DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 09/09/2025 has been entered.
Applicant's response, filed on 09/09/2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of claims
Canceled:
15-287
Amended:
1, 12
Pending:
1-14, 288-292
Withdrawn:
none
Examined:
1-14, 288-292
Independent:
1
Allowable:
none
Drawings
The drawings filed 07/20/2023 are accepted.
Priority
As detailed on the 11/29/2019 filing receipt, this application claims priority to as early as 11/15/2018.
Information Disclosure Statement
The Information Disclosure Statement filed on 09/09/2025 is in compliance with the provisions of 37 CFR 1.97 and have been considered in full. A signed copy of the list of references cited from each IDS is included with this Office Action.
Withdrawn Rejections/Objections
The rejection of claims 1-14 and 288-292 under 35 U.S.C. §112(a), in the Office action mailed 04/09/2025 is withdrawn in view of the amendments and Remarks filed 09/09/2025.
The rejection of claims 1-14 and 288-292 under 35 U.S.C. §102(a)(2) over Callewaert, in the Office action mailed 04/09/2025 is withdrawn in view of the amendments filed 09/09/2025. However, a new rejection is applied as discussed below.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 1-14 and 288-292 is/are rejected under 35 U.S.C. 103 as being unpatentable over Callewaert (U.S. Patent No 2020/0231956 A1, published Jul. 23, 2020, Foreign Application Priority Data Sep. 28, 2017; cited on the 03/20/2023 “Notice of References Cited” form 892) in view of Swaminathan (“A theoretical justification for single molecule peptide sequencing.” PLoS computational biology vol. 11,2 e1004080. 25 Feb. 2015; cited on the attached “Notice of References Cited” form 892). Any newly recited portions herein are necessitated by claim amendment.
Regarding claim 1, Callewaert teaches the recited obtaining the data comprises obtaining a plurality of signals including a first plurality of signals, each of the first plurality of signals corresponding to a first type of molecule and being emitted when the first type of molecule is bound to a terminus of the polypeptide and respective ones of the first plurality of signals at least with "FIG. 15. Schematic representation of the Edman degradation mechanism. Edman degradation entails the coupling of phenyl isothiocyanate (PITC) onto the free N-terminus of a protein/peptide (alkaline conditions), followed by the release of the N-terminal amino acid as a phenylthiohydantoin (PTH) derivative (acidic conditions). The released PTH-amino acid is then identified with chromatography" (Para. [0035]). The recited "first type of molecule" corresponds to "phenyl isothiocyanate (PITC)" of Callewaert. The recited "signals" corresponds to "released PTH-amino acid" that is identified by chromatography of Callewaert. Callewaert also teaches "The method of the application can additionally include a step of determining the cleavage of said N-terminal amino acid by measuring an optical, electrical or plasmonical signal of the surface-immobilized polypeptide, wherein a difference in optical, electrical or plasmonical signal is indicative for cleavage of said N-terminal amino acid. The above methods are also provided wherein said surface-immobilized polypeptide is additionally contacted with one or more N-terminal amino acid binding proteins, wherein the kinetics of the binding events of said one or more binding proteins to said N-terminal amino acid identify or is further informative for said N-terminal amino acid. The above methods can also include a first step of polypeptide denaturation or are provided in which polypeptide denaturing conditions are present during one or more of the steps of said methods, wherein said catalytically active aminopeptidase is a thermophilic and/or solvent resistant aminopeptidase and/or wherein said cleavage-inducing agent is isothiocyanate or isothiocyanate analogues. Above methods are also provided wherein N-terminal amino acid is derivatized. The aminopeptidase from above methods can be any of the aminopeptidase disclosed herein." (Para. [0018])
Callewaert teaches the recited discrete binding events of a plurality of binding events that occur between the first type of molecule and the terminus of the polypeptide occurring prior to a cleavage event of the degradation process at least with "FIG. 15. Schematic representation of the Edman degradation mechanism. Edman degradation entails the coupling of phenyl isothiocyanate (PITC) onto the free N-terminus of a protein/peptide (alkaline conditions), followed by the release of the N-terminal amino acid as a phenylthiohydantoin (PTH) derivative (acidic conditions). The released PTH-amino acid is then identified with chromatography" (Para. [0035]). The recited "first type of molecule" corresponds to "phenyl isothiocyanate (PITC)" of Callewaert. It is noted that cleavage is interpreted to be equivalent to the degradation. Callewaert also teaches "...the identity of the N-terminal amino acid derivative is determined by performing, for example, 20 rounds of antibody binding with antibodies specific for each PITC-derivatized N-terminal amino acid, detection, and stripping. The N-terminal amino acid is removed by raising the temperature or lowering pH, and the cycle is repeated to sequence 12-20 amino acids from each peptide on the slide." (para. [0003]).
Callewaert teaches the recited the cleavage event performed by a second type of molecule different than the first type of molecule at least with "Said N-terminal amino acid can be a derivatized N-terminal amino acid and if so said aminopeptidase binds and cleaves said derivatized N-terminal amino acid. Said N-terminal amino acid can be an N-terminal amino acid derivatized with isothiocyanate or isothiocyanate analogues" (Para. [0006]). The recited "second type of molecule" corresponds to "aminopeptidase" of Callewaert.
Callewaert teaches the recited based on the determined portions of data, determining a value for at least one characteristic of the respective determined portions of data; identifying a portion of a sequence of amino acids of the polypeptide based at least in part on the determined values for the at least one characteristic at least with "...wherein said cleavage-inducing agent is isothiocyanate or isothiocyanate analogues, wherein said residence time is the length of time until said N-terminal amino acid is removed, wherein said N-terminal amino acid is identified by comparing said length of time to a set of reference values for different amino acids." (Para. [0016]) and “…wherein said cleavage-inducing agent binds and cleaves the N-terminal amino acid from said polypeptide; measuring the residence time of said cleavage-inducing agent on said N-terminal amino acid; and comparing said measured residence time to a set of reference residence time values characteristic for said cleavage-inducing agent and a set of N-terminal amino acids to identify or categorize said N-terminal amino acid.” (Para. [0009]). The recited "value" corresponds to "residence time" and "length of time" of Callewaert. Callewaert also teaches (Paragraph [0018]) the method of the application can additionally include a step of determining the cleavage of said N-terminal amino acid by measuring an optical, electrical or plasmonical signal of the surface-immobilized polypeptide, wherein a difference in optical, electrical or plasmonical signal is indicative for cleavage of said N-terminal amino acid (Paragraph [0018]). The identity of the N-terminal amino acid corresponds to the signal value and the characteristic of the signal allows one to determine its identity.
Callewaert further teaches that the N-terminal amino acid of single molecules of peptides are identified (or categorized) using the catalytic properties of an aminopeptidase and the kinetics of the enzymatic reaction (Paragraph [0005]). The method is based on the correlation between the turnover number (kcat) of engineered aminopeptidases and the N-terminal amino acid which it cleaves (Paragraph [0005]). Therefore, by measuring the time the engineered aminopeptidase resides upon addition on the peptide substrate before the N-terminal amino acid is cleaved off, N-terminal amino acid is identified (Paragraph [0005]). This corresponds to the claim limitation of obtaining data during a degradation process of a polypeptide and analyzing the plurality of signals to determine portions of the data corresponding to respective amino acids that are exposed at a terminus of the polypeptide during the degradation process.
Callewaert teaches identifying a portion of a sequence of amino acids of the polypeptide based at least in part on the determined values for the at least one characteristic; with "...the application provides a method to sequence proteins comprising the following step cycle: the N-terminal derivatization of peptides immobilized through a moiety of the peptide C-terminal to the scissile bond, measuring the time it takes for a cleavage-inducing agent to cleave off the N-terminal amino acid, leading to release of the N-terminal amino acid from the immobilisation surface, setting the system ready for the next cycle (FIG. 1)." (Para. [0005]) and “…wherein said cleavage-inducing agent binds and cleaves the N-terminal amino acid from said polypeptide; measuring the residence time of said cleavage-inducing agent on said N-terminal amino acid; and comparing said measured residence time to a set of reference residence time values characteristic for said cleavage-inducing agent and a set of N-terminal amino acids to identify or categorize said N-terminal amino acid.” (Para. [0009]).
Callewaert teaches the application provides a method to sequence proteins comprising the following step cycle: the N-terminal derivatization of peptides immobilized through a moiety of the peptide C-terminal to the scissile bond, measuring the time it takes for a cleavage-inducing agent to cleave off the N-terminal amino acid, leading to release of the N-terminal amino acid from the immobilization surface, setting the system ready for the next cycle (FIG. 1) (Paragraph [0005]). Callewaert also teaches “The invention discloses means and methods for single molecule protein sequencing and/or amino acid identification using cleavage inducing agent.” (Abstract) This corresponds to the claim limitation of identifying the sequence of amino acids of the polypeptide and outputting the identified sequence of amino acids.
Callewaert does not explicitly teach identifying the sequence of amino acids of the polypeptide based on the identified portion of the sequence of amino acids, wherein a total number of amino acids in the identified sequence of amino acids is greater than a total number of amino acids in the portion of the sequence of amino acids; and the total number of amino acids in the identified sequence of amino acids is greater than a total number of the portions of data corresponding to the amino acids that are exposed at the terminus of the polypeptide during the degradation process of claim 1. However, this limitation is taught by Swaminathan.
Swaminathan teaches identifying the sequence of amino acids of the polypeptide based on the identified portion of the sequence of amino acids, wherein a total number of amino acids in the identified sequence of amino acids is greater than a total number of amino acids in the portion of the sequence of amino acids; and the total number of amino acids in the identified sequence of amino acids is greater than a total number of the portions of data corresponding to the amino acids that are exposed at the terminus of the polypeptide during the degradation process with “Mapping the partial sequence back to a reference proteome of potential proteins, such as might be derived from a genome sequence, would determine if the fluorosequence uniquely identifies a peptide, and ultimately, its parent protein.” (page 4, para. 3) and “Matching this partial sequence to a reference protein database identifies the peptide.” (Fig. 1 caption, page 3).
It would have been prima facia obvious to combine the teachings of Callewaert and Swaminathan to arrive at the claimed invention. Swaminathan’s method is capable of generating partial peptide sequences in a highly parallel fashion, scalable to entire proteomes (page 3, Paragraph 1). A person of ordinary skill in the art would have been motivated to modify the method of Callewaert to identify portions of amino acid sequences as taught by Swaminathan for the benefit of utilizing the partial sequence to uniquely identify the peptide from the entire proteomes. Furthermore, there would have been a reasonable expectation of success, since both Callewaert and Swaminathan teach methods that pertain to single molecule peptide sequencing.
With respect to claim 2, Callewaert teaches that the N-terminal amino acid of single molecules of peptides are identified (or categorized) using the catalytic properties of an aminopeptidase and the kinetics of the enzymatic reaction (Paragraph [0005]). The method is based on the correlation between the turnover number (kcat) of engineered aminopeptidases and the N-terminal amino acid which it cleaves (Paragraph [0005]). Therefore, by measuring the time the engineered aminopeptidase resides upon addition on the peptide substrate before the N-terminal amino acid is cleaved off, N-terminal amino acid is identified (Paragraph [0005]). This corresponds to the claim limitation of wherein the data is indicative of amino acid identity at the terminus of the polypeptide during the degradation process.
With respect to claim 3, Callewaert teaches that the N-terminal amino acid of single molecules of peptides are identified (or categorized) using the catalytic properties of an aminopeptidase and the kinetics of the enzymatic reaction (Paragraph [0005]). An aminopeptidase taught by Callewaert is equivalent to amino acid recognition molecule. Therefore, this corresponds to the claim limitation of the data is indicative of signals produced by one or more amino acid recognition molecules binding to different types of terminal amino acids at the terminus during the degradation process.
With respect to claim 4, Callewaert teaches “Surface” as used herein is a synonym for carrier or layer (Paragraph [0077]). The surface or layer of current application is suitable to use in the detection of molecular labels, electrochemical signals, electromagnetic signals, plasmon related events (Paragraph [0077]). Said molecular label can be an optical (comprising but not limited to luminescent and fluorescent labels) or electrical (comprising but not limited to potentiometric, voltametric, coulometric labels) label (Paragraph [0077]).
Callewaert also teaches that in order to detect and measure the “on-time” values or the residence time of the aminopeptidase of the application on the N-terminal amino acid of an immobilized polypeptide or until the N-terminal amino acid of an immobilized polypeptide is cleaved off (see above), said aminopeptidase needs to be detected (Paragraph [0080]). The aminopeptidase can interact cleavage-productively or cleavage non-productively with the substrate within the measured residence time until the N-terminal amino acid is cleaved off (Paragraph [0080]). Of both interaction types, their length, sum of length and average lengths can be part of the measured residence time relevant to the present invention, as these parameters all are part of the measurement that provides information on how long it takes until the aminopeptidase cleaves off the N-terminal amino acid (Paragraph [0080]). The nature of detection is not vital to the invention, as long as the enzyme “on-time” or the residence time of the aminopeptidase can be detected (Paragraph [0080]). In certain embodiments of the application, the “on-time” of the aminopeptidase is detected optically, electrically or plasmonicall(Paragraph [0080]). One way of detecting the aminopeptidases of the application is by fusing it to a molecular label and subsequent detection of the molecular label (Paragraph [0080]). Similar to the above, aminopeptidases can be labelled optically, electrically or plasmonically (Paragraph [0080]). Therefore, Callewaert teaches that the molecular label could be luminescent or fluorescent labels that allows for the “on-time” of the aminopeptidase to be detected optically. This corresponds to the claim limitation of wherein the signals comprise of a luminescent signal generated during the degradation process.
With respect to claim 5, Callewaert teaches to detect the “on-time” values or residence time, two labelling options can be selected (Paragraph [0079]). First, the polypeptides to be sequenced can be labelled for example through their N-terminal amino acids. Alternatively or additionally, internal amino acids can be labelled for example as shown in FIG. 14 (Paragraph [0079]). The labelling of polypeptides can be done using fluorescent probes, such as but not limited to fluorescamine, o-phthalaldehyde, dansyl chloride and coumarinyl isothiocyanate (CITC) (Paragraph [0079]). In particular embodiments, the N-terminal amino acid of the immobilized polypeptide of the application is CITC-derivatized or alternatively phrased labeled with CITC (Paragraph [0079]). The polypeptides can also be electrically labeled (Paragraph [0079]). Electroanalytical methods are a class of techniques by which the presence of an analyte, peptide, enzyme, . . . can be determined by measuring the potential (volts) and/or current (amperes) of the electrical label on the analyte, peptide, enzyme . . . These methods can be broken down into several categories depending on the label (Paragraph [0079]). The three main categories are potentiometry (the difference in electrode potentials is measured), coulometry (the current is measured over time), and voltammetry (the current is measured while the potential is actively altered) (Paragraph [0079]). There are two basic categories of coulometric techniques (Paragraph [0079]). Potentiostatic coulometry involves holding the electric potential constant during the reaction using a potentiostat (Paragraph [0079]). The other, called coulometric titration or amperostatic coulometry, keeps the current (measured in amperes) constant using an amperostat (Paragraph [0079]). A non-limiting example of an electrical label is sulfophenyl isothiocyanate (SPITC) (Paragraph [0079]). SPITC is a negatively charged variant of the phenyl isothiocyanate (PITC) probe that is used in MS de novo peptide sequencing for neutralizing N-terminal fragment ions (Samyn et al. 2004 J Am Soc Mass Spectrom 15:1838-1852) (Paragraph [0079]). In particular embodiments, electrically labeled can be potentiometrically, amperometrically or voltametrically labeled (Paragraph [0079]). This corresponds to the claim limitation of wherein the signals comprise an electrical signal generated during the degradation process.
With respect to claim 6, Callewaert teaches that the present invention relates to the field of biochemistry, more particularly to proteomics, more particularly to protein sequencing, even more particularly to single molecule peptide sequencing (Abstract). The invention discloses means and methods for single molecule protein sequencing and/or amino acid identification using cleavage inducing agent (Abstract). Said cleavage inducing agents which are not specific for one particular amino acid, cleave polypeptides step by step from the N-terminus onwards and provide information on the identity of the cleaved amino acids based on the kinetics of said reaction (Abstract). It is noted that the process of cleaving polypeptides step by step taught by Callewaert is equivalent to series of cleavage events and successive cleavage events. The process of identifying the cleaved amino acids based on the kinetics of said reaction is equivalent to the claim limitation of detecting cleavage events including the cleavage event and determining the portions of the data between successive cleavage events.
With respect to claim 7, Callewaert teaches in claim 17 a method of obtaining sequence information of a polypeptide immobilized on a surface via its C-terminus, the method comprising:
a. contacting the surface-immobilized polypeptide with a cleavage-inducing agent, wherein the agent binds and cleaves the N-terminal amino acid from the polypeptide;
b. measuring the residence time of the cleavage-inducing agent on the N-terminal amino acid of the surface-immobilized polypeptide;
c. allowing the cleavage-inducing agent to cleave off said the N-terminal amino acid; and
d. wherein comparing the measured residence time to a set of reference residence time values characteristic for the cleavage-inducing agent and a set of N-terminal amino acids allows determining the identity of the N-terminal amino acid;
e. repeating the measuring and cleaving one or more times.
Each amino acid of a sequence is considered to be equivalent to individual portions. Repetition of the process taught by Callewaert allows for the sequential measuring, cleaving, and identifying of amino acids resulting in a series of amino acids being identified. Therefore, this corresponds to the claim limitation of determining a type of amino acid for each of the portions.
With respect to claim 8, Callewaert teaches after immobilizing the peptide substrates and determining the single molecule substrate locations in the field-of-view, the fluorescently labeled aminopeptidase is added and the consecutive enzyme residence times on the substrate locations is measured (Paragraph [0151]). Considering that both the enzyme-substrate binding kinetics (KM) and the substrate cleavage kinetics (kcat) depend on the identity of the N-terminal amino acid, by measuring the number of enzyme-substrate ‘on-off’ events and the overall time until substrate cleavage, the identity of the N-terminal amino acid is derived or categorized (FIG. 14) (Paragraph [0151]). Verification of substrate cleavage is derived from a measurable change in frequency of enzyme-substrate ‘on-off’ events before and after cleavage (FIG. 14 below) (Paragraph [0151]). When using a thermophilic aminopeptidase (e.g. T. aquaticus aminopeptidase T) at a far-below optimal temperature, cleave kinetics are significantly reduced leading to an increase in the number of enzyme-substrate ‘on-off’ events (Paragraph [0151]). Callewaert also teaches in Figure 14 the pulse pattern that is observed to be the number of enzyme-substrate ‘on-off’ events and the overall time until substrate cleavage that corresponds to N-terminal amino acid identity. Therefore, this corresponds to the claim limitation of wherein each of the individual portions comprises a pulse pattern, and analyzing the data further comprises determining a type of amino acid for one or more of the portions based on its respective pulse pattern.
With respect to claim 9, Callewaert teaches in Figure 14 the pulse pattern that is observed to be the number of enzyme-substrate ‘on-off’ events and the overall time until substrate cleavage that corresponds to N-terminal amino acid identity. It is interpreted that the event when a pulse is detected corresponds to the time when threshold value is reached or is above threshold. From the data depicted in Figure 4, the amount of time within the portion could be compared with the duration of the portion. Therefore, this corresponds to the claim limitation of determining the type of amino acid further comprises identifying an amount of time within a portion when the data is above a threshold value and comparing the amount of time to a duration of time for the portion.
With respect to claim 10, Callewaert teaches that both the enzyme-substrate binding kinetics (KM) and the substrate cleavage kinetics (kcat) depend on the identity of the N-terminal amino acid, by measuring the number of enzyme-substrate ‘on-off’ events and the overall time until substrate cleavage, the identity of the N-terminal amino acid is derived or categorized (FIG. 14) (Paragraph [0151]). Callewaert also teaches in Figure 14 the pulse pattern that is observed to be the number of enzyme-substrate ‘on-off’ events and the overall time until substrate cleavage that corresponds to N-terminal amino acid identity. Therefore, this corresponds to the claim limitation of wherein the at least one characteristic comprises pulse duration and determining the type of amino acid further comprises identifying at least one pulse duration for each of the one or more portions.
With respect to claim 11, Callewaert teaches that both the enzyme-substrate binding kinetics (KM) and the substrate cleavage kinetics (kcat) depend on the identity of the N-terminal amino acid, by measuring the number of enzyme-substrate ‘on-off’ events and the overall time until substrate cleavage, the identity of the N-terminal amino acid is derived or categorized (FIG. 14) (Paragraph [0151]). Callewaert also teaches in Figure 14 the pulse pattern that is observed to be the number of enzyme-substrate ‘on-off’ events and the overall time until substrate cleavage that corresponds to N-terminal amino acid identity. The off events are interpreted to be equivalent to the interpulse. Therefore, this corresponds to the claim limitation of wherein the at least one characteristic comprises interpulse duration and determining the type of amino acid further comprises identifying at least one interpulse duration for each of the one or more portions.
With respect to claim 12, Callewaert teaches in claim 17 a method of obtaining sequence information of a polypeptide immobilized on a surface via its C-terminus, the method comprising:
a. contacting the surface-immobilized polypeptide with a cleavage-inducing agent, wherein the agent binds and cleaves the N-terminal amino acid from the polypeptide;
b. measuring the residence time of the cleavage-inducing agent on the N-terminal amino acid of the surface-immobilized polypeptide;
c. allowing the cleavage-inducing agent to cleave off said the N-terminal amino acid; and
d. wherein comparing the measured residence time to a set of reference residence time values characteristic for the cleavage-inducing agent and a set of N-terminal amino acids allows determining the identity of the N-terminal amino acid;
e. repeating the measuring and cleaving one or more times.
Each amino acid of a sequence is considered to be equivalent to individual portions. Repetition of the process taught by Callewaert allows for the sequential measuring, cleaving, and identifying of amino acids resulting in a series of amino acids being identified. Therefore, this corresponds to the claim limitation of wherein the sequence of amino acids includes a series of amino acids corresponding to the portions.
Regarding claim 288, Callewaert teaches the recited wherein the first type of molecule is an amino acid recognition molecule, and the second type of molecule is an aminopeptidase at least with "FIG. 15. Schematic representation of the Edman degradation mechanism. Edman degradation entails the coupling of phenyl isothiocyanate (PITC) onto the free N-terminus of a protein/peptide (alkaline conditions), followed by the release of the N-terminal amino acid as a phenylthiohydantoin (PTH) derivative (acidic conditions). The released PTH-amino acid is then identified with chromatography" (Para. [0035]) and with "Said N-terminal amino acid can be a derivatized N-terminal amino acid and if so said aminopeptidase binds and cleaves said derivatized N-terminal amino acid. Said N-terminal amino acid can be an N-terminal amino acid derivatized with isothiocyanate or isothiocyanate analogues" (Para. [0006]). The recited "first type of molecule" corresponds to "phenyl isothiocyanate (PITC)" of Callewaert. The recited "second type of molecule" corresponds to "aminopeptidase" of Callewaert.
Regarding claim 289, Callewaert teaches the recited plurality of signals further comprise a second plurality of signals different from the first plurality of signals; the first plurality of signals correspond to binding events between a first type of amino acid recognition molecule and a first type of amino acid at the terminus of the polypeptide at least with "FIG. 15. Schematic representation of the Edman degradation mechanism. Edman degradation entails the coupling of phenyl isothiocyanate (PITC) onto the free N-terminus of a protein/peptide (alkaline conditions), followed by the release of the N-terminal amino acid as a phenylthiohydantoin (PTH) derivative (acidic conditions). The released PTH-amino acid is then identified with chromatography" (Para. [0035]). The recited "first type of molecule" corresponds to "phenyl isothiocyanate (PITC)" of Callewaert. The recited "first type of amino acid" corresponds to "free N-terminus of a protein/peptide" of Callewaert.
Callewaert teaches the recited the second plurality of signals correspond to binding events between a second type of amino acid recognition molecule and a second type of amino acid at the terminus of the polypeptide at least with "Said N-terminal amino acid can be a derivatized N-terminal amino acid and if so said aminopeptidase binds and cleaves said derivatized N-terminal amino acid. Said N-terminal amino acid can be an N-terminal amino acid derivatized with isothiocyanate or isothiocyanate analogues" (Para. [0006]). The recited "second type of molecule" corresponds to "aminopeptidase" of Callewaert. The recited "second type of amino acid" corresponds to "derivatized N-terminal amino acid" of Callewaert.
Regarding claim 290, Callewaert teaches the recited wherein the plurality of signals corresponds to discrete binding events between one or more amino acid recognition molecules and amino acids that are exposed at the terminus of the polypeptide during the degradation process at least with "Therefore, by measuring the time the engineered aminopeptidase resides upon addition on the peptide substrate before the N-terminal amino acid is cleaved off, N-terminal amino acid is identified. Said aminopeptidase can also be replaced by a chemical cleavage-inducing agent. Similar to what is observed using aminopeptidases, the residence time of chemical cleavage-inducing agents is a read-out for the identity of the N-terminal amino acid to which it binds." (Para. [0005]).
Regarding claim 291, Callewaert teaches the recited wherein the degradation process comprises terminal amino acid cleavage performed by one or more aminopeptidases during the degradation process at least with "Said N-terminal amino acid can be a derivatized N-terminal amino acid and if so said aminopeptidase binds and cleaves said derivatized N-terminal amino acid. Said N-terminal amino acid can be an N-terminal amino acid derivatized with isothiocyanate or isothiocyanate analogues" (Para. [0006]).
Regarding claim 292, Callewaert teaches the recited wherein the first type of molecule comprises an amino acid recognition molecule comprising a fluorophore at least with "In yet another embodiment, the N-terminal amino acid is derivatized (e.g. with biotin, for example using a biotinylated isothiocyanate) such that a binding agent (e.g. an avidin such as streptavidin or neutravidin) that carries a spectroscopically distinguishable label (e.g. a fluorophore) can bind the derivatized N-terminal amino acid" (Para. [0118]).
Regarding claims 13 and 14, Callewaert does not explicitly teach a system comprising: at least one hardware processor; and at least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by the at least one hardware processor, cause the at least one hardware processor to perform the method of claim 1 in claim 13 and at least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by at least one hardware processor, cause the at least one hardware processor to perform the method of claim 1 in claim 14. However, Callewaert teaches making use of computer programs that are available in the art for sequence alignment (Paragraph [0073]). Callewaert teaches Determining the percentage of sequence homology can be done manually, or by making use of computer programs that are available in the art. Examples of useful algorithms are PILEUP (Higgins & Sharp, CABIOS 5:151 (1989), BLAST and BLAST 2.0 (Altschul et al. J. Mol. Biol. 215: 403 (1990) (Paragraph [0073]). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) (Paragraph [0073]). It is well known that computer programs and software have to be executed on a computer. It is also well known that a generic computer system includes hardware processor and a non-transitory computer-readable storage medium. Therefore, Callewaert’s teachings meet the claim limitations of claims 13 and 14. It would have been obvious to one of ordinary skill in the art at the time of the invention to use the generic computer system and hardware of claims 13 and 14 to automate the data analysis of amino acid sequences to save time on sequence comparison.
Response to 35 USC §102 (09/09/2025, Pages 8-9 of remarks)
Applicant argues that the cited paragraphs of Callewaert in the office action fail to describe the language of amended independent claim 1. For example, amended independent claim 1 recites "obtaining data during a degradation process of the polypeptide ... [by] obtaining a plurality of signals", "analyzing the plurality of signals to determine portions of the data corresponding to amino acids that are exposed at the terminus of the polypeptide during the degradation process", and "identifying a sequence of amino acids of the polypeptide based on the identified portion of the sequence of amino acids, wherein a total number of amino acids in the identified sequence of amino acids is greater than a total number of the portions of data corresponding to the amino acids that are exposed at the terminus of the polypeptide during the degradation process." The cited paragraphs of Callewaert do not describe this process. In particular, the cited paragraphs do not describe identifying a sequence of amino acids having a total number of amino acids that is greater than a total number of portions of data determined from the collected signals.
In response, Applicant's arguments are based on amended claims and are persuasive. Therefore, the rejection of claims 1-14 and 288-292 under 35 U.S.C. §102(a)(2) over Callewaert, in the Office action mailed 04/09/2025 is withdrawn in view of the amendments filed 09/09/2025. However, a new rejection is applied as discussed below.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Judicial exceptions (JEs) to 101 patentability
Claims 1-14 and 288-292 are rejected under 35 USC 101 because the claimed inventions are not directed to patent eligible subject matter. After consideration of relevant factors with respect to each claim as a whole, each claim is directed to one or more judicially-recognized exceptions to patentability (JEs), i.e. an abstract idea, a natural phenomenon, a law of nature and/or a product of nature, as identified below. Below, it is not clear that any element or combination of elements in addition to the JE(s), i.e. and "additional elements," either integrate the identified JE(s) into a practical application and/or is a non-conventional additional element, such that it is not clear that any claim is directed to significantly more than the identified JE(s).
MPEP 2106 organizes JE analysis into Steps 1, 2A (1st prong & 2nd prong) and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: www.uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Analysis of claims 1-14 and 288-292
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Independent claim 1 is directed to a 101 process, here a "method comprising: obtaining data during a degradation process of a polypeptide …," with process steps such as " analyzing … and determining…"
[Step 1: claims 1-14 and 288-292: YES]
Step 2A, 1st prong: Do the claims recite a judicially-recognized exception (JE), e.g. a law of nature, a natural phenomenon or product, or an abstract idea (MPEP 2106.04.II.A.1 & .04(a))?
The MPEP at 2106.I, 2nd para. explains that JEs have been court-recognized as: abstract ideas, laws of nature and natural phenomena (including natural products).
MPEP § 2106.04(a)(2) further explains that abstract ideas may be grouped as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations);
• certain methods of organizing human activity (fundamental economic practices or
principles, managing personal behavior or relationships or interactions between people);
and/or
• mental processes (procedures for observing, evaluating, analyzing/ judging and
organizing information).
Regarding the instant claims and with respect to Step 2A, 1st prong, at least preliminarily these claims recite JEs in the form of abstract ideas (claims 1, 6-11 and 13-14) as follows.
Mental processes recited include:
Claims 1, 13, 14 recite: “…analyzing plurality of signals to determine portions to determine portions of the data corresponding to respective amino acids that are sequentially exposed at the terminus of the polypeptide during the degradation process…; …determining a value for at least one characteristic of the first plurality of signals produced by the discrete binding events between the first molecule and the terminus of the polypeptide …; determining the probabilistic assessment and identifying a portion of a sequence of amino acids of the polypeptide based on at least in part on the analyzing determined values for the at least one characteristic; identifying the sequence of amino acids of the polypeptide based on the identified portion of the sequence of amino acids, wherein a total number of amino acids in the identified sequence of amino acids is greater than a total number of amino acids in the portion of the sequence of amino acids; and the total number of amino acids in the identified sequence of amino acids is greater than a total number of the portions of data corresponding to the amino acids that are exposed at the terminus of the polypeptide during the degradation process." The claims recite process of analyzing, determining, identifying and comparing which are data analytics steps and are acts of analyzing, evaluating, organizing and judging information that could be practically performed in the human mind and/or with pen and paper. Acts of evaluating and analyzing data could be practically performed in the human mind and/or with pen and paper because they merely require making observations, evaluations, judgments, and opinions (See MPEP 2106.04(a)(2) subsection III).
Claim 6 recites: “…wherein analyzing the data further comprises detecting cleavage events... and determining the portions of the data between successive cleavage events.” The process of analyzing and determining are data analytics steps that could be performed with the human mind or with pen and paper.
Claim 7 recites: “…wherein analyzing the data further comprises determining a type of amino acid for each of the portions.” The process of analyzing is a data analytics step that could be performed with the human mind or with pen and paper.
Claim 8 recites: “…wherein each of the portions comprises a pulse pattern, and analyzing the data further comprises determining a type of amino acid for one or more of the portions based on its respective pulse pattern.” The process of analyzing and determining are data analytics steps that could be performed with the human mind or with pen and paper.
Claim 9 recites: “…wherein determining the type of amino acid further comprises identifying an amount of time within a portion when the data is above a threshold value and comparing the amount of time to a duration of time for the portion.” The process of determining and identifying are data analytics steps that could be performed with the human mind or with pen and paper.
Claim 10 recites: “…wherein the at least one characteristic comprises pulse duration and determining the type of amino acid further comprises identifying at least one pulse duration for each of the one or more portions.” The process of determining and identifying are data analytics steps that could be performed with the human mind or with pen and paper.
Claim 11 recites: “…wherein the at least one characteristic comprises interpulse duration and determining the type of amino acid further comprises identifying at least one interpulse duration for each of the one or more portions.” The process of determining is a data analytics step could be performed with the human mind or with pen and paper.
At this step of the analysis, elements of claims 1, 6-11 and 13-14 are interpreted as directed to the abstract idea of mental processes including the particularly recited JE steps/elements of " analyzing...," "…determining...," and "identifying...," each of which, including all recitation within each listed element, in at least some embodiments within a BRI, involves only manipulation of data. The above-identified steps/elements are interpreted as directed to the abstract ideas identified below.
BRIs of the claims are analogous to the JE of an abstract idea in the form of a mental process, including obtaining and comparing intangible data. Instant examples of mental process that cause the claim(s) to be directed to the above-identified JE(s) are identified above for claims 1, 6-11 and 13-14. In a BRI, it is not clear that the claim embodiments are limited so as to require complexity precluding analogy to a mental process. Case law, establishing the mental process JE and to which the instant claims are analogized, is presented in MPEP 2106.04(a)(2).III, including examples of analogous mental process JEs.
[Step 2A, 1st prong: claims 1-14 and 288-292: YES]
Step 2A, 2nd prong: Are the above-identified JEs integrated into a practical application (MPEP 2106.04.II.A.2 & .04(d))?
Generally regarding Step 2A, 2nd prong
MPEP 2106.04(d).I lists the following considerations for evaluating whether additional elements integrate a judicial exception into a practical application:
An improvement in the functioning of a computer, or an improvement to other technology or technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to affect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Additionally, the courts have also identified limitations that did not integrate a judicial exception into a practical application:
Merely reciting a phrase such as "apply it" (or an equivalent) along with the judicial exception, or merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP 2106.05(f);
Adding insignificant extra-solution activity to the judicial exception, as discussed in MPEP 2106.05(g); and
Generally linking the use of a judicial exception to a particular technological environment or field of use, as discussed in MPEP 2106.05(h).
At this point in examination, it is not clear that the identified JEs are integrated into a practical application according to any of the "considerations" exemplified in MPEP 2106.04(d).
For example, according to the first consideration at MPEP 2106.04(d)(1), it is not yet clear in the record that application of the above-identified JEs results in an improvement to the technology field notwithstanding the specification at paragraph [0064].
[Step 2A, 2nd prong: claims 1-14 and 288-292: NO]
Step 2B: Do the claims recite a non-conventional arrangement of additional elements (i.e. elements in addition to any identified JE) (MPEP 2106.05)?
All elements of claims 1, 6-11 and 13-14 are part of one or more identified JEs (as described above), except for elements identified here as conventional elements in addition to the above JEs:
The recited " … obtaining data during a degradation process of a polypeptide, wherein obtaining the data comprises obtaining a plurality of signals including a first plurality of signals, each of the first plurality of signals corresponding to a first type of molecule and being emitted when the first type of molecule is bound to a terminus of the polypeptide and respective ones of the first plurality of signals correspond to respective discrete binding events between the first type of molecule and the terminus of the polypeptide occurring prior to a cleavage event of the degradation process performed by a second molecule and outputting the identified sequence of amino acid." steps/elements (claims 1, 13 and 14); “a system comprising: at least one hardware processor; and at least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by the at least one hardware processor, cause the at least one hardware processor to perform the method of claim 1.” steps/elements (claim 13) and “At least one non-transitory computer-readable storage medium storing processor-executable instructions that, when executed by at least one hardware processor, cause the at least one hardware processor to perform the method of claim 1.” steps/elements (claim 14) are conventional elements of a laboratory and/or computing environment, conventional data gathering/input elements, and/or conventional post-processing or output elements, as exemplified by the following evidence.
The use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application or provide significantly more as identified by the courts in Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Also, data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data need