DETAILED ACTION
Applicant’s response filed 07/24/2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 07/24/2025 has been entered.
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 .
Claim Status
Claims 3-4 and 9-13 are cancelled by Applicant.
Claims 14-19 are newly added by Applicant.
Claims 1-2, 5-8 and 14-19 are currently pending and are herein under examination.
Claims 1-2, 5-8 and 14-19 are rejected.
Claims 1-2, 15 and 19 are objected.
Priority
The instant application claims domestic benefit as a 371 filing of International Application PCT/JP2016/076963 filed 09/13/2016, which claims the benefit of priority to Japanese Application No. 2015-181031 filed 09/14/2015. The claims to the benefit of priority are acknowledged. As such, the effective filing date of claims 1-2, 5-8 and 14-19 is 09/14/2015.
Claim Objections
Claims 1-2, 15 and 19 are objected to because of the following informalities:
Claim 1, line 38, recites the word “contacting” which it appears that it should be “contracting” because the specification does not use the word contacting.
Claim 2, line 5, recites the phrase “a database creator that … read”. The word “read” in the phrase should be changed to “reads”.
Claim 2, line 6, recites the word “who” which should be changed to “whose” to correct its grammar.
Claim 15, lines 2-3, recites the phrase “of precursor” which should be “of a precursor” to correct its grammar.
Claim 19, line 5, recites the phrase “positions one” which should be “positions of one” to correct its grammar.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
35 USC 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-2, 5-8 and 19 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
This rejection is newly recited and is necessitated by claim amendment.
Claim 1, lines 11-14, recites the following phrase that renders the claim indefinite: “for a respective target peptide sequence, the database including a variation referencing a corresponding full-length sequence of the precursor proteins, the variation representing a relative position within the corresponding full-length sequence of the precursor proteins”. It is unclear if each target peptide sequence represents a variation in the sequence of all full-length precursor proteins for a single endogenous peptide, or if each target peptide sequence represents a variation in the sequence of a single full-length precursor protein from the plurality of precursor proteins for a single endogenous peptide. To overcome this rejection, it is suggested to clarify what each target peptide sequence represents.
Claim 1, lines 13-14, recites the relative phrase “relative position” which renders the claim indefinite. The term “relative position” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what the position is relative to or if the phrase “relative position” further limits the claim as opposed to just saying “position”. To overcome this rejection, it is suggested to further clarify the relative phrase or to remove it.
Claim 1, lines 16-17 and line 28, recites the phrases “the endogenous peptide” which render the claim indefinite because it is unclear which endogenous peptide is being referenced. Steps (i), (ii) and (iii) recite “the endogenous peptides”, but it is unclear which specific endogenous peptide is being referenced out of the plurality of endogenous peptides. To overcome this rejection, it is suggested to clarify which endogenous peptide is being referenced.
Claim 1, step (viii), recites the phrase “the peptide sequence of the endogenous peptide contained in the peptide sample” lacks antecedent basis. Claim 1, step (vii) recites a similar phrase but is directed toward an “endogenous particle” rather than an “endogenous peptide. To overcome this rejection, it is suggested to change the phrase in step (vii) of “endogenous particle” to “endogenous peptide”.
Claim 1, lines 29-31, recites the phrase “the peptide sequence read from the endogenous peptide sequence database and the full-length sequence of the precursor protein of the endogenous peptide read from the protein sequence database” which renders the claim indefinite because it is unclear which peptide sequence and which full-length sequence is being referenced. Claim 1, steps (i) and (ii) recite “peptide sequences of endogenous peptides from an endogenous peptide sequence database” and “full-length sequences of precursor proteins of the endogenous peptides from a protein sequence database”, but it is unclear which specific ones of the plurality of peptide sequences and full-length sequences are being referenced. To overcome this rejection, it is suggested to clarify which peptide sequence and which full-length sequence are being referenced.
Furthermore, claims 5 and 7 are also rejected because they depend on claim 1, which is rejected, and because they do not resolve the issue of indefiniteness.
Claim 2, lines 9-12, recites the following phrase that renders the claim indefinite: “for a respective target peptide sequence, the database including a variation referencing a corresponding full-length sequence of the precursor proteins, the variation representing a relative position within the corresponding full-length sequence of the precursor proteins”. It is unclear if each target peptide sequence represents a variation in the sequence of all full-length precursor proteins for a single endogenous peptide, or if each target peptide sequence represents a variation in the sequence of a single full-length precursor protein from the plurality of precursor proteins for a single endogenous peptide. To overcome this rejection, it is suggested to clarify what each target peptide sequence represents.
Claim 2, line 12, recites the relative phrase “relative position” which renders the claim indefinite. The term “relative position” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what the position is relative to or if the phrase “relative position” further limits the claim as opposed to just saying “position”. To overcome this rejection, it is suggested to further clarify the relative phrase or to remove it.
Claim 2, line 14 and lines 26-27, recites the phrases “the endogenous peptide” which render the claim indefinite because it is unclear which endogenous peptide is being referenced. Lines 2-12 “the endogenous peptides”, but it is unclear which specific endogenous peptide is being referenced out of the plurality of endogenous peptides. To overcome this rejection, it is suggested to clarify which endogenous peptide is being referenced.
Claim 2, lines 27-29, recites the phrase “the peptide sequence read from the endogenous peptide sequence database and the full-length sequence of the precursor protein of the endogenous peptide read from the protein sequence database” which renders the claim indefinite because it is unclear which peptide sequence and which full-length sequence is being referenced. Lines 2-4 recite the phrase “peptide sequences of endogenous peptides from an endogenous peptide sequence database and full-length sequences of precursor proteins of the endogenous peptides from a protein sequence database”, but it is unclear which specific ones of the plurality of peptide sequences and full-length sequences are being referenced. To overcome this rejection, it is suggested to clarify which peptide sequence and which full-length sequence are being referenced.
Furthermore, claims 6 and 8 are also rejected because they depend on claim 2, which is rejected, and because they do not resolve the issue of indefiniteness.
Claim 19, lines 4-5, recites the phrase “position information indicating relative positions one or more residues of the partial sequence of the endogenous peptide” which renders the claim indefinite. It is unclear what the residue positions are relative to. For examination purposes, this phrase will be interpreted to mean “position information indicating positions of one or more residues of the partial sequence of the endogenous peptide”.
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.
Claims 1-2, 5-8 and 14-19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Any newly recited portions herein are necessitated by claim amendment.
Step 2A, Prong 1:
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomena (Step 2A, Prong 1). In the instant application claims 1, 5 and 7 recite a method, claims 2, 6 and 8 recite a system and claims 14-19 recite a system. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claim 1 recites “(i) reading peptide sequences of endogenous peptides from an endogenous peptide sequence database; (ii) reading full-length sequences of precursor proteins of the endogenous peptides from a protein sequence database; (v) creating a peak list in which peaks included in a mass spectrum obtained by (iv) are extracted; (vi) collating the peak list created by (v) with the target peptide sequence database created by (iii); (vii) determining a peptide sequence narrowed down by (vi) as a peptide sequence of an endogenous particle contained in the peptide sample; wherein configuring the target peptide sequence database generates the target peptide sequences different from the endogenous peptide based on the peptide sequence read from the endogenous peptide sequence database and the full-length sequence of the precursor protein of the endogenous peptide read from the protein sequence database, wherein configuring the target peptide sequence database generates the target peptide sequences by extending and contracting the peptide sequence of the endogenous peptide while leaving a part of the peptide sequence of the endogenous peptide at least one residue, and … generating the target peptide sequences for all endogenous peptides stored in the endogenous peptide sequence database by extending an N-terminal side and contacting a C-terminal side and extending the C-terminal side and contracting the N-terminal side and contracting both the N-terminal side and the C-terminal side and extending both the N-terminal side and the C-terminal side.”
Claim 2 recites “… that reads peptide sequences of endogenous peptides from an endogenous peptide sequence database and full-length sequences of precursor proteins of the endogenous peptides from a protein sequence database … that creates a peak list in which peaks included in a mass spectrum obtained by the mass spectrometry performer are extracted; … that collates the peak list created by the peak list creator with the target peptide sequence database created by the database creator; and … that determines a peptide sequence narrowed down by the collator as a peptide sequence of an endogenous peptide contained in the peptide sample, and wherein … generates the target peptide sequences different from the endogenous peptide based on the peptide sequence read from the endogenous peptide sequence database and the full-length sequence of the precursor protein of the endogenous peptide read from the protein sequence database, wherein … generates the target peptide sequences by extending and contracting the peptide sequence of the endogenous peptide while leaving a part of the peptide sequence of the endogenous peptide of at least one residue, and wherein … generates the target peptide sequences for all endogenous peptides stored in the endogenous peptide sequence database by extending an N-terminal side and contracting a C-terminal side and extending the C-terminal side and contracting the N-terminal side and contracting both the N-terminal side and the C-terminal side and extending both the N-terminal side and C-terminal side.”
Claim 5 recites “wherein the peptide sequences of the endogenous peptides are extended and contracted while referring to a full-length sequence of an assignment protein containing the endogenous peptide.”
Claim 6 recites “. . . extends and contracts the peptide sequences of the endogenous peptides while referring to a full-length sequence of an assignment protein containing the endogenous peptide.”
Claim 7 recites “wherein the peptide sequences of the endogenous peptides are determined by scoring.”
Claim 8 recites “. . . determines the peptide sequences of the endogenous peptides by scoring.”
Claim 14 recites “configure a target peptide sequence database according to peptide sequences respectively containing one or more residues of a partial sequence of an endogenous peptide as target peptide sequences; and index differences between the peptide sequences of the target peptide sequences and a sequence of the endogenous peptide.”
Claim 15 recites “The database and peptide assignment system according to claim 14, wherein the differences are locations of the target peptide sequences on a full-length sequence of precursor protein of the endogenous peptide.”
Claim 16 recites “… perform peptide sequence assignment using a reduced search space provided by the configured target peptide sequence database.”
Claim 17 recites “… extract the target peptide sequences from the target peptide database that match a mass- to-charge ratio of a peptide sequence to be analyzed within a predetermined tolerance range as peptide sequence candidates; and using a scoring logic, score each of the peptide sequence candidates based on the matching result.”
Claim 18 recites “… rank the peptide sequence candidates based on the scores, and select a peptide sequence candidate with a highest score among the peptide sequence candidates.”
Limitations reciting a mental process.
The above cited limitations in claims 1-2, 7-8 and 14-18 are recited at such a high level of generality that they equate to a mental process because they are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), which the courts have identified as concepts that can be practically performed in the human mind. Below are the limitations in these claims that recite a mental process under their broadest reasonable interpretation (BRI):
The BRI of reading data from a database includes searching through the database and writing down data observed in the database. The BRI of creating a peak list includes a human drawing a graph using data obtained from a mass spectrum. The BRI of collating a peak list and data within a database includes combining and organizing information. The BRI of determining a peptide sequence as an endogenous peptide contained in the peptide sample includes making a determination and analyzing data. The BRI of generating a target peptide sequence includes writing down the sequence of a peptide. The BRI of generating a target peptide sequence by extending and contracting a peptide sequence includes writing down and modifying the sequence of a peptide. The BRI of determining a peptide sequence of an endogenous peptide by using scoring includes matching peak intensities, as stated in specification para. [43]. The BRI of configuring a target peptide database that is not stored in memory includes writing down sequences and organizing them on paper (claim 14). The BRI of indexing differences between sequences includes performing sequence alignment. The BRI of performing sequencing assignment includes organizing data. The BRI of extracting target peptides from the database that match a mass-to-charge ratio includes selecting data and writing it down by using the database as a reference. The BRI of using scoring logic to score each peptide includes using the formulas listed in specification paras. [49-51]. The BRI of ranking and selecting a peptide sequence includes analyzing data and making determinations. All of these limitations can be practically performed by a human either with their mind or by using pen and paper and thus equate to a mental process.
Limitations reciting a mathematical concept.
The above cited limitations in claims 7-8 and 17 recite a mathematical concept because these they are similar to organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)), which the courts have identified as mathematical concepts. Below are the limitations in these claims that recite a mathematical concept under their broadest reasonable interpretation (BRI):
The BRI of scoring includes performing calculations. This interpretation is reinforced by the specification in para. [43] which states “Each of the peptide sequence candidates searched for is scored using matching peak intensities, peak numbers, and the like. As a score calculation method, various score calculation methods used in database search using protein databases can be adopted”. The specification in paras. [49-51] shows equations that can be used for scoring. Therefore, these limitations equate to reciting a mathematical concept.
Limitations included in the judicial exception.
The above cited limitations in claims 5-6 and 15 are included in the judicial exception recited in claims 1-2 and 14 because they further limit the judicial exception but do not change it to recite an additional element.
As such, claims 1-2, 5-8 and 14-19 recite an abstract idea (Step 2A, Prong 1: Yes).
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to a computer, technology, or technical field (MPEP § 2106.04(d)(1) and 2106.5(a)), require a particular treatment or prophylaxis for a disease or medical condition (MPEP § 2106.04(d)(2)), implement the recited judicial exception with a particular machine that is integral to the claim (MPEP § 2106.05(b)), effect a transformation or reduction of a particular article to a different state or thing (MPEP § 2106.05(c)), nor provide some other meaningful limitation (MPEP § 2106.05(e)). Rather, the claims include limitations that equate to instructions to implement an abstract idea on a computer (MPEP § 2106.05(f)) and to insignificant extra-solution activity (MPEP § 2106.05(g)). The instant claims recite the following additional elements:
Claim 1 recites “A computer-implemented peptide assignment method comprising performing the following steps by using at least one processor: (iii) based on the peptide sequences of the endogenous peptides, read from the endogenous peptide sequence database, whose peptide sequences are known among endogenous peptides produced in vivo and on the full-length sequences of the precursor proteins of the endogenous peptides read from the protein sequence database, configuring a target peptide sequence database that stores target peptide sequences with a reduced search space, for a respective target peptide sequence, the database including a variation referencing a corresponding full-length sequence of the precursor proteins, the variation representing a relative position within the corresponding full-length sequence of the precursor proteins, wherein the target peptide sequences contain one or more residues of a partial sequence of the endogenous peptide; (iv) performing mass spectrometry on a peptide sample by using a mass spectrometer; and (viii) outputting the peptide sequence of the endogenous peptide contained in the peptide sample determined by (vii), as an analysis result, … wherein the method further comprises performing the following step by using the at least one processor:”
Claim 2 recites “A peptide assignment system comprising: a reader …; a database creator that, based on the peptide sequences of the endogenous peptides, read from the endogenous peptide sequence database, who peptide sequences are known among endogenous peptides produced in vivo and on the full-length sequences of the precursor proteins of the endogenous peptides read from the protein sequence database, configures a target peptide sequence database that stores target peptide sequences with a reduced search space, for a respective target peptide sequence, the database including a variation referencing a corresponding full-length sequence of the precursor proteins, the variation representing a relative position within the corresponding full-length sequence of the precursor proteins, wherein the target peptide sequences contain one or more residues of a partial sequence of the endogenous peptide; a mass spectrometry performer that performs mass spectrometry on a peptide sample; a peak list creator … a collator … a peptide determiner … at least one processor configured to execute a program in order to function as the reader, the database creator, the mass spectrometry performer, the peak list creator, the collator and the peptide determiner, the database creator … the database creator … the database creator … ”
Claim 6 recites “The peptide assignment system according to claim 2, wherein the database creator . . .”
Claim 8 recites “The peptide assignment system according to claim 2, wherein the peptide determiner . . .”
Claim 14 recites “A database and peptide assignment system for target peptide sequences, comprising: a Central Processing Unit (CPU) communicable with at least one database including endogenous peptides and full-length sequences of precursor proteins of the endogenous peptides configured to:”
Claim 15 recites “The database and peptide assignment system according to claim 14,”
Claim 16 recites “The database and peptide assignment system according to claim 14, wherein the CPU is further configured to …”
Claim 17 recites “The database and peptide assignment system according to claim 16, wherein the CPU is further configured to:”
Claim 18 recites “The database and peptide assignment system according to claim 17, wherein the CPU is further configured to:”
Claim 19 recites “The database and peptide assignment system according to claim 18, wherein the CPU is further configured to: output a final table including a protein ID identifying a protein associated with the selected peptide sequence candidate, a protein name identifying a name of the protein, position information indicating relative positions one or more residues of the partial sequence of the endogenous peptide and sequence information indicating the selected peptide sequence candidate.”
Regarding the above cited limitations in claims 1-2, 6, 8 and 14-19 of (i) the at least one processor, (ii) the peptide assignment system comprising the reader, the database creator, the mass spectrometry performer, the peak list creator, the collator, the peptide determiner, and the at least one processor configured to execute a program in order to function as the reader, the database creator, the mass spectrometry performer, the peak list creator, the collator and the peptide determiner, (iii) the database and peptide assignment system comprising a CPU, and (iv) storing data in a database. There are no limitations that these components require anything other than a generic computing system. Therefore, these limitations equate to mere instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983.
Regarding the above cited limitations in claims 1 and 2 of configuring a database that stores target peptide sequences, performing mass spectrometry on a peptide sample by using a mass spectrometer, and outputting the peptide sequence as an analysis result. These limitations equate to insignificant extra-solution activity of mere data gathering and outputting because they collect data used to perform the judicial exception in claims 1 and 2 of creating a peak list, collating data, and determining a peptide sequence as a peptide sequence of an endogenous peptide contained in the peptide sample and because they output the result of the judicial exception.
Regarding the above cited limitation in claim 18, this limitation equates to insignificant, extra-solution activity of data outputting because it outputs the results of the judicial exception in claim 18 of selecting a peptide sequence candidate.
As such, claims 1-2, 5-8 and 14-19 are directed to an abstract idea (Step 2A, Prong 2: No).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The instant claims recite the following additional elements:
Claim 1 recites “A computer-implemented peptide assignment method comprising performing the following steps by using at least one processor: (iii) based on the peptide sequences of the endogenous peptides, read from the endogenous peptide sequence database, whose peptide sequences are known among endogenous peptides produced in vivo and on the full-length sequences of the precursor proteins of the endogenous peptides read from the protein sequence database, configuring a target peptide sequence database that stores target peptide sequences with a reduced search space, for a respective target peptide sequence, the database including a variation referencing a corresponding full-length sequence of the precursor proteins, the variation representing a relative position within the corresponding full-length sequence of the precursor proteins, wherein the target peptide sequences contain one or more residues of a partial sequence of the endogenous peptide; (iv) performing mass spectrometry on a peptide sample by using a mass spectrometer; and (viii) outputting the peptide sequence of the endogenous peptide contained in the peptide sample determined by (vii), as an analysis result, … wherein the method further comprises performing the following step by using the at least one processor:”
Claim 2 recites “A peptide assignment system comprising: a reader …; a database creator that, based on the peptide sequences of the endogenous peptides, read from the endogenous peptide sequence database, who peptide sequences are known among endogenous peptides produced in vivo and on the full-length sequences of the precursor proteins of the endogenous peptides read from the protein sequence database, configures a target peptide sequence database that stores target peptide sequences with a reduced search space, for a respective target peptide sequence, the database including a variation referencing a corresponding full-length sequence of the precursor proteins, the variation representing a relative position within the corresponding full-length sequence of the precursor proteins, wherein the target peptide sequences contain one or more residues of a partial sequence of the endogenous peptide; a mass spectrometry performer that performs mass spectrometry on a peptide sample; a peak list creator … a collator … a peptide determiner … at least one processor configured to execute a program in order to function as the reader, the database creator, the mass spectrometry performer, the peak list creator, the collator and the peptide determiner, the database creator … the database creator … the database creator … ”
Claim 6 recites “The peptide assignment system according to claim 2, wherein the database creator . . .”
Claim 8 recites “The peptide assignment system according to claim 2, wherein the peptide determiner . . .”
Claim 14 recites “A database and peptide assignment system for target peptide sequences, comprising: a Central Processing Unit (CPU) communicable with at least one database including endogenous peptides and full-length sequences of precursor proteins of the endogenous peptides configured to:”
Claim 15 recites “The database and peptide assignment system according to claim 14,”
Claim 16 recites “The database and peptide assignment system according to claim 14, wherein the CPU is further configured to …”
Claim 17 recites “The database and peptide assignment system according to claim 16, wherein the CPU is further configured to:”
Claim 18 recites “The database and peptide assignment system according to claim 17, wherein the CPU is further configured to:”
Claim 19 recites “The database and peptide assignment system according to claim 18, wherein the CPU is further configured to: output a final table including a protein ID identifying a protein associated with the selected peptide sequence candidate, a protein name identifying a name of the protein, position information indicating relative positions one or more residues of the partial sequence of the endogenous peptide and sequence information indicating the selected peptide sequence candidate.”
Regarding the above cited limitations in claims 1-2, 6, 8 and 14-19 of (i) the at least one processor, (ii) the peptide assignment system comprising the reader, the database creator, the mass spectrometry performer, the peak list creator, the collator, the peptide determiner, and the at least one processor configured to execute a program in order to function as the reader, the database creator, the mass spectrometry performer, the peak list creator, the collator and the peptide determiner, and (iii) the database and peptide assignment system comprising a CPU. Therefore these limitations equate to instructions to implement an abstract idea on a generic computing environment, which the courts have established does not provide an inventive concept in Intellectual Ventures I LLC v. Capital One Bank (USA), 792 F.3d 1363, 1367, 115 USPQ2d 1636, 1639 (Fed. Cir. 2015).
Regarding the above cited limitations in claims 1-2 and 19 of outputting the peptide sequence as an analysis result and outputting a final table, these limitations equate to receiving/transmitting data over a network because they are performed by a computer processor, which the courts have established as WURC limitation of a generic computer in buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014).
Regarding the above cited limitations in claims 1-2 of configuring a target peptide database that stores target peptides, this limitation equates to storing information in memory, which the courts have established as a WURC function of a generic computer in Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015).
Regarding the above cited limitations in claims 1 and 2 of performing mass spectrometry and a mass spectrometer in combination with a generic computing device, these limitations equate to be WURC limitations because Grayson (American Society for Information Science and Technology, 190-202; published 2004; previously cited on PTO892 mailed 05/22/2024) discloses a review on the evolution of mass spectral databases, application for the identification of unknown compounds from mass spectra, and application of computers in acquisition, reduction and analysis of mass spectral data (abstract; pg. 197, col 1, para. 2 – col. 2, para. 4). Grayson therefore teaches that performing mass spectrometry is WURC when in combination with a generic computer.
When these additional elements are considered individually and in combination, they do not provide an inventive concept because they equate to WURC functions/components of a generic computer and to WURC limitations of a generic computer with mass spectrometry. Therefore, these additional elements do not transform the claimed judicial exception into a patent-eligible application of the judicial exception and do not amount to significantly more than the judicial exception itself (Step 2B: No).
As such, claims 1-2, 5-8 and 14-19 are not patent eligible.
Response to Arguments under 35 USC 101
Applicant's arguments filed 07/24/2025 have been fully considered but they are not persuasive.
Applicant argues that the claims improve database search techniques by generating a database that contains target peptide sequences based on peptide sequences of endogenous peptides, wherein the target peptide contains one or more residues of partial sequence of the endogenous peptide. The target peptide database is structured in such a way that it reduces search space, enhances sensitivity, and reduces computational cost. Applicant also appears to equate the configuration of the target peptide database as a data structure analogous to the self-referential table in Enfish (pg. 6, para. 4-5 of Applicant’s remarks). Applicant’s arguments are not persuasive for the following reasons:
Configuring the target peptide database in claim 1, step (iii), and in claim 2, lines 8-12, have been identified as reciting an additional element. However, the target peptide database equates to nothing more than insignificant, extra-solution activity of necessary data gathering for performing the recited judicial exception in claim 1, step (vi), and in claim 2, lines 19-20, of collating the peak list with the target peptide sequence database. The results of the collating step are then used in the judicial exception of determining a peptide sequence as a peptide sequence of an endogenous peptide. The alleged improvement in technology appears to be a result of the judicial exception itself (i.e., collating the peak list with the target peptide sequence database and determining a peptide sequence as an endogenous peptide). The judicial exception alone cannot provide the improvement (MPEP 2106.05(a)).
Regarding Applicant’s analogy of the target peptide database and the self-referential table of Enfish, there are no limitations that discuss a structure of the data in the database. Rather, the target peptide database merely stores data, without any specific data structure. As such, the target peptide database is not being interpreted as having a particular data structure.
Applicant’s remarks to claims 1 and 2 regarding a variance and claim 14 performing indexing are noted (pg. 6, para. 5 of Applicant’s remarks). However, it is unclear what purpose the remarks have in relation to Applicant’s arguments for an improvement in technology.
Claim Rejections - 35 USC § 102
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.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 14-18 are rejected under 35 USC 102(a)(1) as being anticipated by Falth et al. (“Falth”; Journal of proteome research 7, no. 7 (2008): 3049-3053; previously cited on PTO892 mailed 06/06/2023 as NPL ref. V).
This rejection is newly recited and is necessitated by claim amendment.
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
Claim 14:
A database and peptide assignment system for target peptide sequences, comprising: a Central Processing Unit (CPU) communicable with at least one database including endogenous peptides and full-length sequences of precursor proteins of the endogenous peptides configured to:
Falth discloses a database called SwePep designed for endogenous peptides and mass spectrometry (title). Falth states “SwePep is a Java Enterprise Edition (J2EE) application … The SwePep database is implemented as a relational database using MySql database management system” (pg. 3050, col. 2, para. 1-2), which indicates that the SwePep database requires use of a computer that inherently contains a processor. Falth teaches “The SwePep database is designed for endogenous peptides and mass spectrometry. It contains information about the peptides such as mass, pI, precursor protein and potential post-translational modifications” (abstract).
configure a target peptide sequence database according to peptide sequences respectively containing one or more residues of a partial sequence of an endogenous peptide as target peptide sequences; and
Falth teaches “The CID tandem mass spectra stored in SwePep were collected from analysis of different brain regions from the mouse. They were analyzed on an LTQ (Thermo Fisher Scientific) mass spectrometer by capillary liquid chromatography electrospray ionization tandem mass spectrometry (nanoLC-ESI MS/MS)2,11,21 and identified by searching the spectra against SwePep Mouse precursors using X! Tandem. All identifications are stored in the database, even if the scores are below the suggested threshold (log(e) >-2)” (pg. 3051, col. 1, para. 2 – col. 2, para. 1). The endogenous peptides identified in the CID tandem mass spectra (target peptide sequences) are stored in the SwePep database (target peptide sequence database). The identified endogenous peptides contain partial sequences of endogenous peptides because they are compared against precursors of the endogenous peptides (Figures 2 & 3).
Falth also teaches “we have extended the SwePep database to include tandem mass spectra of identified endogenous peptides. Tandem mass spectra of 219 unique peptides that have been identified with a significant score have been added to the SwePep database and the peptides are linked to their corresponding tandem mass spectra” (pg. 3050, col. 1, last para.). This indicates that the identified endogenous peptides have associated sequences in the database.
index differences between the peptide sequences of the target peptide sequences and a sequence of the endogenous peptide.
Falth discloses scoring the identified endogenous peptides with the endogenous peptides stored in the database (Figures 1 & 2) (pg. 3050, col. 1, last para.).
Regarding claim 15, Falth discloses scoring experimental spectral data to already identified peptides in the database (pg. 3049, col. 2, para. 2). Figure 2 shows experimental spectral being scored against an already identified Proenkephalin precursor.
Regarding claim 16, the search space is reduced in the SwePep database because more peptides are added that identified over time, allowing researches to focus on peptides that are not identified using the database. Falth teaches “Many peptides are identified over and over again from different experiments by searching experimental spectra against sequence collections with search engines such as X! Tandem3 and Mascot. Since only a small amount of the generated tandem mass spectra in a typical peptidomics experiment are assigned to a sequence, the time and effort should be used to identifying those spectra instead of identifying the same peptides repeatedly. A possible solution for this problem is to collect tandem mass spectra and then use spectral library algorithms to match experimental spectra to already identified spectra. This is a fast way to reidentify already identified peptides and the effort can instead be put into identifying sequences for the large part of the spectra that never get assigned to a sequence” (pg. 3049, col. 2, para. 2).
Regarding claim 17, Falth teaches that the identified endogenous peptides are stored in the SwePep database (pg. 350, col. 1, last para.). Falth also teaches that peptides in the database can be used to identify peptides by using mass-to-charge ratio as seen on the y-axis of Figures 2A and 2B, which uses a score in the form of, for example log(e) = -4.0, as seen in the caption of Figure 2.
Regarding claim 18, Falth teaches that only identified endogenous peptides with a score above a threshold score are stored in the tandem mass spectra database (pg. 3050, col. 1, last para.).
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 19 is rejected under 35 USC 103 as being unpatentable over Falth et al. (“Falth 2008”; Journal of proteome research 7, no. 7 (2008): 3049-3053; previously cited on PTO892 mailed 06/06/2023 as NPL ref. V), as applied to claims 14 and 16-18 in the rejection above under 35 USC 102, in view of Falth et al. (“Falth 2006”; Molecular & Cellular Proteomics 5, no. 6 (2006): 998-1005; previously cited on PTO892 mailed 06/06/2023 as NPL ref. U).
This rejection is newly recited and is necessitated by claim amendment.
The limitations of claims 14 and 16-18 have been taught in the rejection above by Falth 2008 in section Claim Rejections - 35 USC § 102.
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
Regarding claim 19, Falth 2008 teaches the CPU (pg. 3050, col. 2, para. 1-2) as well as an identified/selected endogenous peptide based upon scoring above a threshold (pg. 3050, col. 1, last para.). However, Falth 2008 does not teach a table that displays all of the listed limitations recited in instant claim 19.
Falth 2006 discloses the original paper for the SwePep database designed for endogenous peptides and mass spectrometry. Falth 2006 shows in Table II an output table. The table contains columns for: a UniProt accession number (a protein ID identifying a protein associated with the selected peptide sequence candidate), a Peptide name (a protein name identifying a name of the protein), a Peptide sequence which contains amino acids and numerical positions of the amino acids (position information indicating relative positions one or more residues of the partial sequence of the endogenous peptide and sequence information indicating the selected peptide sequence candidate).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the instant invention to have modified the method of Falth 2008 to include the output table of Falth 2006 because both methods use the same SwePep database and because the output table provides additional information regarding the identified endogenous peptides. One of ordinary skill in the art would have had a reasonable expectation of success for the combination because both Falth 2008 and Falth 2006 operate using the same SwePep database.
Conclusion
No claims are allowed.
Claims 1-2 and 5-8 are free from the prior for the same reasons described in the Conclusion of the Office actioned mailed 06/06/2023.
Notable, but not relied upon, prior art includes: Falth et al. (Molecular & Cellular Proteomics 6, no. 7 (2007): 1188-1197; newly cited).
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Noah A. Auger whose telephone number is (703)756-4518. The examiner can normally be reached M-F 7:30-4:30 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowronek can be reached on (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685