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 .
Claim Status
Claims 16-25 are newly added.
Claims 1-25 are currently pending and under exam herein.
Claims 1-25 are rejected.
Claims 7, 11, and 22-23 are objected to.
Priority
Applicant’s claim for domestic benefit to the earlier filed international application PCT/EP2022/053387, filed February 11, 2022, which claims benefit to U.S. Provisional Application No. 63/156,971, filed March 5, 2021, under 35 U.S.C. 119(e) is acknowledged. At this point in examination, the effective filing date of claims 1-25 is March 5, 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted September 1, 2023, complies with the provisions of 37 CFR 1.97. Accordingly, the IDS is being considered by the examiner.
Specification
The abstract of the disclosure is objected to because it contains legal phraseology (i.e., said data and said extraction width window). A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
The disclosure is objected to because of the following informalities: Figure 2a does not have a description in the brief description of the drawings. Appropriate correction is required.
Claim Objections
Claim 7 is objected to because of the following informalities: The word ‘using’ should be removed to make the claim grammatically correct.
Claim 11 is objected to because of the following informalities: The words “is used” should be removed to make the claim grammatically correct.
Claim 22 is objected to because of the following informalities: The words “is used” should be removed to make the claim grammatically correct.
Claim 23 is objected to because of the following informalities: The claim contains a typo “rang” that should be changed to range.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are:
A device for chemical analysis in claim 15.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. However, the specification does not provide any structure for the device.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112
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 1-25 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.
Regarding claim 1, the recitation of the limitation "the targeted peptide precursor identification" lacks sufficient antecedent basis. Claims 2-25 are also rejected because they depend from claim 1 and do not resolve the issue of indefiniteness. For the purposes of examination, the recited limitation will be treated as the first appearance. It is suggested to remove the word ‘the’ to overcome this rejection.
Regarding claim 3, the limitation “it accesses said single array” renders the claim indefinite because it is not clear what ‘it’ is referring to and therefore how accessing said single array may be accomplished. Claim 6 is also rejected because it depends from claim 3 and does not solve the issue of indefiniteness. For the purposes of examination, it will be interpreted that the data from the single array is used in the analysis.
Regarding claim 4, the recitation of the limitation "the building of the first ion trace and the determination of the apex retention time" lacks sufficient antecedent basis. Claim 5 is also rejected because it depends from claim 4 and does not solve the issue of indefiniteness. For the purposes of examination, the recited limitation will be treated as the first appearance. It is suggested to amend the claim 4 to depend from claim 3 to overcome this rejection.
Regarding claim 8, the recitation of the limitation "it accesses said single array" lacks sufficient antecedent basis and it is not clear what ‘it’ is referring to and therefore how accessing said single array may be accomplished. Claims 9 and 20 are also rejected because they depend from claim 8 and do not resolve the issue of indefiniteness. For the purposes of examination, the recited limitation will be treated as the first appearance and that data from the single array is used in the analysis. It is recommended to amend claim 8 to depend from claim 2 to overcome this rejection.
Regarding claim 15, claim limitation “a device for chemical analysis” invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The disclosure is devoid of any structure that performs the function in the claim and there is no clear association between the structure and the function in the specification. Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Claim 25 is also rejected because it depends from claim 15 and does not resolve the issue of indefiniteness. For the purposes of examination, a device for chemical analysis will be interpreted as a computer.
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
Regarding claim 17, the recitation of the limitation "it accesses said single array" lacks sufficient antecedent basis and it is not clear what ‘it’ is referring to and therefore how accessing said single array may be accomplished. For the purposes of examination, the recited limitation will be treated as the first appearance and that data from the single array is used in the analysis. It is recommended to amend claim 17 to depend from claim 2 to overcome this rejection.
Regarding claim 18, the recitation of the limitation "the building of the first ion trace and the determination of the apex retention time and also the peak width" lacks sufficient antecedent basis. For the purposes of examination, the recited limitation will be treated as the first appearance. It is recommended to amend the claim to depend from claim 17 to overcome this rejection.
Regarding claim 19, the recitation of the limitation "it accesses said single array" lacks sufficient antecedent basis and it is not clear what ‘it’ is referring to and therefore how accessing said single array may be accomplished. For the purposes of examination, the recited limitation will be treated as the first appearance and that data from the single array is used in the analysis. It is recommended to amend claim 19 to depend from claim 2 to overcome this rejection.
Regarding claim 20, the recitation of the limitation "also the peak width in the retention time dimension" lacks sufficient antecedent basis. For the purposes of examination, the recited limitation will be treated as the first appearance. It is recommended to amend claim 8 to provide the antecedent basis for the claim limitation.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 15 and 25 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Regarding claim 15, claim limitation “a device for chemical analysis” invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The disclosure is devoid of any structure that performs the function in the claim and there is no clear association between the structure and the function in the specification. The claim is indefinite and was rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph above.
MPEP 2181(IV) and 2163.03(VI) state, limitations interpreted under 35 U.S.C. 112(f) that are rejected as being indefinite for failure to disclose sufficient corresponding structure also lack written description. Claim 25 is also rejected because it depends from claim 15 and does not resolve the issue of lack of written description.
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.
Claim 15 is rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Claim 15 does not fall within at least one of the four categories of patent eligible subject matter because it is directed to a product without physical or tangible form (i.e., software per se) (MPEP 2106.03(I)).
Claims 1-25 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Step 1:
The first part of the eligibility analysis evaluates whether a claim falls within any statutory category (MPEP 2106.03). Claims 1-25 recites steps taken in the analysis of mass spectrometry data. Although claim 15 is not a statutory category of invention, for the purpose of compact prosecution, the subject matter eligibility analysis will proceed. The claims are directed to a process and fall within one of the statutory categories of invention (Step 1: YES).
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 phenomenon (Step 2A, prong 1). In the instant application, the claims recite the following limitations that equate to those concepts:
Claims 1 and 14-15 recite: method for the targeted peptide precursor identification from sample mass spectroscopic intensity data acquired as a function of mass to charge ratio, of retention time as well as of ion mobility; wherein for peptide precursor identification from the sample mass spectroscopic intensity data, in a first step for at least three reference peptide precursors, from the database of reference peptide precursor data, said sample mass spectroscopic intensity data is analysed in the respective reference peptide precursor region of interest of mass to charge ratio, retention time as well as ion mobility dimension, and from that analysis empirically an adjusted center in the ion mobility dimension for each reference peptide precursor is determined and an ion mobility extraction width window in the ion mobility dimension, is determined, and wherein in a second step for the identification of further peptide precursors from said sample mass spectroscopic intensity data, said empirically determined ion mobility extraction width window in the ion mobility dimension, is used.
Claim 2 recites: wherein for the analysis in the first and/or the second step, for a given retention time the data are merged into a single array with three dimensions, mass to charge ratio dimension, intensity dimension, and ion mobility index dimension, sorted by mass to charge ratio.
Claim 3 recites: wherein in said first step for each reference peptide precursor the analysis considers a range in the retention time dimension as a retention time window, and for each retention time value in that retention time window, it accesses said single array for that retention time for building a first ion trace for that reference peptide precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding reference peptide are summed up over the full range in the ion mobility dimension to a single data point for that retention time value, these single data points as a function of the retention time value building together said first ion trace in the retention time dimension, followed by peak detection in the first ion trace to determine the apex retention time.
Claim 4 recites: wherein the building of the first ion trace and the determination of the apex retention time for that reference peptide precursor is followed by extraction of a second ion trace at said trace apex retention time by accessing said single array for that trace apex retention time for building a second ion trace for that reference peptide precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding reference peptide are extracted and represented as a function of the ion mobility dimension, building together said second ion trace in the ion mobility dimension, followed by peak detection in the second ion trace to determine the apex ion mobility value and the peak width for that reference peptide precursor.
Claim 5 recites: wherein the peak detection in the second ion trace is followed by a non-linear or linear ion mobility regression using the apex ion mobility values and the peak widths of the at least three reference peptide precursors to determine said adjusted center in the ion mobility dimension for each reference peptide precursor and to determine said window in the ion mobility dimension.
Claim 6 recites: wherein said first step is carried out for a first set of at least 3, or at least 5, or at least 7, or at least 10, or at least 100, or at least 1000 reference peptide precursors considering the full range in the retention time dimension as retention time window for building the first ion trace, and wherein said first step is carried out a second time with a larger set of reference peptide precursors than the first time, or at least 10, or at least 100, or at least 1000, or at least 2000, or at least 5000 reference peptide precursors, and wherein a retention time window is used for building the first ion trace based on the peak width in the retention time dimensions determined in the first run of the first step.
Claim 8 recites: wherein in said second step after the determination of the precursors in the data, for each precursor the analysis considers a range in the retention time dimension as a retention time window, and for each retention time value in that retention time window, it accesses said single array for that retention time for building a first ion trace for that precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding precursor are summed up over the full range in the ion mobility dimension to a single data point for that retention time value, these single data points as a function of the retention time value building together said first ion trace in the retention time dimension, followed by peak detection in the first ion trace to determine the apex retention time.
Claim 9 recites: wherein the step of peak detection in the first ion trace to determine the apex retention time is followed by extraction of a second ion trace at said trace apex retention time by accessing said single array for that trace apex retention time for building a second ion trace for that precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding precursor are extracted and represented as a function of the ion mobility dimension, building together said second ion trace in the ion mobility dimension, followed by peak detection in the second ion trace to determine the apex ion mobility value and the peak width for that precursor for scoring and/or identification of the precursor.
Claim 10 recites: wherein in the first step also in the mass to charge ratio dimension and/or in the retention time dimension an extraction width window in the respective dimension, is determined, and in the second step for the identification of further peptide precursors from said sample mass spectroscopic intensity data, said empirically determined extraction width window in the respective dimension as a variable function of the respective dimension is used.
Claim 13 recites: wherein at least one, or at least 2, or at least 5, or at least 7 reference peptide precursors are based on a corresponding number of proteins or peptides spiked into the sample to be analysed prior to analysis.
Claim 14 recites: wherein at least one or for the majority or for each peptide precursor in the database based on empirical measurements an associated ion mobility extraction width window is determined…
Claim 16 recites: wherein in a first step for at least three reference peptide precursors, or for all reference peptide precursors from the database of reference peptide precursor data, said sample mass spectroscopic intensity data is analysed in the respective reference peptide precursor region of interest of mass to charge ratio, retention time as well as ion mobility dimension, and from that analysis empirically an adjusted center in the ion mobility dimension for each reference peptide precursor is determined and an ion mobility extraction width window in the ion mobility dimension, as a variable function of the ion mobility dimension, is determined, and wherein in a second step for the identification of further peptide precursors from said sample mass spectroscopic intensity data, said empirically determined ion mobility extraction width window in the ion mobility dimension, as a variable function of the ion mobility dimension is used.
Claim 17 recites: wherein in said first step for each reference peptide precursor the analysis considers a range in the retention time dimension as a retention time window, or the full retention time dimension, and for each retention time value in that retention time window, it accesses said single array for that retention time for building a first ion trace for that reference peptide precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding reference peptide are summed up over the full range in the ion mobility dimension to a single data point for that retention time value, these single data points as a function of the retention time value building together said first ion trace in the retention time dimension, followed by peak detection in the first ion trace to determine the apex retention time and also the peak width in the retention time dimension for that reference peptide precursor.
Claim 18 recites: wherein the building of the first ion trace and the determination of the apex retention time and also the peak width in the retention time dimension for that reference peptide precursor is followed by extraction of a second ion trace at said trace apex retention time by accessing said single array for that trace apex retention time for building a second ion trace for that reference peptide precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding reference peptide are extracted and represented as a function of the ion mobility dimension, building together said second ion trace in the ion mobility dimension, followed by peak detection in the second ion trace to determine the apex ion mobility value and the peak width for that reference peptide precursor.
Claim 19 recites: wherein in said second step after the determination of the precursors in the data, for each precursor the analysis considers a range in the retention time dimension as a retention time window, determined based on an analysis of reference peptide precursors, and for each retention time value in that retention time window, it accesses said single array for that retention time for building a first ion trace for that precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding precursor are summed up over the full range in the ion mobility dimension to a single data point for that retention time value, these single data points as a function of the retention time value building together said first ion trace in the retention time dimension, followed by peak detection in the first ion trace to determine the apex retention time and also the peak width in the retention time dimension for that precursor.
Claim 20 recites: wherein the step of peak detection in the first ion trace to determine the apex retention time and also the peak width in the retention time dimension for that precursor is followed by extraction of a second ion trace at said trace apex retention time by accessing said single array for that trace apex retention time for building a second ion trace for that precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding precursor are extracted and represented as a function of the ion mobility dimension , building together said second ion trace in the ion mobility dimension , followed by peak detection in the second ion trace to determine the apex ion mobility value and the peak width for that precursor for scoring and/or identification of the precursor.
Claim 21 recites: wherein in the first step also in the mass to charge ratio dimension and/or in the retention time dimension an extraction width window in the respective dimension, as a variable function of the respective dimension, is determined, and in the second step for the identification of further peptide precursors from said sample mass spectroscopic intensity data, said empirically determined extraction width window in the respective dimension as a variable function of the respective dimension is used.
Claim 24 recites: wherein for the majority or for each peptide precursor in the database based on empirical measurements an associated ion mobility extraction width window is determined…
The limitation in claims 1 and 14-15 of targeted peptide precursor identification is a recitation of a mathematical analysis performed on mass spectrometry data and the limitations of determining an adjusted center and extraction window width are recitations of mathematical calculations performed in the analysis to align/calibrate the sample data. The limitation of the second step of using the ion mobility extraction window to identify further precursors is also reciting mathematical analysis on the mass spectrometry data. The limitation in claim 2 further limits the mathematical analysis in claim 1 by describing the arrangement of the data that is used to perform the mathematical calculations. The limitations in claim 16 further limit the mathematical analysis by determining the extraction window width as a variable function of the ion mobility dimension.
The limitations in claims 3-4, 8-9, and 17-20 further limit the analysis in claim 1 by reciting mathematical calculations and mental processes to build 1 first and second ion trace. Particularly, claims 3 and 17 further limit the analysis in the first step in claim 1 by reciting additional mathematical calculations to build the first ion trace. Claims 4 and 18 further limit the analysis in the first step of claim 1 by reciting the mental process of observing and evaluating data to build the second ion trace. Likewise, claims 8 and 19 further limit the analysis in the second step of claim 1 by reciting additional mathematical calculations to build the first ion trace and claims 9 and 20 further limit the second step by reciting the mental process of observing and evaluating data to build the second ion trace.
The limitations of claim 5 further limit the analysis in the first step of claim 1 by reciting additional mathematical calculations to use in determining the adjusted center and ion mobility window. The limitations in claim 6 further limit the first step of the analysis in claim 1 by repeating the analysis by using more data and output from the first iteration as input into the second iteration. The limitations in claims 10 and 21 further limit the first step of the analysis in claim 1 by reciting additional mathematical calculations to determine the extraction window width in the m/z and retention time dimension and the second step of the analysis is further limited by incorporating the additional windows.
The limitations in claim 13 further limit the analysis in claim 1 by indicating the particular reference peptide precursors used in mathematical calculations. The limitations in claims 14 and 24 further limit the analysis in claim 1 by providing alternative numbers for how many reference peptide precursors or peptide precursors an extraction window width is determined.
Therefore, these limitations fall under the “Mathematical concepts” and “Mental processes” groupings of abstract ideas (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 (Step 2A, prong 2). The claims recite the following additional elements:
Claim 1 recites: …using a database of reference peptide precursor data for retrieval of a region of interest for at least three reference peptide precursors in the mass to charge ratio, the retention time as well as in the ion mobility dimension…
Claim 7 recites: wherein using a database of reference peptide precursor data for a region of interest for at least 5, or at least 7, or at least 10, or at least 100, or at least 500, or at least 1000 reference peptide precursors in the mass to charge ratio, the retention time as well as in the ion mobility dimension is retrieved for carrying out the first step.
Claim 11 recites: wherein the sample mass spectroscopic intensity data acquired as a function of mass to charge ratio, of retention time as well as of ion mobility are determined using an LC tandem mass spectroscopy method, used.
Claim 12 recites: wherein the sample mass spectroscopic intensity data acquired as a function of mass to charge ratio, of retention time as well as of ion mobility are determined from a biological sample in a data independent manner on the complete mass range, and through the entire chromatography, disregarding of the content of the sample.
Claim 14 and 24 recite: determined ion extraction mobility windows are stored in a database.
Claim 15 recites: performing the steps in claim 1 on a processor.
Claim 22 recites: wherein the sample mass spectroscopic intensity data acquired as a function of mass to charge ratio (m/z), of retention time as well as of ion mobility are determined using an LC tandem mass spectroscopy method, selected from the group of LC-MRM or LC-SWATH is used.
Claim 23 recites: wherein the sample mass spectroscopic intensity data acquired as a function of mass to charge ratio (m/z), of retention time as well as of ion mobility are determined from a biological sample in a data independent manner on the mass rang, 200-2000 Thomson, and through the entire chromatography, disregarding of the content of the sample.
Claim 25 recites: a tangible computer-readable storage medium with program instructions to perform the steps in claim 1.
The additional element in claim 1 of a database of reference peptide precursors is insignificant extra-solution activity of data gathering that is required for the recited judicial exception (MPEP 2106.05(g)). The additional elements in claim 7 further limit the database by reciting alternative amounts of reference precursors stored. Similarly, the additional elements of claims 11-12 and 22-23 are data gathering steps needed to obtain mass spectroscopy data necessary to perform the judicial exception. The additional elements in claims 14 and 24 of storing extraction window widths in a database are an insignificant application of storing data generated from the judicial exception without placing significant limits on the claim.
The additional elements in claims 15 and 25 of a processor performing the judicial exception and a tangible computer-readable storage medium are instructions to apply the judicial exception in a generic computer environment by invoking computer components to perform steps in the recited judicial exception (MPEP 2106.05(f)).
Therefore, the judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies/uses the recited judicial exception in some other meaningful way and the claims are directed to the judicial exception (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). Claims 15 and 25 recite additional elements that equate to mere instructions to apply the recited judicial exception in a generic computing environment. Claims that amount to nothing more than instructions to apply the judicial exception using a generic computer do not render an abstract idea eligible. Alice Corp., 576 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. The additional elements recited in claims 11-12 and 22-23 amount to well-understood, routine and conventional (WURC) activity because paragraphs 0002-0003 show that data-independent acquisition as a mass spectrometric approach is known to those of ordinary skill in the art. The additional elements in claims 1, 7, 14, and 24 also recite computer functions that the courts have ruled to be WURC such as receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information); OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network); buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network) and storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93.
As such, the combination of additional elements recited in the claims is well-understood, routine, and conventional. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transform the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: NO) and claims 1-25 are not patent eligible.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-2, 7, 11-15, 22-25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Meier et al. (Nature Communications, vol. 12, no. 1, p. 1185; referred to as Meier et al. 1), as evidenced by Meier et al. (Nature Methods, vol. 17, no. 12, pp. 1229-36; referred to as Meier et al. 2). The italicized text corresponds to the instant claim limitations.
Regarding claim 1, Meier et al. 1 teach performing a validation of their predicted collisional cross section (CCS) values by replacing experimental CCS values in a spectral library with their predictions and analyzing data from a data-independent acquisition parallel accumulation serial fragmentation (diaPASEF) experiment (p. 6, Deep learning accurately predicts peptide CCS values, paragraph 4) disclosing method for the targeted peptide precursor identification from sample mass spectroscopic intensity data acquired as a function of mass to charge ratio, or retention time as well as of ion mobility, using a database of reference peptide precursor data for retrieval of a region of interest for at least three reference peptide precursors in the mass to charge ratio, the retention time as well as in the ion mobility dimension... PASEF data combines ion mobility separation of analytes with liquid chromatography-mass spectrometry which allows analysis of samples in the three dimensions of ion mobility, mass to charge ratio, and retention time (p. 2, Introduction, paragraphs 1-2). Additionally, CCS values are derived from measurements taken in the ion mobility dimension (p. 2, Introduction, paragraph 3) and Figure 1b shows the spectral library made from the 24 HeLa fractions has 1,171,851 CCS measurements (p. 2-3, Results paragraph 1).
Meier et al. 1 performed targeted data analysis using Spectronaut software which automatically performs alignment of the diaPASEF data to the reference library and optimized the ion mobility extraction window (p. 6, Deep learning accurately predicts peptide CCS values, paragraph 4) which discloses … wherein for peptide precursor identification from the sample mass spectroscopic intensity data, in a first step for at least three reference peptide precursors, from the database of reference peptide precursor data, said sample mass spectroscopic intensity data is analyzed in the respective reference peptide precursor region of interest of mass to charge ratio, retention time as well as ion mobility dimension, and from that analysis empirically an adjusted center in the ion mobility dimension for each reference peptide precursor is determined and an ion mobility extraction width window in the ion mobility dimension is determined, ... Alignment of the diaPASEF data to the spectral library corrects any linear shifts of peaks that may be due to variations of the gas flow (p. 3, Evaluating the accuracy, precision, and utility of TIMS CCS measurements, paragraphs 1-3). The results of the targeted analysis showed that a similar number of peptides were identified between the original CCS values of the spectral library and the CCS values predicted by Meier et al. (Id.) which discloses … and wherein in a second step for the identification of further peptide precursors from said sample mass spectroscopic intensity data, said empirically determined ion mobility extraction width window in the ion mobility dimension is used.
Regarding claim 2, Meier et al. 1 teach using the MaxQuant software to create their CCS dataset which creates a four-dimensional isotope cluster in the mass, retention time, ion mobility, and intensity dimension (p. 2, Construction of a very large-scale peptide CCS dataset, paragraph 2). Figure 1e shows a two-dimensional presentation of the data in CCS vs. m/z space sorted by m/z (p. 3). Since CCS values are derived from ion mobility measurements (p. 2, Construction of a very large-scale peptide CCS dataset, paragraph 2), the CCS axis can be seen as a transformed ion mobility dimension. These teachings disclose the limitations of wherein for the analysis in the first and/or the second step, for a given retention time the data are merged into a single array with three dimensions, mass to charge ratio dimension, intensity dimension, and ion mobility index dimension, sorted by mass to charge ratio.
Regarding claim 7, the previous teachings from Meier et al. 1 of making a spectral library from the 24 HeLa fractions dataset they created (p. 6, Deep learning accurately predicts peptide CCS values, paragraph 4) which contains 1,171,851 CCS measurements (p. 2-3, Results paragraph 1; Figure 1b) discloses wherein using a database of reference peptide precursor data for a region of interest for at least 5, or at least 7, or at least 10, or at least 100, or at least 500, or at least 1000 reference peptide precursors in the mass to charge ratio, the retention time as well as in the ion mobility dimension is retrieved for carrying out the first step.
Regarding claim 11, Meier et al. 1 teach analyzing data from a diaPASEF experiment of Meier et al. 2 (p. 6, Deep learning accurately predicts peptide CCS values, paragraph 4). Meier et al. 2 teaches that the data from the whole-proteome HeLa sample was obtained by liquid chromatography tandem mass spectrometry (p. 1237, Liquid chromatography; Mass spectrometry; Spectral library generation) which discloses wherein the sample mass spectroscopic intensity data acquired as a function of mass to charge ratio, of retention time as well as of ion mobility are determined using an LC tandem mass spectroscopy method is used.
Regarding claims 12 and 23, Meier et al. 2 shows the diaPASEF data used in Meier et al. 1 was scanned over a 400-1,200 m/z mass range after the sample went through a chromatography column coupled to the mass spectrometer (p. 1237, Liquid chromatography, paragraphs 1-3; Mass spectrometry, paragraph 2) which discloses the claim 12 limitation of wherein the sample mass spectroscopic intensity data acquired as a function of mass to charge ratio, of retention time as well as of ion mobility are determined from a biological sample in a data independent manner on the complete mass range, and through the entire chromatography, disregarding of the content of the sample and the claim 23 limitation of wherein the sample mass spectroscopic intensity data acquired as a function of mass to charge ratio (m/z), of retention time as well as of ion mobility are determined from a biological sample in a data independent manner on the mass rang, 200-2000 Thomson, and through the entire chromatography, disregarding of the content of the sample.
Regarding claim 13, Meier et al. 2 shows that the diaPASEF data used in Meier et al. 1 was spiked with tryptic yeast digest and Mobi-DIK analysis identified 1,394 yeast proteins in the samples (p. 1233, Label-free quantification benchmark) and Meier et al. 1 teach that their peptide CCS dataset included peptides from whole-cell proteomes of budding yeast (p. 2, Results, paragraph 1) which shows the spectral library had peptide precursors that were spiked-in the sample data and therefore discloses wherein at least one, or at least 2, or at least 5, or at least 7 reference peptide precursors are based on a corresponding number of proteins or peptides spiked into the sample to be analysed prior to analysis.
Regarding claims 14 and 24, Meier et al. 1 teach depositing output files at the ProteomeXchange Consortium via the PRIDE partner repository (p. 10, Data Availability) which discloses the claim 14 limitations of method for the generation of a peptide precursor database, wherein at least one or for the majority of for each peptide precursor in the database based on empirical measurement an associated ion mobility extraction width window is determined and stored in the database and using a method according to claim 1 and the claim 24 limitations of wherein for the majority or for each peptide precursor in the database based on empirical measurements an associated ion mobility extraction width window is determined and stored in the database determined from sample mass spectroscopic intensity data acquired as a function of mass to charge ratio, of retention time as well as of ion mobility.
Regarding claims 15 and 25, Meier et al. 1 teach using the Spectronaut software for targeted data analysis which uses library values to score peptide signals and to restrict the data extraction window in the ion mobility dimension (p. 6, Deep learning accurately predicts peptide CCS values, paragraph 4) which discloses the claim 15 limitations of a computer program product, whose contents include a program with instructions being executed on the processor so as to control a device for chemical analysis using a method according to claim 1. Additionally, it is inherent that software must be stored on computer-readable storage media from where it is called by the computer system when the processor executes the software instructions. Thus, disclosing the claim 25 limitation of a computer program product according to claim 15, on … a tangible computer-readable storage medium.
Regarding claim 22, Meier et al. 2 shows that the diaPASEF data used in Meier et al. 1 was acquired by LC-SWATH tandem mass spectrometry because they defined 32 isolation windows of 25 Th width through the analyzed mass range to obtain the spectra data (p. 1237, Mass spectrometry, paragraph 2). Additionally, Meier et al. 2 shows that OpenSWATH software was used for targeted data extraction (p. 1237, Targeted data extraction). These teachings disclose wherein the sample mass spectroscopic intensity data acquired as a function of mass to charge ratio (m/z), of retention time as well as of ion mobility are determined using an LC tandem mass spectroscopy method, selected from the group … LC-SWATH is used.
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.
Claims 3-6, 8-9, 17-20 are rejected under 35 U.S.C. 103 as being unpatentable over Meier et al. (Nature Communications, vol. 12, no. 1, p. 1185; referred to as Meier et al. 1) as applied to claims 1-2 above, and further in view of Yu et al. (Molecular & Cellular Proteomics, vol. 19, no. 9, pp. 1575-85; IDS document 9/1/2023) and Meier et al. (Nature Methods, vol. 17, no. 12, pp. 1229-36; referred to as Meier et al. 2). The italicized text corresponds to the instant claim limitations.
The limitations of claims 1-2 have been taught by Meier et al. 1.
Regarding claim 6, Meier et al. 1 teach targeted analysis in the Spectronaut software makes use of peptide library values to restrict the data extraction window in the ion mobility dimension, thereby removing interfering signals from precursors with similar mass and retention time (p. 6, Deep learning accurately predicts peptide CCS values, paragraph 4) which discloses … and wherein said first step is carried out a second time with a larger set of reference peptide precursors than the first time, or at least 10, or at least 100, or at least 1000, or at least 2000, or at least 5000 reference peptide precursors, and wherein a retention time window is used for building the first ion trace based on the peak width in the retention time dimensions determined in the first run of the first step.
Meier et al. 1 appear to be silent on the limitations of claims 3-5, 8-9, and 17-20, and the claim 6 limitations of wherein said first step is carried out for a first set of at least 3, or at least 5, or at least 7, or at least 10, or at least 100, or at least 1000 reference peptide precursors considering the full range in the retention time dimension as retention time window for building the first ion trace. However, these limitations were known in the art prior to the effective filing date of the invention as taught by Yu et al. and Meier et al. 2.
Regarding claim 3, Yu et al. teach the IonQuant Algorithm that performs peak tracing by locating ion mobility indexes from a indexed four-dimensional space corresponding to a precursor, collecting m/z indexes within the tolerance of the theoretical m/z, and traversing all qualified peaks within the retention time range and generating a curve by tracing and Gaussian smoothing and reports the boundaries and apex locations (p. 1577-1578, Results and Discussion, paragraphs 1-2; Figure 1B) which discloses wherein in said first step for each reference peptide precursor the analysis considers a range in the retention time dimension as a retention time window, and for each retention time value in that retention time window, it accesses said single array for that retention time for building a first ion trace for that reference peptide precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding reference peptide are summed up over the full range in the ion mobility dimension to a single data point for that retention time value, these single data points as a function of the retention time value building together said first ion trace in the retention time dimension, followed by peak detection in the first ion trace to determine the apex retention time.
Regarding claim 4, Yu et al. teach that after tracing all peaks in the retention time and m/z dimension, IonQuant traces the ion mobility dimension by clustering adjacent peaks to form 4-D features and the algorithm reports the boundaries, apex location, and volume of each detected ion feature (Id.) which discloses wherein the building of the first ion trace and the determination of the apex retention time for that reference peptide precursor is followed by extraction of a second ion trace at said trace apex retention time by accessing said single array for that trace apex retention time for building a second ion trace for that reference peptide precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding reference peptide are extracted and represented as a function of the ion mobility dimension, building together said second ion trace in the ion mobility dimension, followed by peak detection in the second ion trace to determine the apex ion mobility value and the peak width for that reference peptide precursor.
Regarding claim 5, Meier et al. 2 teach using OpenSWATH software to perform m/z correction by quadratic regression of the difference in ppm mass tolerance (p. 1237, Targeted data extraction) which discloses wherein the peak detection in the second ion trace is followed by a … linear ion mobility regression using the apex ion mobility values and the peak widths of the at least three reference peptide precursors to determine said adjusted center in the ion mobility dimension for each reference peptide precursor and to determine said window in the ion mobility dimension.
Regarding claim 6, the teaching of Yu et al. of the steps of the IonQuant algorithm cited above (p. 1577-1578, Results and Discussion, paragraphs 1-2; Figure 1B) disclose wherein said first step is carried out for a first set of at least 3, or at least 5, or at least 7, or at least 10, or at least 100, or at least 1000 reference peptide precursors considering the full range in the retention time dimension as retention time window for building the first ion trace…
Regarding claim 8, the same limitations as claim 3 are recited except they are performed in the second step on other precursors and therefore the teachings of Yu et al. applied to claim 3 above (p. 1577-1578, Results and Discussion, paragraphs 1-2; Figure 1B) also disclose the limitations wherein in said second step after the determination of the precursors in the data, for each precursor the analysis considers a range in the retention time dimension as a retention time window, and for each retention time value in that retention time window, it accesses said single array for that retention time for building a first ion trace for that precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding precursor are summed up over the full range in the ion mobility dimension to a single data point for that retention time value, these single data points as a function of the retention time value building together said first ion trace in the retention time dimension, followed by peak detection in the first ion trace to determine the apex retention time.
Regarding claim 9, the same limitations as claim 4 are recited except they are performed in the second step on other precursors and have an intended use, therefore the teachings Yu et al. applied to claim 4 above (p. 1577-1578, Results and Discussion, paragraphs 1-2; Figure 1B) also disclose the limitations wherein the step of peak detection in the first ion trace to determine the apex retention time is followed by extraction of a second ion trace at said trace apex retention time by accessing said single array for that trace apex retention time for building a second ion trace for that precursor, in that the intensity values that fall within a mass to charge ratio window of the corresponding precursor are extracted and represented as a function of the ion mobility dimension, building together said second ion trace in the ion mobility dimension, followed by peak detection in the second ion trace to determine the apex ion mobility value and the peak width for that precursor for scoring and/or identification of the precursor.
Regarding claim 17, the same limitations as claim 3 are recited except with the addition of alternatively considering the full retention time dimension and determining the peak width in the retention time dimension. As cited above, Yu et al. teaches all these limitations.
Regarding claim 18, the same limitations as claim 4 are recited except with the addition of the second trace is preceded by the determination of the peak width in the retention time dimension. All these limitations read on the teachings of Yu et al. cited above.
Regarding claim 19, the same limitations as claim 8 are recited except for the addition of the retention time window is determined based on an analysis of reference peptide precursors and determining the peak width in the retention time dimension. Since the data from reference peptide precursors was obtained by performing a mass spectrometry analysis on those peptides before they were stored in a database, the above cites teachings of Yu et al. disclose all the limitations of claim 19.
Regarding claim 20, the same limitations as claim 9 are recited except for the addition of the second trace is preceded by the determination of the peak width in the retention time dimension. All these limitations read on the teachings of Yu et al. cited above.
An invention would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive the claimed invention. Meier et al. 1 teach using MaxQuant to analyze raw MS files (p. 9-10, Data processing), and Yu et al. teach IonQuant outperforms MaxQuant in terms of number of quantified proteins while maintaining good quantification precision and accuracy (Abstract). Therefore, an ordinary artisan would have been motivated by the superior performance of IonQuant over MaxQuant to modify the teachings of Meier et al. 1 with those of Yu et al. There would be a reasonable expectation of success because both references utilize the same four-dimensional parallel accumulation serial fragmentation (PASEF) data from mass spectrometry.
In regard to claim 6, a person having ordinary skill in the art would be motivated to also optimize the retention time window in the same fashion as Meier et al. 1 taught for optimizing the ion mobility window (p. 6, Deep learning accurately predicts peptide CCS values, paragraph 4) because Meier et al. 1 teach that there are shifts in retention time data collected during mass spectrometry experiments which hinder peptide identification (p. 3, Evaluating the accuracy, precision, and utility of TIMS CCS measurement). Yu et al. also teach that there are many spectral preprocessing steps such as mass calibration and retention time alignment/calibration (p. 1577, Label-Free Quantification). Meier et al. 2 teach using curated reference peptide to re-calibrate raw diaPASEF data in the m/z, retention time, and ion mobility dimensions (p. 1237, Targeted data extraction). It would be obvious to one of ordinary skill in the art to repeat calibration steps with more data to obtain a better retention time window width. Repeating a step/duplicating a part does not provide patentable significance to an invention (MPEP 2144(VI)(B)).
Furthermore, A person of ordinary skill would also be motivated to use quadratic regression to correct ion mobility values in the same way Meier et al. 2 corrected m/z values to lower the deviation between experimental values and reference values because Meier et al. 2 teach that the deviation in data values from experimental runs and library values defines the precision of each precursor in the data (p. 1233, Single-run proteome analysis, paragraph 2). There would be a reasonable expectation of success because Meier et al. 2 also uses the same four-dimensional diaPASEF data obtained from mass spectrometry and shows that this type of regression is already done for m/z values. The invention of claims 3-6, 8-9, and 17-20 are therefore prima facie obvious.
Claims 10, 16, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Meier et al. (Nature Communications, vol. 12, no. 1, p. 1185; referred to as Meier et al. 1) as applied to claim 1 above, and further in view of Bruderer et al. (PROTEOMICS, vol. 16, nos. 15-16, pp. 2246-56). The italicized text corresponds to the instant claim limitations.
The limitations of claim 1 have been taught by Meier et al. 1.
Regarding claim 10, Bruderer et al. teach high precision iRT (indexed retention times) implemented in the Spectronaut software that uses segmented regression for generating spectral libraries and DIA analysis (p. 2247, Introduction, paragraphs 5-7). Indexed retention times are used to normalize retention times from spectral libraries that may be made up of heterogenous data-dependent acquisition (DDA) data or having different gradient lengths than data-independent acquisition which can help in obtaining a more accurate elution time for peptides and shown to improve sensitivity and speed in targeted DIA analyses (p. 2247, Introduction, paragraph 3-4). Bruderer et al. teach Spectronaut performs segmented regression based on 21,155 reference anchor points split into bins and estimates window width based on anchor points in each bin (p. 2249, iRT ~ RT and RT ~ iRT segmented regression and extraction window width estimation as implemented in Spectronaut; Figure 1). These teachings disclose wherein in the first step also in the mass to charge ratio dimension and/or in the retention time dimension an extraction width window in the respective dimension, is determined, and in the second step for the identification of further peptide precursors from said sample mass spectroscopic intensity data, said empirically determined extraction width window in the respective dimension as a variable function of the respective dimension is used.
Regarding claim 16, the same teachings cited above by Bruderer et al. disclose wherein in a first step for at least three reference peptide precursors, or for all reference peptide precursors from the database of reference peptide precursor data, said sample mass spectroscopic intensity data is analysed in the respective reference peptide precursor region of interest of mass to charge ratio, retention time as well as ion mobility dimension, and from that analysis empirically an adjusted center in the ion mobility dimension for each reference peptide precursor is determined and an ion mobility extraction width window in the ion mobility dimension, as a variable function of the ion mobility dimension, is determined, and wherein in a second step for the identification of further peptide precursors from said sample mass spectroscopic intensity data, said empirically determined ion mobility extraction width window in the ion mobility dimension, as a variable function of the ion mobility dimension is used.
Regarding claim 21, the same limitations are recited in claim 10 with the addition that the width of the extraction windows is determined as a variable function of the respective dimension. The above cited teachings of Bruderer et al. do determine the width of the retention time window as a variable of the retention time dimension and therefore disclose all the limitations.
An invention would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive the claimed invention. One of ordinary skill in the art would be motivated to modify the teachings of Meier et al. 1 of optimizing ion mobility windows using Spectronaut to make the optimization determine the window width as a variable function of the ion mobility dimension because Bruderer et al. showed that their high precision iRT values increased the number of peptide identifications compared to no RT prediction and linear iRT regression (p. 2253, Discussion, paragraph 3) and there would be a reasonable expectation of success because Bruderer et al. teach that their segmented regression approach is generally applicable (p. 2247, Introduction, paragraph 6). An ordinary artisan would further be motivated to apply the same technique to the m/z dimension in order to further increase peptide identification accuracy and would have a reasonable expectation of success because Bruderer et al. already demonstrated the technique on retention time data. The invention of claims 10, 16, and 21 are therefore prima facie obvious.
Conclusion
No claims are allowed.
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/T.Y.O./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
