artificially. In some embodiments, artificially is in vitro. In some embodiments, the peptide is a fragment of a protein. In some embodiments, the peptide is at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 97, 99 or 100% of a protein. Each possibility represents a separate embodiment of the invention. In some embodiments, the peptide is a native protein. In some embodiments, the peptide is a naturally occurring peptide. In some embodiments, the peptide is not a cleaved peptide. In some embodiments, the peptide is not a digested peptide. In some embodiments, the peptide is not produced by cleaving or digesting an intact protein.
In some embodiments, the peptide comprises at least 2, 3, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2500, or 3000, amino acids. Each possibility represents a separate embodiment of the invention. In some embodiments, the peptide comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 20 or 25 of the first amino acid. Each possibility represents a separate embodiment of the invention.
In some embodiments, the readout is embodied in an electronic file. In some embodiments, the readout is an electronic file. In some embodiments, the readout is further representative of at least a portion of a second amino acid along the peptide. In some embodiments, the readout is further representative of at least a portion of a third amino acid along the peptide. In some embodiments, the readout is representative of at least a portion of 1, 2, 3, 4, or 5 amino acids along the peptide. Each possibility represents a separate embodiment of the invention.
It will be understood by a skilled artisan that when referring herein to a first amino acid and a second amino acid reference is being made to different types or species of amino acids and not single individual amino acids along a chain. Thus, a first amino acid might be, for example, lysine; and a second amino acid might be, for example, cysteine. In some embodiments, the first, second, third or any amino acid recited herein is a specific amino acid species. As used herein, the term “amino acid species” refers to any specific amino acid, such as lysine, cysteine, methionine, alanine, histidine etc. In some embodiments, the first, second, third or any amino acid recited herein is a type of amino acid. In some embodiments, a type of amino acid refers to group of amino acids with a common structure or characteristic. Types of amino acids include, but are not limited to, aromatic amino acids, non-polar amino acids, charged amino acids, and polar amino acids. In some embodiments, an amino acid is a naturally occurring amino acid. In some embodiments, an amino acid comprises artificial amino acids. In some embodiments, the amino acid is a mammalian amino acid. In some embodiments, the mammal is human. In some embodiments, an amino acid is selected from: aspartic acid, threonine, serine, glutamic acid, proline, glycine, alanine, valine, cysteine, methionine, isoleucine, leucine, tyrosine, phenylalanine, lysine, histidine, arginine, tryptophan asparagine, and glutamine.
In some embodiments, the amino acid is an amino acid that can be uniquely labeled. It will be understood by a skilled artisan that while the labeling of three specific amino acids (lysine, cysteine and methionine) is embodied in the examples section hereinbelow, such illustration is merely by way of example. Lysine, cysteine and methionine can be uniquely labeled by separate chemistries and thus can be analyzed together. Use of another three amino acids or a combination of only 1 or 2 of the exemplified amino acids with other amino acids that can be uniquely labeled would result in a similar analysis. Even a labeling with less specificity, such as a label that marks two amino acids uniquely, can be employed. Similarly, higher combinations, mixes or four unique labels or five unique labels will work on the same principle and may allow for more rapid identification, or identification with worse resolution. In some embodiments, the first and second amino acids are different amino acids. In some embodiments, the first, second and third amino acids are different amino acids. In some embodiments, the first and any subsequent amino acids are different amino acids. In some embodiments, different amino acids can be differentially and/or uniquely labeled. Examples of unique amino acid labeling include, but are not limited to, labeling the thiol group of cysteine, labeling the amine group of lysine, labeling the sulfur of methionine, labeling the indole side chain of tryptophan, labeling the phenolic side chain of tyrosine, and labeling the glutamyl/aspartyl side chains of glutamic acid and aspartic acid. Commercial kits for such labeling are known in the art and include, but are not limited to, the STELLA+lysine labeling kit, the Monolith NHS kit (amine reactive), and the Monolith Maleimide kit (cysteine reactive). Additionally, artificial amino acids may be used during protein/peptide synthesis such that the artificial amino acids may be specifically labeled. Similarly, natural amino acids may be post-translationally modified to generate a moiety for specific labeling.
In some embodiments, the readout is a linear readout. A linear readout refers to a presentation of the amino acids as they appear in the sequence of the peptide, if the peptide is viewed linearly as a single string of amino acids. The linearity of the peptide can be considered from its N-terminus to C-terminus or in the reverse. Either direction is still considered linear. In some embodiments, the readout is from N-terminus to C-terminus. In some embodiments, the readout is from C-terminus to N-terminus. In some embodiments, the readout is from N-terminus to C-terminus or C-terminus to N-terminus. In some embodiments, the linear readout is representative of the order of amino acids along the peptide. In some embodiments, the linear readout is representative of the relative position of the amino acids along the peptide. In some embodiments, the readout is representative of the linear pattern of the amino acid. In some embodiments, the readout is a low-resolution linear pattern of the amino acid. In some embodiments, the readout is a low-resolution linear positioning of the amino acid along the peptide. In some embodiments comprising representation of more than one amino acid, the linear readout represents relative information on the order and/or position of the more than one amino acids.
In some embodiments, the first amino acid is selected from lysine, cysteine and methionine. In some embodiments, the second amino acid is selected from lysine, cysteine and methionine. In some embodiments, the third amino acid is selected from lysine, cysteine and methionine. In some embodiments, the first, second and third amino acids are lysine, cysteine and methionine.
As used herein, “a portion” of an amino acid refers to at least one of all of the particular amino acids along the peptide. A peptide may have many residues of one particular amino acid, and a portion refers to at least one of those residues. In some embodiments, a portion is at least 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 97, 99 or 100% of all residues of the amino acid along the peptide. Each possibility represents a separate embodiment of the invention. In some embodiments, a portion is at least 60%. In some embodiments, a portion is at least 70%. In some embodiments, a portion is at least 80%. In some embodiments, a portion is at least 90%. In some embodiments, a portion is not 100%. In some embodiments, a portion does not comprise 100%. It will be understood by a skilled artisan that not every portion must be the same percentage. For example, labeling of a first amino acid may be less efficient than labeling of a second amino acid, and therefore the portion of the first amino acid may be smaller than the portion of the second amino acid. Similarly, for any other conditions that may affect the size of the portion represented in the readout, it need not be such that each amino acid be represented by the same size portion or by the same number of amino acid residues.
As will be understood by a skilled artist, specific methods of labeling of amino acids have varying labeling efficiencies depending on the method of labeling and the target amino acid. Because this inefficiency in labeling is generally unbiased, different residues of a peptide may be labeled each time a given peptide is labeled. Further, most label scanning/detecting technologies also lack 100% accuracy and thus correctly labeled amino acids may be missed or not detected. Similarly, depending on the resolution of the scanning device, two labeled amino acids that are in close proximity may not be uniquely detected, and/or their relative position may not be identifiable. The resolution may also depend on other factors such as the velocity of the peptide as it is being scanned, the medium in which it is being scanned (viscosity, electrical properties, etc.) and the general physical conditions (pH, temp, etc.) during scanning. All of these issues may lead to an imperfect readout in which not every amino acid that should be detected is, but rather only a portion of the amino acids are present in the readout. The methods of the invention are unexpectedly useful in that even with such degenerate readouts for a peptide, the peptides true identity can be accurately assessed.
In some embodiments, the machine learning model is a machine learning classifier. In some embodiments, the machine learning model is a machine learning algorithm. In some embodiments, the algorithm is a supervised learning algorithm. In some embodiments, the algorithm is an unsupervised learning algorithm. In some embodiments, the algorithm is a reinforcement learning algorithm. In some embodiments, the machine learning model is a Convolutional Neural Network (CNN).
In some embodiments, the machine learning model predicts the identity of the peptide. In some embodiments, the machine learning model outputs the identity of the peptide. In some embodiments, the machine learning model predicts the sequence of the peptide. In some embodiments, the machine learning model predicts with at least 70, 75, 80, 85, 90, 95, 97, 99 or 100% accuracy. Each possibility represents a separate embodiment of the invention. In some embodiments, the machine learning model predicts at most 2 possibilities for the identity of the peptide. In some embodiments, the machine learning model further outputs a confusion matrix for the peptide. In some embodiments, the confusion matrix indicates the probability for correct identification.
In some embodiments, the machine learning model is trained on readouts of a set of peptides. In some embodiments, the machine learning model is trained on a training set of readouts. In some embodiments, the peptide to be identified is in the set of peptides. In some embodiments, the peptide to be identified is predicted to be in the set of peptides. In some embodiments, the readouts of the training set represent at least a portion of the first amino acid along a peptide from the set of peptides. In some embodiments, the readouts of the training set represent at least a portion of 1, 2, 3, 4, or 5 amino acids along the peptide from the set of peptides. In some embodiments, the readouts of the training set represent at least a portion of the first amino acid and a portion of the second amino acid and optionally a portion of the third amino acid along the peptide from the set of peptides.
In some embodiments, the set of peptides is a set of peptides with known sequences. In some embodiments, the set of peptides is a set of peptides with known readouts. In some embodiments, the set of peptides is a set of peptides expected to be in a sample. In some embodiments, the peptide to be analyzed in from the sample. In some embodiments, the sample is a bodily fluid. In some embodiments, a bodily fluid is selected from at least one of blood, plasma, serum, tissue, urine, gastric fluid, intestinal fluid, saliva, bile, tumor fluid, breast milk, interstitial fluid, stool and cerebral spinal fluid. In some embodiments, the sample is a biopsy. In some embodiments, the biopsy is a liquid biopsy. In some embodiments, the sample is protein panel. Protein panels are well known in the art, such as, for non-limiting example, a cytokine panel, oncogene panel, surface marker panel and a clinical biomarker panel.
In some embodiments, the set of peptides are the proteins found in a proteome. In some embodiments, the proteome is full organism proteome. In some embodiments, the organism is a mammalian. In some embodiments, the mammal is a human. In some embodiments, the peptide to be analyzed is from the proteome. In some embodiments, the set of peptides are proteins found in a bodily fluid. In some embodiments, the peptide to be analyzed is in the bodily fluid. In some embodiments, the proteome is an organ, tissue or fluid proteome. In some embodiments, the fluid is a bodily fluid. In some embodiments, the tissue is tumor tissue. In some embodiments, the tissue is a tumor. In some embodiments, the set pf proteins are proteins found in plasma. In some embodiments, the protein to be analyzed is from plasma.
In some embodiments, the set of proteins comprises at least 2, 5, 7, 10, 12, 15, 20, 25, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 5000, 10000, 15000, 20000, or 25000 proteins. Each possibility represents a separate embodiment of the invention.
The sequences of proteins that may be used for generation of simulated traces are easily accessible to one skilled in the art. For example, amino acid sequences can be found in the Pubmed, Uniprot and Swissprot databases. Additionally, the expected protein makeup of whole organism genomes are also available on these databases. Further, the proteome or expected proteome for various tissues and fluids can be found, for example, at the Human Protein Atlas, or the Tissues database, as well as at the above databases that provide whole proteome data.
In some embodiments, the analyzed readout is the same type of readout as the readouts of the training set. In some embodiments, the training set comprises a plurality of readouts. In some embodiments, each readout represents at least a portion of a first amino acid along a peptide. In some embodiments, each readout represents at least a portion of a second amino acid along a peptide. In some embodiments, each readout represents at least a portion of a third amino acid along a peptide. In some embodiments, each readout represents at least a portion of a fourth amino acid along a peptide. In some embodiments, each readout represents at least a portion of a fifth amino acid along a peptide.
In some embodiment, the training set comprises at least 10, 15, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 readouts representative of a peptide. Each possibility represents a separate embodiment of the invention. In some embodiments, the training set comprises at least 2, 5, 7, 10, 12, 15, 20, 25, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 5000, 10000, 15000, 20000, or 25000 proteins. Each possibility represents a separate embodiment of the invention. In some embodiments, the training set comprises at least 10, 15, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 readouts representative of each peptide from the set. Each possibility represents a separate embodiment of the invention.
In some embodiments, the training set comprises labels identifying the peptide associated with each readout. In some embodiments, the training set comprises labels identifying the peptide represented in each readout. In some embodiments, the training set comprises labeled readouts, wherein the label identifies the peptide associated with the readout. In some embodiments, the training set comprises labeled readouts, wherein the label identifies the peptide represented in the readout.
In some embodiments, the readouts of the training set comprise at least 10, 15, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 readouts representative of a peptide from the set. Each possibility represents a separate embodiment of the invention. In some embodiments, the readouts of the training set comprise at least 50 readouts representative of a peptide from the set. In some embodiments, the readouts of the training set comprise at least 80 readouts representative of a peptide from the set. In some embodiments, the readouts of the training set comprise at least 10, 15, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 readouts representative of each peptide from the set. Each possibility represents a separate embodiment of the invention. In some embodiments, the readouts of the training set comprise at least 50 readouts representative of each peptide from the set. In some embodiments, the readouts of the training set comprise at least 80 readouts representative of each peptide from the set.
In some embodiments, the readouts of the training set are simulated readouts. In some embodiments, the training set comprises simulated readouts. In some embodiments, the simulated readouts are based on a known sequence for a peptide. In some embodiments, the simulated readouts are based on a known sequence for each peptide. In some embodiments, the simulations are generated with a non-ideal condition. In some embodiments, the condition is selected from non-ideal labeling efficiency and non-ideal detection resolution. In some embodiments, the condition is selected from non-ideal labeling efficiency, non-ideal detection resolution, and non-ideal conditions during detection. In some embodiments, non-deal conditions during detection are selected from non-ideal pH, non-ideal temperature, non-ideal speed of the peptide. In some embodiments, the condition is selected from non-ideal labeling efficiency, non-ideal detection resolution, and non-deal velocity of the peptide as it is detected. In some embodiments, the simulations are based on a known sequence when only a portion of an amino acid is represented in the simulated readout. In some embodiments, the simulations are based on a known sequence when at least a portion of an amino acid is not represented in the simulated readout.
It will be understood, that given a known sequence of a protein, simulated readouts can be generated with only a certain percentage of labeling or only with a given spatial resolution or generally with any desired constraint. Several readouts for each condition can be generated, as labeling only 80% of an amino acid for example, can lead to numerous permutations of a simulated readout. For an illustrative example, if a peptide comprises four lysine residues {K1, K2, K3 and K4}, a 75% labeling can result in 4 different possibilities: {K1, K2, K3}, {K1, K2, K4}, {K1, K3, K4} and {K2, K3, K4}. In some embodiments, the training set comprises simulation of every possibility for a given condition. In some embodiments, the training set comprises at least 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 95, 97, 99 or 100% of every possibility for a given condition. Each possibility represents a separate embodiment of the invention. In some embodiments, the training set comprises a plurality of simulated condition. In some embodiments, the training set comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 simulated conditions. Each possibility represents a separate embodiment of the invention.
In some embodiments, the method further comprises receiving a readout representative of the peptide to be analyzed. In some embodiments, the method further comprises receiving a readout representative of a target peptide. In some embodiments, a target peptide is a peptide to be analyzed. In some embodiments, the target peptide is a peptide in a sample. In some embodiments, the target peptide is a peptide expected to be in a sample. In some embodiments, the target peptide is in the sample. In some embodiments, the target peptide is from the sample. In some embodiments, the method further comprises an inference stage. In some embodiments, the inference stage comprises applying the machine learning model to a target readout. In some embodiments, the machine learning model is the trained machine learning model. In some embodiments, the target readout represents at least a portion of a first amino acid along a target peptide. In some embodiments, the target readout represents at least a portion of a second amino acid along a target peptide. In some embodiments, the target readout represents at least a portion of 1, 2, 3, 4 or 5 amino acids along a target peptide. Each possibility represents a separate embodiment of the invention.
In some embodiments, the method further comprises receiving a readout representative of at least a portion of a first amino acid along a peptide. In some embodiments, the received readout is a linear readout. In some embodiments, the received readout is of at least a portion of a first amino acid and at least a portion of a second amino acid and optionally at least a portion of a third amino acid, fourth amino acid or fifth amino acid along the peptide.
In some embodiments, the method further comprises labeling at least a portion of an amino acid with a label along the peptide. In some embodiments, the received readout and/or the readout to be analyzed is generated by labeling at least a portion of an amino acid with a label along the peptide. In some embodiments, the amino acid is the first amino acid and the label is a first label. In some embodiments, the amino acid is the second amino acid and the label is a second label. In some embodiments, the amino acid is the third amino acid and the label is a third label. In some embodiments, each different amino acid is labeled with a different label. Thus, if three amino acids are to be part of the readout then those three amino acids are labeled each with a distinct label.
In some embodiments, the method further comprises detecting the labels linearly along the peptide. In some embodiments, the detecting the labels linearly along the peptide is to produce the readout. In some embodiments, the received readout and/or the readout to be analyzed are produced by detecting the labels linearly along the peptide. In some embodiments, detecting linearly comprises detecting the order along the peptide. In some embodiments, the detecting linearly comprises detecting the relative order of more than one amino acid along the peptide. In some embodiments, detecting linearly comprises detecting a low-resolution pattern of the amino acid along the peptide. In some embodiments, detecting linearly comprises detecting the low-resolution position of the amino acid along the peptide. In some embodiments, all labeled amino acids are detected. In some embodiments, at least 1, 2, 3, 4, or 5 labeled amino acids are detected. Each possibility represents a separate embodiment of the invention.
In some embodiments, each labeled amino acid along the peptide is detected. In some embodiments, at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 97, 99 or 100% of the labeled amino acids along the peptide are detected. Each possibility represents a separate embodiment of the invention. Depending on the resolution of the detecting device not all labels may be uniquely detected. Further, the experimental conditions during detection may result in non-ideal detection causing either missing of a label or incorrect ordering of a label.
In some embodiments, the detecting comprises passing the labeled peptide through a nanopore. In some embodiments, a label is uniquely detectable as it passes through the nanopore. In some embodiments, the nanopore comprises a sensor. In some embodiments, the nanopore is coupled to a sensor. In some embodiments, the sensor is configured for detection of the label. In some embodiments, the sensor is configured for detection at the nanopore. In some embodiments, the sensor is configured for detection at the exit of the nanopore. In some embodiments, the sensor is configured for detection of the label at the nanopore or at the exit of the nanopore. In some embodiments, each label is uniquely detectable as it passes through the nanopore. In some embodiments, a label comprises a fluorophore or a fluorescent moiety. In some embodiments, the nanopore comprises or is coupled to an optical sensor. In some embodiments, the optical sensor is configured to detect fluorescence at the nanopore. In some embodiments, the optical sensor is configured to detect fluorescence at the exit of the nanopore. In some embodiments, a label comprises a bulky group. In some embodiments, the nanopore comprises or is coupled to an electrical sensor. In some embodiments, electrical sensor is configured to detect electrical current at the nanopore. In some embodiments, the electrical sensor is configured to detect electrical voltage at the nanopore. In some embodiments, the electrical sensor is configured to detect electrical current, voltage or both at the nanopore.
Different fluorochromes have distinct excitation ranges and emission ranges allowing for unique detection by a single sensor or by a plurality of sensors. In some embodiments, a dedicated sensor detects each label. These fluorochromes and their excitation and emission ranges are well known in the art. Some non-limiting examples of fluorochromes and their maximum excitation and emission wavelengths (nm) include: 7-AAD (7-Aminoactinomycin D) 546, 647; Acridine Orange (+DNA) 500, 526; Acridine Organe (+RNA) 460, 650; Allophycocyanin (APC) 650, 660; Aniline Blue 370, 509; BODIPY® FL 505, 513; CF640R 642, 662; Cy5® 649, 670; Cy5.5® 675, 694; Cy7® 743, 767; DAPI 358, 461; EGFP 489, 508; Fluorescein (FITC) 494, 518; Pacific Blue 410, 455; PE (R-phycoerythrin) 480 and 565, 575; PE-Cy5480 and 650, 670; PE-Cy7480 and 743, 767; Propidium Iodide (PI) 536, 617; and YFP (Yellow Fluorescent Protein) 513, 527. Spectra for fluorochromes can also be found at the following websites: probes.com/servlets/spectra/and clontech.com/gfp/excitation.shtml as well as many others known to those skilled in the art. Detection of each
According to some embodiments, the nanopore is an ion-conducting nanopore. In some embodiments, the nanopore is a solid-state nanopore. In some embodiments, the nanopore is a plasmonic nanopore. In some embodiments, the nanopore is a plasmonic nanowell.
In some embodiments, the nanopore is part of a nanopore apparatus. In some embodiments, the nanopore is in a film. The production of nanopores in a film is well known in the art. Fabrication of nanopores in thin membranes has been shown in, for example, Kim et al., Adv. Mater. 2006, 18 (23), 3149 and Wanunu, M. et al., Nature Nanotechnology 2010, 5 (11), 807-814. Further, methods of such fabrication of films in silicon wafers, and methods of producing nanopores therein are provided herein in the Materials and Methods section. In some embodiments, the nanopore is produced with a transition electron microscope (TEM). In some embodiments, the nanopore is produced with a high-resolution aberration-corrected TEM or a noncorrected TEM.
According to some embodiments, the nanopore apparatus comprises a film, and wherein the film comprises at least one nanopore. In some embodiments, the nanopore apparatus further comprises a first and a second fluidic reservoir separate by the film and connected via the nanopore. In some embodiments, the nanopore apparatus further comprises first and second electrodes configured to electrically contact fluid placed in the first reservoir and fluid placed in the second reservoir, respectively. In some embodiments, the electrodes are configured to generate an electrical current that drives a protein to be analyzed through the nanopore.
In some embodiments, the nanopore is naked in that it does not comprise a protein for facilitating transfer through the nanopore. In some embodiments, the labeled protein passes through the nanopore via the electrical current generated by the electrodes. In some embodiments, the labeled protein is denatured. In some embodiments, the protein is denatured with a surfactant. In some embodiments, the surfactant is sodium dodecyl sulfate (SDS). In some embodiments, the labeled protein is uniformly labeled by a charge to induce transfer through the nanopore. In some embodiments, the charge is a negative charge. In some embodiments, the nanopore apparatus further comprises a sensor or detector for detecting a label as it passes through the nanopore. In some embodiments, the label is detected at the nanopore. In some embodiments, the label is detected at the exit of the nanopore. In some embodiments, the label is detected while exiting the nanopore.
In some embodiments, the readout is a linear trace of the peptide as it passes through the nanopore. In some embodiments, the linear trace is a linear-temporal trace. In some embodiments, the readout represents the time of each label along the peptide as it passes through the nanopore. In some embodiments, the time of passage is roughly proportional to position along the peptide. It will be understood by a skilled artisan that different amino acids will pass through a naked nanopore at different speeds and with different translocation rates. Since the movement is not linear, the temporal trace does not perfectly correlate to positions along the peptide, although a low-resolution positioning can be discerned. Although precise positioning is not known, the time traces can be analyzed by the machine learning model to better distinguish between peptides with similar orders of labeled amino acids, but with different positions temporally. In some embodiments, linear-temporal traces are used for training the machine learning model.
In some embodiments, the nanopore comprises a diameter not greater than 1, 2, 3, 4, 5, 7, 10, 15, 20, 15, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150 nm. Each possibility represents a separate embodiment of the invention. In some embodiments, the nanopore comprises a diameter not greater than 5 nm. In some embodiments, the nanopore comprises a diameter not greater than 7 nm. In some embodiments, the nanopore comprises a diameter not greater than 100 nm. In some embodiments, the nanopore comprises a diameter of about 5 nm. In some embodiments, the nanopore comprises a diameter between 0.5 and 5, 0.5 and 7, 0.5 and 10, 0.5 and 15, 0.5 and 20, 1 and 5, 1 and 7, 1 and 10, 1 and 15, 1 and 20, 3 and 5, 3 and 7, 3 and 10, 3 and 15, 3 and 20, 5 and 7, 5 and 10, 5 and 15, or 5 and 20 nm. Each possibility represents a separate embodiment of the invention. The width of an amino is ˜2 nm and the Kuhn length for a polypeptide is ˜7 nm, therefore nanopores in this size range are ideal. However, as demonstrated hereinbelow, even far worse spatial resolution can still be used as part of the method of the invention.
In some embodiments, the nanopore comprises a resolution not greater than 1, 2, 3, 4, 5, 7, 10, 15, 20, 15, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150 nm. Each possibility represents a separate embodiment of the invention. In some embodiments, the nanopore comprises a resolution not greater than 5 nm. In some embodiments, the nanopore comprises a resolution not greater than 7 nm. In some embodiments, the nanopore comprises a resolution not greater than 100 nm. In some embodiments, the nanopore comprises a resolution of about 5 nm. In some embodiments, the nanopore comprises a resolution between 0.5 and 5, 0.5 and 7, 0.5 and 10, 0.5 and 15, 0.5 and 20, 1 and 5, 1 and 7, 1 and 10, 1 and 15, 1 and 20, 3 and 5, 3 and 7, 3 and 10, 3 and 15, 3 and 20, 5 and 7, 5 and 10, 5 and 15, or 5 and 20 nm. Each possibility represents a separate embodiment of the invention.
In some embodiments, the nanopore comprises a plasmonic structure. In some embodiments, the structure is a nano-structure. Such nanopores are known in the art as plasmonic nanopores. In some embodiments, the plasmonic structure is configured to localize electromagnetic excitation below a wavelength of light. In some embodiments, the wavelength below a wavelength of light is a particular wavelength. In some embodiments, the particular wavelength is a wavelength of the fluorescent label to be detected. In some embodiments, the plasmonic structure is configured to amplify localized fluorescence emission at the nanopore. In some embodiments, the amplification is at a plurality of wavelengths. In some embodiments, the amplification is at a particular wavelength. In some embodiments, the plurality of wavelengths comprise wavelengths of the fluorochrome labels.
The plasmonic nanopores and nanowells can be configured to enhance specific excitation and thereby specific flourochromes. Configurations of nanowells to enhance excitation at specific or multiple plasmonic resonances are well known in the art and comprise using particular geometries, dimensions, materials, refractive indecies or a combination thereof. Examples of these geometries, materials and dimensions can be found in Fermamdez-Garcia, et al., Design Considerations for Near-filed Enhancement in Optical Antennas, Contemporary Physics, 2014, and may include for example rod, ellipsoid, bowtie, disk and square geometries; gold, silver aluminum and copper nanowells; as well as diameters measuring about 40, 30, 20, 10 and 5 nm. Configurations of plasmonic nanopores and methods of producing plasmonic nanopores can be found in International Patent Publication WO2019/123467, which is herein incorporated by reference in its entirety.
In some embodiments, the method can be for identifying a plurality of peptides in a sample. In some embodiments, readouts from the plurality of peptides are analyzed. In some embodiments, the sample is passed through the nanopore and the peptides are analyzed. In some embodiments, the sample is provided to the first reservoir of the nanopore apparatus and the peptides are detected to produce readouts for each protein. In some embodiments, the apparatus comprises an array of nanopores so that a plurality of peptides is detected simultaneously.
As used herein, the terms “electronic document” and “electronic file” are interchangeable and refer broadly to any document/file containing data and stored in a computer-readable format. Electronic document formats may include, among others, Portable Document Format (PDF), Digital Visual Interface (DVI), text files (txt), Comma Separated Vector (CSV), binary files, NumPy array files (npy), PostScript, word processing file formats, such as docx, doc, and Rich Text Format (RTF), and/or XML Paper Specification (XPS).
In some embodiments, the labels denote the identity of the peptide. In some embodiments, the labels identify the peptide by name. In some embodiments, the labels are the name of the peptide. In some embodiments, the labels are the protein abbreviate of the name of the protein. For example, the abbreviate for Albumen is known in the art to be ALB. In some embodiments, the labels are database numbers for the proteins. In some embodiments, the labels are sequences of the proteins. In some embodiments, the labels are tags for the proteins.
In some embodiments, the one or more new documents/file contain readouts from a peptide to be identified. In some embodiments, the one or more new documents/files contain readouts from a peptide from a sample. In some embodiments, the training set comprises readouts of a set of peptides in, or expected to be in, the sample. In some embodiments, the training set comprises readouts of proteins found in a proteome. In some embodiments, the training set comprises readouts of all proteins found in a proteome. In some embodiments, the training set comprises readouts for at least 2, 5, 7, 10, 12, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 5000, 10000, 15000, 20000, or 25000 proteins. Each possibility represents a separate embodiment of the invention. In some embodiments, the training set comprises readouts for at least 15 proteins. In some embodiments, the training set comprises readouts for at least 16 proteins. In some embodiments, the training set comprises readouts for at least 50 proteins. In some embodiments, the training set comprises at least 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 readouts representative of a peptide from the set. Each possibility represents a separate embodiment of the invention. In some embodiments, the training set comprises at least 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 readouts representative of each peptide from the set. Each possibility represents a separate embodiment of the invention. In some embodiments, the training set comprises at least 50 readouts representative of a peptide from the set. In some embodiments, the training set comprises at least 50 readouts representative of each peptide from the set. In some embodiments, the training set comprises at least 80 readouts representative of a peptide from the set. In some embodiments, the training set comprises at least 80 readouts representative of each peptide from the set.
In some embodiments, the one or more new electronic documents are one new document. In some embodiments, the one or more new electronic documents are a plurality of documents. In some embodiments, the one or more new electronic documents are proteins from a sample. In some embodiments, the one or more new electronic documents comprise a readout of a peptide to be analyzed. In some embodiments, the one or more new electronic documents comprise a readout of a peptide from a sample. In some embodiments, the one or more new electronic documents comprise a readout of a peptide as it passes through a nanopore. In some embodiments, the one or more new electronic documents comprise a linear temporal trace of a labeled peptide as it passes through a nanopore.
In some embodiments, the labeled peptide is labeled at at least a portion of one amino acid. In some embodiments, the labeled peptide is labeled at at least a portion of a plurality of amino acids. In some embodiments, the labeled peptide is labeled at at least a portion of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids. Each possibility represents a separate embodiment of the invention. In some embodiments, the labeled peptide is labeled at at least a portion of two amino acids. In some embodiments, the labeled peptide is labeled at at least a portion of three amino acids. In some embodiments, the amino acids are the first, second, third amino acid or a combination thereof.
In some embodiments, the at least one hardware processor trains a machine learning model. In some embodiments, the model is based, at least in part, on a training set. In some embodiments, the model is based on a training set. In some embodiments, the at least one hardware processor applies the machine learning model to a target readout. In some embodiments, the target readout is a linear readout. In some embodiments, the target readout represents at least a portion of a first amino acid along a target peptide. In some embodiments, the target readout represents at least a portion of a second amino acid along a target peptide. In some embodiments, the target readout represents at least a portion of a third amino acid along a target peptide. In some embodiments, the target readout represents at least a portion of 1, 2, 3, 4 or 5 amino acids along a target peptide. Each possibility represents a separate embodiment of the invention.
According to some embodiments, the system further comprises means for producing the plurality of electronic documents. In some embodiments, the system further comprises a nanopore. In some embodiments, the system further comprises a nanopore apparatus. In some embodiments, the means for producing the plurality of electronic documents is the nanopore apparatus.
In some embodiments, the present invention may be configured for automatic document classification based, at least in part, on content-based assignment of one or more predefined categories (classes) to documents. By classifying the content of a document, it may be assigned one or more predefined classes or categories, thus making it easier to manage and sort. Such classes may be specific families of proteins, proteins with particular functions, proteins from particular sources or any class of protein or category of protein such as would be useful to the user.
Typically, multi-class machine learning classifiers are trained on a training set of documents, where each document belongs to one of a certain number of distinct classes (e.g., invoices, scientific papers, resumes, letters). The training set may be labeled with the correct classes (e.g., for supervised learning), or may not be labeled (e.g., in the case of unsupervised learning). Following a training stage, the classifier may be able to predict the most probable class for each document in a test set of documents. Although document classification may be based on textual content alone, for some types of documents, the task of classification can be significantly enhanced by also generating features from the visual structure of the document. This is based on the idea that documents in the same category often also share similar layout and structure features.
In some embodiments, following a multi-modal training stage, a trained classifier of the present invention may be configured for classifying electronic documents based on a multi-modal input comprising both representations of the documents. In other embodiments, the trained classifier may be configured for classifying electronic documents based on only a single modality input (e.g., textual content or raster image alone), with improved classification accuracy as compared to a classifier which has been trained solely based on a single modality.
In some embodiments, the present invention may employ one or more types of neural networks to further generate data representations of the multi-modal inputs. For example, raw input text from an electronic document may be processed so as to generate a data representation of the text as a fixed-length vector. Similarly, images of the electronic document (e.g., thumbnails or raster images) may be processed to extract image features.
In some embodiments, the neural network models employed by the present invention to generate textual data representations may be selected from the group consisting of Neural Bag-of-Words (NBOW); recurrent neural network (RNN), Recursive Neural Tensor Network (RNTN); Dynamic Convolutional Neural Network (DCNN); Long short-term memory network (LSTM); and recursive neural network (RecNN). See, e.g., Pengfei Liu et al., “Recurrent Neural Network for Text Classification with Multi-Task Learning”, Proceedings of the Twenty-Fifth International Joint Conference on Artificial Intelligence (IJCAI-16). Convolutional neural network (CNN) may be used, e.g., to extract image features which represent the physical visual structure of a document.
In some embodiments, the present invention may further be configured for employing a common representation learning (CRL) framework, for learning a common representation of the two views of data (i.e., textual and visual). CRL is associated with multi-view data that can be represented in multiple forms. The learned common representation can then be used to train a model to reconstruct all the views of the data from each input. CRL of multi-view data can be categorized into two main categories: canonical-based approaches and autoencoder-based methods. Canonical Correlation Analysis (CCA)-based approaches comprise learning a joint representation by maximizing correlation of the views when projected to the common subspace. Autoencoder (AE) methods learn a common representation by minimizing the error of reconstructing the two views. AE-based approaches use deep neural networks that try to optimize two objective functions. The first objective is to find a compressed hidden representation of data in a low-dimensional vector space. The other objective is to reconstruct the original data from the compressed low-dimensional subspace. Multi-modal autoencoders (MAE) are two-channeled models which specifically perform two types of reconstructions. The first is the self-reconstruction of view from itself, and the other is the cross-reconstruction where each view is reconstructed from the other. These reconstruction objectives provide MAE the ability to adapt towards transfer learning tasks as well. In the context of CRL, each of these approaches has its own advantages and disadvantages. For example, though CCA based approaches outperform AE based approaches for the task of transfer learning, they are not as scalable as the latter.
The present invention may be a system, a method, and/or a computer program product. The computer program product may include a computer readable storage medium (or media) having computer readable program instructions thereon for causing a processor to carry out aspects of the present invention.
The computer readable storage medium can be a tangible device that can retain and store instructions for use by an instruction execution device. The computer readable storage medium may be, for example, but is not limited to, an electronic storage device, a magnetic storage device, an optical storage device, an electromagnetic storage device, a semiconductor storage device, or any suitable combination of the foregoing. A non-exhaustive list of more specific examples of the computer readable storage medium includes the following: a portable computer diskette, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or Flash memory), a static random access memory (SRAM), a portable compact disc read-only memory (CD-ROM), a digital versatile disk (DVD), a memory stick, a floppy disk, a mechanically encoded device having instructions recorded thereon, and any suitable combination of the foregoing. A computer readable storage medium, as used herein, is not to be construed as being transitory signals per se, such as radio waves or other freely propagating electromagnetic waves, electromagnetic waves propagating through a waveguide or other transmission media (e.g., light pulses passing through a fiber-optic cable), or electrical signals transmitted through a wire. Rather, the computer readable storage medium is a non-transient (i.e., not-volatile) medium.
Computer readable program instructions described herein can be downloaded to respective computing/processing devices from a computer readable storage medium or to an external computer or external storage device via a network, for example, the Internet, a local area network, a wide area network and/or a wireless network. The network may comprise copper transmission cables, optical transmission fibers, wireless transmission, routers, firewalls, switches, gateway computers and/or edge servers. A network adapter card or network interface in each computing/processing device receives computer readable program instructions from the network and forwards the computer readable program instructions for storage in a computer readable storage medium within the respective computing/processing device.
Computer readable program instructions for carrying out operations of the present invention may be assembler instructions, instruction-set-architecture (ISA) instructions, machine instructions, machine dependent instructions, microcode, firmware instructions, state-setting data, or either source code or object code written in any combination of one or more programming languages, including an object oriented programming language such as Java, Smalltalk, C++ or the like, and conventional procedural programming languages, such as the “C” programming language or similar programming languages. The computer readable program instructions may execute entirely on the user's computer, partly on the user's computer, as a stand-alone software package, partly on the user's computer and partly on a remote computer or entirely on the remote computer or server. In the latter scenario, the remote computer may be connected to the user's computer through any type of network, including a local area network (LAN) or a wide area network (WAN), or the connection may be made to an external computer (for example, through the Internet using an Internet Service Provider). In some embodiments, electronic circuitry including, for example, programmable logic circuitry, field-programmable gate arrays (FPGA), or programmable logic arrays (PLA) may execute the computer readable program instructions by utilizing state information of the computer readable program instructions to personalize the electronic circuitry, in order to perform aspects of the present invention.
These computer readable program instructions may be provided to a processor of a general-purpose computer, special purpose computer, or other programmable data processing apparatus to produce a machine, such that the instructions, which execute via the processor of the computer or other programmable data processing apparatus, create means for implementing the functions/acts specified in the flowchart and/or block diagram block or blocks. These computer readable program instructions may also be stored in a computer readable storage medium that can direct a computer, a programmable data processing apparatus, and/or other devices to function in a particular manner, such that the computer readable storage medium having instructions stored therein comprises an article of manufacture including instructions which implement aspects of the function/act specified in the flowchart and/or block diagram block or blocks.
The computer readable program instructions may also be loaded onto a computer, other programmable data processing apparatus, or other device to cause a series of operational steps to be performed on the computer, other programmable apparatus or other device to produce a computer implemented process, such that the instructions which execute on the computer, other programmable apparatus, or other device implement the functions/acts specified in the flowchart and/or block diagram block or blocks.
As used herein, the term “about” when combined with a value refers to plus and minus 10% of the reference value. For example, a length of about 1000 nanometers (nm) refers to a length of 1000 nm+−100 nm.
It is noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a polynucleotide” includes a plurality of such polynucleotides and reference to “the polypeptide” includes reference to one or more polypeptides and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.
In those instances where a convention analogous to “at least one of A, B, and C, etc.” is used, in general such a construction is intended in the sense one having skill in the art would understand the convention (e.g., “a system having at least one of A, B, and C” would include but not be limited to systems that have A alone, B alone, C alone, A and B together, A and C together, B and C together, and/or A, B, and C together, etc.). It will be further understood by those within the art that virtually any disjunctive word and/or phrase presenting two or more alternative terms, whether in the description, claims, or drawings, should be understood to contemplate the possibilities of including one of the terms, either of the terms, or both terms. For example, the phrase “A or B” will be understood to include the possibilities of “A” or “B” or “A and B.”
It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments pertaining to the invention are specifically embraced by the present invention and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations of the various embodiments and elements thereof are also specifically embraced by the present invention and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.
Additional objects, advantages, and novel features of the present invention will become apparent to one ordinarily skilled in the art upon examination of the following examples, which are not intended to be limiting. Additionally, each of the various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below finds experimental support in the following examples.
Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.
Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Culture of Animal Cells—A Manual of Basic Technique” by Freshney, Wiley-Liss, N. Y. (1994), Third Edition; “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference. Other general references are provided throughout this document.
The theoretical identification values were calculated using the human proteome Swiss-Prot database, which contains 20,328 entries. For each entry we extracted the number of the target amino acids (C, K and M), as well as their order of appearance. For example, the p53 protein would either be characterized by its C, K, M counts (10, 20, 12, respectively) or by the sequence below: MKMMMKKCKMCKCMKMCCCMCCMMCC KKKKKKKMK (SEQ ID NO: 1), in which all intervening amino acids were deleted. Proteins having identical characteristic sequences (or C, K and M counts) are grouped together. A protein is identified when it is the sole member of a group. In the case of p53, both the C, K and M counts and the characteristic sequence gave a unique identification. The pie charts (
Each protein primary sequence was transformed into a string (B(i)) to which was assigned a value of 1, 2 or 3 corresponding to each of the three aa tags (K, C, and M), respectively; and 0 for all other aa in the protein sequence. To account for partial or nonspecific labelling a set of randomly selected labeled positions in the string were omitted according to a given labeling efficiency (ηL), and a set of artificial labeled positions were inserted according to a given nonspecific labeling efficiency (ηNS). It is important to note that nonspecific labeling did not affect all aa equally. For instance, in generating a barcode for lysine (K) positions, nonspecific labeling could only be inserted at positions of either threonine, serine or tyrosine (amino acids which have been shown to compete with NHS-ester-based labeling) with a probability of typically 1%. The strings were generated for the entire Swiss-Prot data base and were re-generated each time to simulate an uneven labelling of the same protein data sets, as well as whenever different values of ηL and ηNS were used.
The three-dimensional near field enhancement of the plasmonic structure (2D vertical cross-section shown in
The excitation field was modeled as a total-field scattering-field source (TFSFS) and the spatial sampling frequency was set to 5 nm−1 (taking 60 frequency points over the 500-800 nm wavelength range). The FDTD boundary conditions consisted of 8-layer PMLs (perfectly matched layers) symmetric in the x axis and antisymmetric in the y axis thus minimizing the reflections and the computational cost, respectively. Frequency domain power monitors only were incorporated in the simulation to determine the near field enhancement in the vicinity of the nanopore. All numerical simulations were performed using Lumerical FDTD Solutions (Lumerical, Inc).
To simulate the translocation of the linearized protein through the nanopore, there was assumed a unidirectional motion with steps of a single aa length (Δ≈0.35 nm) and an average velocity u (cm/s). To account for thermal fluctuations in this process, a random noise term δu was added at each step (δu can be positive or negative). Hence the simulation step time of the i-th aa was defined as τi=Δ/(u+δu). The average protein velocity value was typically ˜0.2 cm/s, based on experiments using SDS denatured proteins in solid-state nanopores as shown in
K
fl,j,n(t)=kfl,jPj,n(t) Eq. 1
where j=1 . . . 3 correspond to each of the three excitation/emission channels, kfl the fluorescence transition rate and Pn(t) the occupation probability of the excited molecular state S1. The fluorophores are excited by up to three laser lines corresponding to the three channels, that form sub-wavelength excitation volumes by means of a plasmonic nanostructure or total internal reflection. The axial full width at half maximum of our Gaussian excitation volume Iex is defined as ξ and is allowed to vary from 5 nm to 200 nm in order to account for broad possible experimental conditions. The emitted light from the three-color channels is assumed to be acquired with given efficiencies ηj, which include both the optical transmission efficiencies and the photodetector efficiencies. The photon counts Iij at each channel j during each step i of the protein translocation is then determined by summing the emissions of all the fluorophores n that resides within the excitation volume. Namely:
where kbg is the background emission rate, ti the time at which step the translocation occurred such that ti−ti-1=τi, kex,j(n) is the excitation rate of the fluorophore n of channel j, σex,j is its absorption coefficient, λex,j is the excitation wavelength and τSI,j is its excited state lifetime.
The number of cycles (S0→S1→S0) undergone by each fluorophore was capped to account for photobleaching according to a decaying exponential distribution. Specifically, the maximum number of cycles performed by each fluorophore before photobleaching was given by a random number drawn from a decaying exponential distribution with a characteristic decay of ˜106. Finally, we applied a Poisson distribution to the photon counts Iij to simulate shot noise.
To include energy transfer (such as Førster Energy Transfer and homo-transfer) in this system a 2D distance matrix was calculated for each fluorophore in the system. The distances between the labelled aa's (or fluorophores) in each linearized protein were subsequently used to calculate the Forster energy transfers of each fluorophore from and to each of its neighboring emitters. As a proxy for the exact energy transfer, two additional transition rates accounting for energy gain and loss were incorporated in the fluorophore two-state model:
where Em←n=(1+(|xn−xn|/R0,m←n)6)−1 is the FRET energy transfer efficiency from fluorophore n to m, xn is the position of fluorophore n along the denatured protein and R0,m←n is the Forster-radius of the (n, m) dye pair when considering an energy transfer from fluorophore n to m. The transition rates kex,j(n) and kj(n) in Eq. 4 were corrected to account for FRET accordingly:
The code was implemented using MATLAB, and the optical readouts of the three channels were determined by running this procedure for each labeling string.
For the purpose of a multi-class (the human proteome comprises more than twenty thousand proteins) classification of time-series that exhibit specific patterns, convolutional neural networks (CNN) were used that have shown great promise in the field of pattern recognition, including image classification, which similarly requires tens of thousands of classes. Specifically, the python deep learning package Keras was used on a four GPU architecture (NVIDIA Tesla K40), which leads to a CNN whole-proteome training time of −2 h only. The CNN model relied on four sequential layers—a convolutional layer, a normalization layer in which dropout was applied and a pooling layer—followed by a multi-layer perceptron. In brief, the convolutional layer filters (at a given step or stride size) the translocation time-series with a large set of kernels of a specific size. The resulting activation or feature map it provides is further transformed by the normalization layer such as the mean and standard deviation of the activation map approach zero and one, respectively. Next, the dropout circumvents overfitting of the CNN to the training dataset by setting a random subset of activations to zero. The last pooling layer performs a down-sampling operation on the activation map to further prevent overfitting of the training dataset and the computational load. The multi-layer perceptron consists of a single densely connected neural network layer, each neuron outputting the probability of belonging to the class it represents (‘softmax’ activation function).
The hyper-parameters were optimized according to standard procedures, that is maximizing the accuracy of the CNN trained over five to ten epochs per hyper-parameter set. Once finely adjusted, the CNN was trained using twenty epochs to yield the greatest accuracy. The protein identification accuracy as determined by the CNN was calculated as the fraction of correctly classified translocation events from the test dataset. The dataset was randomly partitioned into five pairs of training and testing sub-sets, and for which the identification accuracy was determined. The final accuracy was calculated as the average between them where a typical test set included ˜400,000 translocation events.
Solid-state nanopores were fabricated using a laser drilling method in 17 nm-thick SiNx membranes as is known in the art. Human serum albumin (Biological Industries Inc. 30-O595-A) was first treated by TCEP (5 mM) at room temperature for 30 min to break disulfide bonds and subsequently denatured at 90° C. for 5 min in PBS with 2% sodium-dodecyl sulfate (SDS). The resulting albumin concentration was further diluted (100:1) to <1 nM in buffer (PBS/0.4M NaCl/0.1% SDS/1 mM EDTA) for nanopore translocation experiments performed under a 300 mW bias. A custom-made LabVIEW interface was used to acquire and analyze each event. Scatter plots and dwell-time distributions were generated using Igor Pro (Wavemetrics).
In the method of the invention, proteins extracted from any source (serum, tissue or cells), are denatured using urea and SDS (
The theoretical likelihood of protein ID can be tested by calculating the percentages of unique matches of all proteins in the human Swiss-Prot database based on the number and the order of appearance of three amino-acids only. Simply counting the number of K, C and M residues in each protein identifies 72% of the total proteins uniquely, and another 14% identified as either one of two proteins in which one of them is the correct match (See Materials and Methods). Moreover, the percentage of uniquely identified proteins is close to 99% with the determination of the KCM order of appearance along all proteins in the human proteome database (
The theoretical analysis shown in
To illustrate this method, u
+δui where
u
is its average velocity, and the random term δui accounts for thermal fluctuations in its motion. Since the SDS-coated biopolymers have a Kuhn length of approximately 7 nm, they can be assumed to be partially-stretched (unfolded) wormlike polymers during translocation through a sub ˜5 nm pore. Moreover, when threaded through a 3 nm pore, the roughly 2 nm wide SDS-coated proteins are confined laterally in a small volume in the nanopore proximity where the electromagnetic field remains nearly constant. Hence, in this study the protein translocations can be treated as one dimensional. The excitation profile calculated from the FDTD simulations was approximated by a one-dimensional Gaussian function as shown in
The labeling efficiency was modeled by randomly positioning fluorophores at the K, C and M amino-acid, such that in each protein only a fraction Γi of them (j represents K, C or M) was actually labelled (indicated by purple arrows in
In order to estimate the translocation velocity of SDS-denatured polypeptides electrical translocation measurements using SDS-denatured albumin (585 amino-acids) proteins were performed using ˜4 nm-wide solid-state nanopores, as described in the Materials and Methods section. Representative translocation events measured at a bias voltage of V=300 mV, in which a single blockage current level is observed, are shown in
Initial focus is placed on simulated optical signals calculated for two proteins having nearly the same length: the EGF precursor, and its receptor EGFR (1208 and 1210 amino acids, respectively). Under near-ideal experimental conditions (100% labelling, 0.5 nm resolution, and velocity of 0.035 cm/s) their tri-color fingerprints were readily distinguishable from each other, despite similar K, C and M compositions, and followed the actual K,C,M amino acid order in each protein (
The similarity among repeated translocations of the same proteins, which were subject to different labeling and random velocity fluctuations, was tested by evaluating the Pearson correlation coefficients between all pairs of 50 translocation repeats of the same protein. The results, showed in all cases high values (0.85-0.97) when considering autocorrelation (
Next the simulations were vastly scaled-up to include thousands of different proteins, each one repeated hundreds of times under different labeling efficiencies, translocation velocities and spatial resolutions. The accurate classification of noisy, low-resolution, time-dependent signals is often encountered in areas such as image and speech recognition and is effectively handled by Convolutional Neural Networks (CNN) approaches. It was postulated that, provided sufficient training, the CNN approach would be able to identify most proteins based on the tri-color fingerprints. To check this hypothesis, deep-learning whole-proteome analyses were set up. First, the CNN network was trained using a large dataset containing at least 80 individual nanopore passages of each protein in the Swiss-Prot database. Then the CNN was presented with new protein translocation events and queried as to the protein identity. This procedure was repeated at least 5 times for whole-proteome analysis allowing the establishment of the mean ID accuracy and its standard deviation, for 16 different experimental conditions (
In addition to the mean accuracies, the CNN algorithm produces a “confusion matrix”, which presents the number of times each and every protein x was identified as protein y (where x and y could be any of the proteins in the set). This information was used to calculate the probability density function (pdf) of correct ID for each and every classification set, namely the likelihood that a given protein is correctly identified with probability p. The pdf of correct ID calculated for the case of 30 nm resolution and 80% labelling efficiency (
The results for misclassified proteins were also analyzed. Specifically, it was of interest to know whether a misclassified protein is likely to be a specific protein, or randomly misclassified. To investigate the degree of randomness in misclassification, first were selected proteins that had at least 10% misclassified events. Then, was determined the fraction of identical mismatch ri=maxi nij/Ni for each protein i, where nij is the number of translocation events misidentified to protein j and Ni the total number of misclassified translocation events. With this a high ri was characteristic of a deterministic misidentification, i.e. protein i is consistently mistaken with another specific protein j, and conversely a low ri was indicative of a rather random misidentification. As shown in the right panel of
The performance of this approach for clinically relevant applications, including whole human plasma proteome and a cytokine panel, was evaluated. In both studies, the CNN training was kept at the whole human proteome, rather than restricting it to the clinical subset. Next, nanopore translocation traces of the plasma/cytokines proteins were presented and the classification accuracy was evaluated as before. Interestingly for the high-spatial resolutions (20 nm and 30 nm) the correct ID of the 3852 plasma proteins was only slightly larger than the whole proteome accuracy at the different labelling efficiencies, reflecting the fact that there is a small set of proteins that are hard to be classified in both cases (
The cytokine panel (CytokineMAP) contains 16 proteins involved in inflammation, immune response and repair. The CNN classification was evaluated under 16 different experimental conditions (
Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.
This application claims the benefit of priority of U.S. Provisional Patent Application Nos. 62/750,357, filed Oct. 25, 2018, and 62/753,140, filed Oct. 31, 2018, the contents of which are all incorporated herein by reference in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/IL2019/051149 | 10/24/2019 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62750357 | Oct 2018 | US | |
| 62753140 | Oct 2018 | US |
