DETAILED ACTION
The amendment and RCE filed on 03/20/2026 has been entered and fully considered. Claim 4, 6 and 12 are canceled. Claims 1-3, 5, 7-11 and 13-15 are pending, of which claims 1 and 10-11 are amended, and claim 7 is newly added.
Response to Amendment
In response to amendment, the examiner maintains rejection over the prior art established in the previous Office 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 Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 1-3, 5, 7-11 and 13-15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Pett et al. (Angew. Chem. Int. Ed. 2018) (Pett).
Regarding claim 1, Pett teaches a mass spectrometry method comprising:
preparing a sample containing a glycan including a plurality of sialic acids (page 9322, par 1);
generating a plurality of oxonium ions by ionizing the glycan having the plurality of sialic acids modified in the performing step and dissociating the ionized glycan under the same dissociation condition, wherein the plurality of oxonium ions include a first oxonium ion derived from the first modified form and a second oxonium ion derived from the second modified form, and a mass of the first oxonium ion is different from a mass of the second oxonium ion (Fig. 1B, page 9321, par 0);
detecting, in a first mass spectrometry intensities of the first oxonium ion and the second oxonium ion included in the plurality of oxonium ions generated in the generating step (Fig. 1B, page 9321, par 0);
calculating relative values of intensities of the detected first oxonium ion and second oxonium ion (Fig. 1C, 1D, page 9321, par 0); and
calculating a ratio of a number of sialic acids modified into the first modified form corresponding to the first oxonium ion and a number of sialic acids modified into the second modified form corresponding to the second oxonium ion in the glycan contained in the sample based on the relative values (Fig. 1C, 1D, page 9321).
Pett repeatedly teaches quantitative or semi-quantitative calculations of oxonium-ion intensity ratios, including:
MS² LacNAc-to-Neu5Ac oxonium-ion intensity ratio (L/N) (page 9321, Fig. 1C, 1D);
CF-normalized ratios (Ln/Nn) used to distinguish glycopeptide isomers quantitatively (page 9321, left column);
Measured numerical Ln/Nn ratios for each glycopeptide isomer in Figures 2B and 3D–F (pages 9322–9323);
Pett explicitly describes “threshold values” and “ratio differences” between α2,3 and α2,6 isomers (page 9322, par 1-2).
These quantitative intensity ratios are directly analogous to the claimed “relative values of intensities of the plurality of oxonium ions” and are used for isomer characterization. Pett therefore teaches calculating ratios of oxonium-ion intensities, even though the article describes the use as “differentiation.” Quantitative differentiation is still quantitative analysis.
Pett also fairly suggests that sialic acids can be modified differently, in order to generate a substantial mass difference (More recent strategies utilize derivatization steps to form esters/amides of a2,6-linked sialic acids, while a2,3-linked sialic acids form lactones, which generate a substantial mass difference.[7]” (page 9320, par 2). It would have been obvious to one of ordinary skill in the art to perform a linkage-specific modification on the plurality of sialic acids included in the glycan to classify the plurality of sialic acids into at least a first group and a second group depending on linkage types thereof, wherein the first group is modified into a first modified form having a first mass and the second group is modified into a second modified form having a second mass different from the first mass as suggested by Pett, in order to obtain differential mass of ions of linkage type sialic acid for easier analysis.
The court has ruled that a reference must be considered for all that it teaches, and not limited to its preferred embodiments. Applied Materials, 692 F.3d at 1298; Merck, 874 F.2d at 807. Thus, Pett’s discussion of known prior approaches — including derivatization-based differentiation of α2,3- and α2,6-linked sialic acids — is properly considered part of the prior art and supports that detecting diagnostic ions from differently modified sialic acids and comparing their relative intensities would have been obvious to a POSITA.
Regarding claim 2, Pett fairly suggests that wherein the plurality of sialic acids are amide-modified (page 9320, par 2).
Regarding claim 3, Pett teaches that wherein the first mass spectrometry is performed by tandem mass spectrometry (HCD-MS2) in two or more stages (page 9321, par 0).
Regarding claim 5, Pett fairly suggests that wherein a2,3-sialic acid, a2,8-sialic acid or a2,9-sialic acid, and a2,6-sialic acid are each modified differently (page 9320, par 2).
Regarding claim 7, Pett teaches that the mass spectrometry method comprising:
performing chromatography of the sample before the first mass spectrometry (C18 nano-LC-MS) (page 9321, par 0).
Regarding claim 8, Pett teaches that the mass spectrometry method comprising:
outputting an extracted ion chromatogram including a peak corresponding to at least one of the plurality of oxonium ions (Fig. 3, page 9322, par 2).
Regarding claim 9, Pett teaches that the mass spectrometry method comprising:
performing mass separation of ions generated by ionization of the sample based on scanned m/z, performing dissociation of the mass-separated ions, and performing second mass spectrometry for detecting oxonium ions from the ions generated by the dissociation (Fig. 1-3); and
obtaining at least one of a time during which a molecule containing a glycan from which the detected oxonium ion is derived is eluted in the chromatography and a mass of the molecule, based on a result of the second mass spectrometry (Fig. 3).
Regarding claim 10, Pett discloses a mass spectrometry apparatus comprising:
a measurement unit configured to generate a plurality of oxonium ions by ionizing a glycan having a plurality of sialic acids each in a linkage type-specific manner and dissociating the ionized glycan under the same dissociation condition, wherein the plurality of oxonium ions include a first oxonium ion derived from a first form having a first mass and a second oxonium ion derived from a second form having a second mass different from the first mass, and a mass of the first oxonium ion is different from a mass of the second oxomum ion (page 9321, par 0);
a data acquisition portion configured to acquire data obtained by detecting, in a first mass spectrometry intensities of the first oxonium ion and the second oxonium ion included in the plurality of oxonium ions (page 9321, par 0); and
a calculation portion configured to calculate relative values of intensities of the detected first oxonium ion and second oxonium ion based on the data (page 9321, par 0), and calculate a ratio of a number of sialic acids in the first form corresponding to the first oxonium ion and a number of sialic acids in the second form corresponding to the second oxonium ion in the glycan based on the relative values (Fig. 1, page 9321, par 0).
Pett repeatedly teaches quantitative or semi-quantitative calculations of oxonium-ion intensity ratios, including:
MS² LacNAc-to-Neu5Ac oxonium-ion intensity ratio (L/N) (page 9321, Fig. 1C, 1D);
CF-normalized ratios (Ln/Nn) used to distinguish glycopeptide isomers quantitatively (page 9321, left column);
Measured numerical Ln/Nn ratios for each glycopeptide isomer in Figures 2B and 3D–F (pages 9322–9323);
Pett explicitly describes “threshold values” and “ratio differences” between α2,3 and α2,6 isomers (page 9322, par 1-2).
These quantitative intensity ratios are directly analogous to the claimed “relative values of intensities of the plurality of oxonium ions” and are used for isomer characterization. Pett therefore teaches calculating ratios of oxonium-ion intensities, even though the article describes the use as “differentiation.” Quantitative differentiation is still quantitative analysis.
Pett also fairly suggests that sialic acids can be modified in a linkage type-specific manner, in order to generate a substantial mass difference (More recent strategies utilize derivatization steps to form esters/amides of a2,6-linked sialic acids, while a2,3-linked sialic acids form lactones, which generate a substantial mass difference.[7]” (page 9320, par 2). It would have been obvious to one of ordinary skill in the art to modify a2,6-linked sialic acids and a2,3-linked sialic acids in a linkage type-specific manner, in order to obtain differential mass of ions of linkage type sialic acid for easier analysis.
Regarding claim 11, Pett discloses a non-transitory computer readable medium containing a program for making a processor perform
a generating process of generating a plurality of oxonium ions by ionizing a glycan having a plurality of sialic acids each modified in a linkage type-specific manner and dissociating the ionized glycan under the same dissociation condition, wherein the plurality of oxonium ions include a first oxonium ion derived from a first modified form having a first mass and a second oxonium ion derived from a second modified form having a second mass different from the first mass, and a mass of the first oxonium ion is different from a mass of the second oxomum ion (page 9321, par 0);
a data acquisition process of acquiring data obtained by detecting intensities of the first oxonium ion and the second oxonium ion included in the plurality of oxonium ions generated in the generating process (Fig. 1B, page 9321, par 0); and
a calculation process of calculating relative values of intensities of detected first oxonium ion and second oxonium ion based on the data, and calculating a ratio of a number of sialic acids in the first form corresponding to the first oxonium ion and a number of sialic acids in the second form corresponding to the second oxonium ion in the glycan based on the relative values (Fig. 1C, 1D, page 9321, par 0).
Pett also fairly suggests that sialic acids can be modified in a linkage type-specific manner, in order to generate a substantial mass difference (More recent strategies utilize derivatization steps to form esters/amides of a2,6-linked sialic acids, while a2,3-linked sialic acids form lactones, which generate a substantial mass difference.[7]” (page 9320, par 2). It would have been obvious to one of ordinary skill in the art to modify a2,6-linked sialic acids and a2,3-linked sialic acids in a linkage type-specific manner, in order to obtain differential mass of ions of linkage type sialic acid for easier analysis.
Regarding claim 13, Pett teaches that the mass spectrometry method further comprising:
estimating a structure of the glycan based on the ratio (Fig. 1C, 1D, page 9321, par 0).
Regarding claim 14, Pett discloses that wherein the calculation portion is further configured to estimate a structure of the glycan based on the ratio (Fig. 1C, 1D, page 9321, par 0).
Regarding claim 15, Pett discloses that wherein the calculation process further includes estimating a structure of the glycan based on the ratio (Fig. 1C, 1D, page 9321, par 0).
Response to Arguments
Applicant's arguments filed 03/20/2026 have been fully considered but they are not persuasive.
1. The amended “ratio of a number of sialic acids” does not patentably distinguish over Pett
Amended claim 1 recites, inter alia, calculating:
“a ratio of a number of sialic acids modified into the first modified form … and a number of sialic acids modified into the second modified form … based on the relative values” .
Applicant argues that this limitation requires determining an actual numerical or molar proportion of sialic acids within a glycan and is not met by Pett’s normalized intensity ratios.
This argument is not persuasive.
Under the broadest reasonable interpretation (BRI), the claimed “ratio of a number of sialic acids … based on the relative values” encompasses determining a relative proportion or abundance inferred from measured signal intensities. The claim does not recite:
any absolute counting method,
any calibration standard,
any requirement for exact stoichiometric quantification, or
any specific mathematical transformation beyond being “based on” relative intensity values.
Accordingly, the claimed “ratio of a number” reasonably reads on Pett’s use of quantitative intensity ratios that correlate signal intensity with relative abundance of linkage types.
2. Pett’s intensity-ratio analysis reasonably corresponds to relative compositional ratios
Applicant argues that Pett is limited to qualitative assignment and does not calculate the number of α2,3 vs. α2,6 sialic acids. This argument is not persuasive.
Pett explicitly teaches:
measuring oxonium-ion intensities,
calculating ratios of those intensities (e.g., L/N, Ln/Nn), and
correlating those ratios with linkage-type composition.
Even if Pett describes the use as “assignment” or “diagnostic,” the analysis is inherently quantitative, as it relies on measured signal intensities and defined ratio values. A ratio that correlates with the presence and relative abundance of linkage types necessarily reflects the relative number (i.e., proportion) of those species in the sample.
The claim does not require determining an exact integer count of sialic acids per molecule. Rather, it requires calculating a ratio “based on” relative intensity values, which Pett expressly performs.
3. The “qualitative vs. quantitative” distinction is not commensurate with the claim scope
Applicant asserts that Pett performs only qualitative, trend-based analysis across varying collision energies, whereas the claimed invention provides quantitative compositional analysis under a single condition.
This argument is not persuasive for at least the following reasons:
First, Pett’s analysis is not purely qualitative. Pett provides measured numerical ratios, normalized ratios, and threshold values, which are inherently quantitative.
Second, the claim does not require:
a “single dissociation condition” yielding a specific technical advantage,
any exclusion of multi-condition analysis, or
any defined accuracy or precision of the calculated ratio.
Third, even if Pett evaluates trends across conditions, selecting a particular condition and using the resulting intensity ratios for compositional estimation would have been an obvious matter of routine optimization for a POSITA.
Thus, Applicant’s asserted distinction is not commensurate with the scope of the claims.
4. The Examiner’s rationale is supported and does not rely on hindsight
Applicant contends that the rejection relies on “conclusory statements” and improper hindsight. This argument is not persuasive.
The rejection is based on the following articulated reasoning:
Pett teaches that different sialic acid linkage types produce distinguishable oxonium-ion signals.
Pett further teaches calculating intensity ratios of these ions and correlating them with linkage-type composition.
It is a well-established principle in mass spectrometry that signal intensity is proportional to analyte abundance, and thus ratios of intensities are used to estimate relative quantities.
In view of these teachings, it would have been obvious to a POSITA to use Pett’s intensity-ratio analysis to determine the relative proportion (i.e., ratio of number) of differently modified sialic acids in a glycan.
This reasoning is grounded in Pett’s express disclosures and general knowledge in the art, not Applicant’s disclosure.
5. Linkage-specific modification remains obvious in view of Pett
Although not the primary focus of the current arguments, the claim continues to recite linkage-specific modification.
As previously stated, Pett explicitly acknowledges known derivatization strategies that modify α2,3- and α2,6-linked sialic acids differently, producing distinguishable masses and fragment ions. These teachings render the claimed modification step obvious.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to XIAOYUN R XU, Ph. D. whose telephone number is (571)270-5560. The examiner can normally be reached M-F 8am-5pm.
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/XIAOYUN R XU, Ph.D./ Primary Examiner, Art Unit 1797
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