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 .
Election/Restrictions
Applicant’s election without traverse of group I and species A in the reply filed on 4/9/26 is acknowledged.
Claims 7 and 19-24 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention/species, there being no allowable generic or linking claim.
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 1-6, 8-18, and 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.
Claim 1 recites, “having a relatively high transmission region and one or more relatively low transmission regions.” These regions are repeatedly referred to throughout the claims. Terms of degree will fail for indefiniteness unless they “provide objective boundaries for those of skill in the art” when read in light of the specification and the prosecution history. Interval Licensing LLC v. AOL, Inc., 766 F.3d 1364, 1370–71 (Fed. Cir. 2014), cert. denied, 136 S. Ct. 59 (2015). In the instant case, neither the disclosure nor the claims provides objective boundaries for distinguishing a relatively high transmission region from a relatively low transmission regions. As such, one of ordinary skill in the art cannot discern whether a given set of transmission regions infringes upon the claimed invention. Accordingly, the limitations at issue make the claims indefinite.
Claims 11 and 12 rely upon the widths of “relatively low transmission region. For the same reasons as noted with respect to the transmission regions of claim 1, these limitations at issue make the claims indefinite.
All of the claims, either directly or through their dependencies, recite determinations of ranges or overlaps of relatively high transmission region and relatively low transmission regions. Without clarity as to what these regions are, all such determination limitations are indefinite.
Claim Rejections - 35 USC § 102
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 1-6, 8-18, and 25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ludwig, Christina, et al. "Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial." Molecular systems biology 14.8 (2018): MSB178126 [hereinafter Ludwig].
Regarding Claim 1:
Ludwig discloses a method for acquiring mass spectral data of a sample across at least a portion of an m/z range, the m/z range comprising a plurality of sets of m/z sub-ranges, each set comprising one or more m/z sub-ranges (see Fig. 1), comprising:
determining a first set of m/z sub-ranges of the plurality of sets of m/z sub-ranges and determining a second set of m/z sub-ranges of the plurality of sets of m/z sub-ranges (the various MS2 ranges of Fig. 1b; alternatively, the MS1 windows of Fig. 5b), the first set comprising a first m/z sub-range and the second set comprising a second m/z sub-range (the first half of the MS2 ranges vs the second half of the MS2 ranges, as shown in Fig. 1b; alternatively, the MS1 windows of Fig. 5b);
mass filtering the sample to isolate ions in the first set of m/z sub-ranges using a first mass filter and performing mass analysis on the sample across the first set of m/z sub-ranges to obtain a first partial mass spectral data set (as shown in Fig. 1b; alternatively, as shown Fig. 5b),
the first mass filter having a first response profile corresponding to the first m/z sub-range, the first response profile having a relatively high transmission region and one or more relatively low transmission regions (as shown by the trapezoids in Fig. 4); and
mass filtering the sample to isolate ions in the second set of m/z sub-ranges using a second mass filter and performing mass analysis on the sample across the second set of m/z sub-ranges to obtain a second partial mass spectral data set (as shown in Fig. 1b, the second mass filter is the same quadrupole with different transmission characteristics; alternatively, as shown and described in Fig. 5b),
the second mass filter having a second response profile corresponding to the second m/z sub-range, the second response profile having a relatively high transmission region and one or more relatively low transmission regions (as shown by the trapezoids in Fig. 4);
wherein the step of determining the first and second sets of m/z sub-ranges comprises setting the first and second sets of m/z sub-ranges such that the relatively high transmission region of the first response profile at least partially overlaps the relatively high transmission region of the second response profile (pg 12-13 – Offset isolation windows intra-run; also as shown and described in Fig. 4D; alternatively, as shown and described in Fig. 5b)).
Regarding Claim 2:
Ludwig discloses the method of claim 1, wherein determining the first and second sets of m/z sub-ranges comprises:
determining whether the relatively high transmission region of the first response profile at least partially overlaps the relatively high transmission region of the second response profile (as can be seen in Fig. 4D, the high transmission areas of the windows are determined to overlap); and
based on determining that the relatively high transmission region of the first response profile does not at least partially overlap the relatively high transmission region of the second response profile, adjusting the first and/or second sets of m/z sub-ranges such that the relatively high transmission region of the first response profile at least partially overlaps the relatively high transmission region of the second response profile. Since the considition precedent does not occur, Ludwig anticipates the claim by describing the alternative.
Regarding Claim 3:
Ludwig discloses the method of claim 1, wherein:
the first set of m/z sub-ranges comprises a first plurality of m/z sub-ranges and the first mass filter has a plurality of response profiles each comprising, for each m/z sub-range of the first set: a relatively high transmission region; and one or more relatively low transmission regions (see trapezoids of Fig. 4);
the second set of m/z sub-ranges comprises a second plurality of m/z sub-ranges and the second mass filter has a plurality of response profiles each comprising, for each m/z sub-range of the second set: a relatively high transmission region; and one or more relatively low transmission regions (see trapezoids of Fig. 4);;and
the step of determining the first and second sets of m/z sub-ranges comprises setting the first and second sets of m/z sub-ranges such that: each relatively high transmission region of each response profile of the first mass filter at least partially overlaps a relatively high transmission region of a response profile of the second mass filter (as is shown and described in Fig. 4D).
Regarding Claim 4:
Ludwig discloses the method of claim 1, wherein each response profile has a relatively high transmission region between a plurality of relatively low transmission regions. As shown in Fig. 4B-D.
Regarding Claim 5:
Ludwig discloses the method of claim 1, wherein each response profile is substantially trapezoidal. As shown in Fig. 4B-D.
Regarding Claim 6:
Ludwig discloses the method of claim 1, wherein the first mass filter and the second mass filter are the same mass filter. As shown in Fig. 1 and described with respect to SWATH-MS in box 1.
Regarding Claim 8:
Ludwig discloses the method of claim 1, wherein the relatively high transmission region of the first response profile and/or the second response profile is a region having at least 90% transmission of ions, at least 95% transmission of ions or at least 99% transmission of ions. As shown in Fig. 4B-D.
Regarding Claim 9:
Ludwig discloses the method of claim 1, wherein determining the first and second sets of m/z sub-ranges comprises:
determining a first trapezoidal fit of the first response profile and/or a second trapezoidal fit of the second response profile based on mass spectral data obtained using the first mass filter and the second mass filter (pg 11 – Section : Should adjacent precursor isolation windows be overlapping? And Fig. 4B-D show obtaining said profiles); and
determining the relatively high transmission region of the first response profile and the relatively high transmission region of the second response profile based on the first and/or second trapezoidal fits (pg 11 – Section : Should adjacent precursor isolation windows be overlapping? describes the determination of high and low transmission regions. Fig. 4B-D demonstrate the regions.).
Regarding Claim 10:
Ludwig discloses the method of claim 1, wherein determining the first and second sets of m/z sub-ranges comprises determining a degree of overlap for the first and second response profiles based on a width of at least one of the first and/or the second response profiles. As shown in Fig. 4B-D and described on page 11– Section : Should adjacent precursor isolation windows be overlapping?.
Regarding Claim 11:
Ludwig discloses the method of claim 1, wherein determining the first and second sets of m/z sub-ranges comprises determining a degree of overlap for the first and second response profiles based on a width of a relatively low transmission region of at least one of the first and/or the second response profiles. As shown in Fig. 4B-D and described on page 11– Section : Should adjacent precursor isolation windows be overlapping?.
Regarding Claim 12:
Ludwig discloses the method of claim 1, wherein the relatively high transmission region of the first response profile overlaps the relatively high transmission region of the second response profile by an amount that is greater than: a width of a relatively low transmission region of the first response profile; and/or a width of a relatively low transmission region of the second response profile. As shown in Fig. 5B.
Regarding Claim 13:
Ludwig discloses the method of claim 1, wherein:
each set of m/z sub-ranges comprises a plurality of m/z sub-ranges and wherein each m/z sub-range in a given set of m/z sub-ranges at least partially overlaps an m/z sub-range of a different set of m/z sub-ranges. As shown in Figs. 1 and 4.
Regarding Claim 14:
Ludwig discloses the method of claim 1, further comprising performing mass analysis on one or more m/z sub-ranges of a respective set using different ion optics settings. Fig. 1, each sub-ranges is subject to mass analysis. Further, each sub-range is subject to different transmission characteristics, i.e., different ion optics settings.
Regarding Claim 15:
Ludwig discloses the method of claim 1, wherein each mass analysis is a MS1 mass analysis. As shown in Fig. 5b.
Regarding Claim 16:
Ludwig discloses the method of claim 1, wherein the m/z sub-ranges of each of the sets of m/z sub-ranges collectively span the m/z range. As shown in Figs. 1, 4.
Regarding Claim 17:
Ludwig discloses the method of claim 1, wherein each set of m/z sub-ranges comprises a plurality of m/z sub-ranges that are spaced apart. As shown in Figs. 1, 4.
Regarding Claim 18:
Ludwig discloses the method of claim 1, further comprising receiving the sample from a chromatograph and obtaining time-dependent mass spectral data for the sample. As described with respect to and in Fig. 6; Pg 8 – section Setting up liquid chromatography for SWTH-MS.
Regarding Claim 25:
Ludwig discloses a computer-readable medium having stored thereon processor-executable instructions for the method of claim 1. Pg 9 – Setting up the SWATH-MS data acquisition method. --indicates that SWATH-MS is operated at least in part by computer.
Conclusion
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WYATT STOFFA
Primary Examiner
Art Unit 2881
/WYATT A STOFFA/Primary Examiner, Art Unit 2881
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