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 Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-4 and 11 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by US 2013/0206979 A1 [Bonner]
Regarding Claim 1:
Bonner discloses a mass spectrometer (Figs. 2, 4), comprising:
a first mass filter (paras 93-94) for receiving a plurality of precursor ions and having a transmission bandwidth configured to allow transmission of ions having m/z ratios within a desired range (Fig. 2, Fig. 5 (510), paras 54-57 all discuss precursor scans across m/z ranges with the above features);
a second mass filter disposed downstream of said first mass filter (Fig. 4 (410), paras 93-94) for selecting, from among ions transmitted by the first mass filter, ions having a target m/z ratio (Fig. 5 (510), para 93) within a transmission window thereof for mass analysis (Fig. 2, the transmission window appears to be an extensive range as fragment ions are detected throughout the m/z range); and
a controller coupled (Fig. 1) to said first mass filter for setting the transmission bandwidth of said first mass filter so as to encompass at least two m/z ratios such that at least one of said m/z ratios is within the transmission window of said second mass filter (paras 35-39),
wherein the controller is configured to change the transmission bandwidth of the first mass filter over time such that any two consecutive transmission bandwidths of said first mass filter have at least one m/z ratio in common (para 54).
Regarding Claim 2:
Bonner discloses the mass spectrometer of claim 1, wherein said controller is coupled to said second mass filter for moving said transmission window of said second mass filter for selecting a different target m/z ratio (para 114 -the product ion transmission window is scanned so as to allow detection of all ions through the second filter. If it weren’t scanned, then resolved detection of m/z would not be possible.).
Regarding Claim 3:
Bonner discloses the mass spectrometer of claim 2, wherein said controller is configured to correlate time-variation of the transmission bandwidth of said first mass filter with time variation of said transmission window of said second mass filter so as to allow mass analysis of ions having different m/z ratios transmitted through said first mass filter by said second mass filter as the transmission bandwidth of said first mass filter is shifted over time (as described in paras 53-57, 82, 94).
Regarding Claim 4:
Bonner discloses the mass spectrometer of claim 3, wherein said controller is configured to set the ion transmission bandwidth of said first mass filter to an initial ion transmission bandwidth and to set the ion transmission window of said second mass filter so as to allow passage of ions having an m/z ratio encompassed by said initial bandwidth of said first mass filter. Para 93 – the ms/ms detects all sample product ion spectra for each window, which would include the ions noted above.
Regarding Claim 11:
Bonner discloses the mass spectrometer of claim 1, further comprising an ion source positioned upstream of said first mass filter for generating said plurality of precursor ions. In that first filter of the mass spectrometer of Bonner filters ions, it inherently has an upstream ion source. Further, Fig. 4 demonstrates a typical MS system with what one of ordinary skill in the art would instantly recognize as a diagram drawing on a generic ion source preceding a quadrupole.
Claim Rejections - 35 USC § 103
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 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.
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 5-6, 9-10, 14, 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Bonner in view of US 9,911,585 [Zabrouskov].
Regarding Claim 5:
Bonner discloses the mass spectrometer of claim 1, but fails to teach that said controller is configured to adjust the transmission window of said second mass filter to capture a next m/z ratio of interest and to shift the ion transmission bandwidth of said first mass filter to cover said next m/z ratio and another m/z ratio of interest.
Zabrouskov teaches another MS/MS technique (abstract) comprising two filters (11:66-12:53 wherein a controller is configured to adjust the transmission window of said second mass filter to capture a next m/z ratio of interest and to shift the ion transmission bandwidth of said first mass filter to cover said next m/z ratio and another m/z ratio of interest (see Fig. 2a, wherein changes to transmission windows of the second filter (44) are timed to correspond to changes in window of the first filters (42a-d, 46a-d).
It would have been obvious to one of ordinary skill in the art before the effective time of filing to use the above noted MS2 scanning arrangement of Zabrouskov in Bonner. One would have been motivated to do so in order to ensure product ion isolation corresponding to the precursor windows. Zabrouskov 13:35-49.
Regarding Claim 6:
Bonner discloses the mass spectrometer of claim 2, but fails to teach that said controller is further configured to adjust the transmission window of said second mass filter and shift the transmission bandwidth of said first mass filter substantially concurrently.
Zabrouskov teaches another MS/MS technique (abstract) comprising two filters (11:66-12:53) wherein a controller is configured to substantially concurrently: 1) adjust the transmission window of said second mass filter to capture a next m/z ratio of interest; and 2) shift the ion transmission bandwidth of said first mass filter to cover said next m/z ratio and another m/z ratio of interest (see Fig. 2a, wherein changes to transmission windows of the second filter (44) are timed to correspond to changes in window of the first filters (42a-d, 46a-d).
It would have been obvious to one of ordinary skill in the art before the effective time of filing to use the above noted MS2 scanning arrangement of Zabrouskov in Bonner. One would have been motivated to do so in order to ensure product ion isolation corresponding to the precursor windows. Zabrouskov 13:35-49.
Regarding Claim 9:
Bonner discloses the mass spectrometer of claim 2, but fails to teach that said controller is configured to set the transmission bandwidth of said first mass filter to allow transmission of ions having three or more m/z ratios.
Zabrouskov teaches another MS/MS technique (abstract) comprising two filters (11:66-12:53) wherein a controller is configured the transmission bandwidth of said first mass filter to allow transmission of ions having three or more m/z ratios. Fig. 2a (42a-d, 46a-d).
It would have been obvious to one of ordinary skill in the art before the effective time of filing to use the above noted MS2 scanning arrangement of Zabrouskov in Bonner. One would have been motivated to do so in order to ensure product ion isolation corresponding to the precursor windows. Zabrouskov 13:35-49.
Regarding Claim 10:
Bonner discloses the mass spectrometer of claim 1, but fails to teach that the transmission bandwidth of any of the first mass filter and the second mass filter is less than about 2000 Da.
Zabrouskov teaches another MS/MS technique (abstract) comprising two filters (11:66-12:53) wherein a transmission bandwidth of any of the first mass filter and the second mass filter is less than about 2000 Da. See Fig. 2a (42a-d, 46a-d).
It would have been obvious to one of ordinary skill in the art before the effective time of filing to use the above noted MS2 scanning arrangement of Zabrouskov in Bonner. One would have been motivated to do so in order to ensure product ion isolation corresponding to the precursor windows. Zabrouskov 13:35-49.
Regarding Claim 14:
Bonner discloses the mass spectrometer of claim 1, but fails to teach that said transmission bandwidth of the first mass filter has an m/z width greater than an m/z width of the transmission bandwidth of the second mass filter.
Zabrouskov teaches another MS/MS technique (abstract) comprising two filters (11:66-12:53) wherein transmission bandwidth of the first mass filter has an m/z width greater than an m/z width of the transmission bandwidth of the second mass filter. See Fig. 2a (42a-d, 46a-d) are the first filter’s windows and they are clearly greater in m/z width than the second filter’s windows (44).
It would have been obvious to one of ordinary skill in the art before the effective time of filing to use the above noted MS2 scanning arrangement of Zabrouskov in Bonner. One would have been motivated to do so in order to ensure product ion isolation corresponding to the precursor window. Zabrouskov 13:35-49.
Regarding Claim 18:
Bonner discloses a system for performing a data-independent acquisition (DIA) method for mass spectrometry (Fig. 2, para 39), comprising:
a first mass filter (paras 93-94) for receiving a plurality of precursor ions (Fig. 5 (510), paras 54-57 all discuss precursor scans with the above features);
a second mass filter disposed downstream of said first mass filter (Fig. 4 (410), paras 93-94) for receiving ions exiting said first mass filter (Fig. 5 (510), para 93); and
a controller (Fig. 1) operably coupled to said first mass filter and said second mass filter to configure the second mass filter to provide a plurality of ion selection windows over a DIA mass analysis cycle such that said mass selection windows collectively span a precursor ion mass range associated with the DIA analysis (para 39).
However, Bonner fails to teach that said controller further configures the first mass filter to provide a plurality of ion transmission bandwidths such that each of said ion transmission bandwidths is configured to prefilter the precursor ions for at least one respective one of said ion selection windows of the second mass filter such that each of the ion transmission bandwidths of the first mass filter has an m/z width greater than an m/z width of said one respective ion selection window of the second mass filter.
Zabrouskov teaches another MS/MS technique (abstract) comprising two filters (11:66-12:53) wherein a controller configures the first mass filter to provide a plurality of ion transmission bandwidths such that each of said ion transmission bandwidths is configured to prefilter the precursor ions (Fig. 2a (42a-d, 46a-d)) for at least one respective one of said ion selection windows of the second mass filter (Fig. 2a (44)) such that each of the ion transmission bandwidths of the first mass filter has an m/z width greater than an m/z width of said one respective ion selection window of the second mass filter (see Fig. 2a, wherein changes to transmission windows of the second filter (44) are timed to correspond to changes in window of the first filters (42a-d, 46a-d).
It would have been obvious to one of ordinary skill in the art before the effective time of filing to use the above noted MS2 scanning arrangement of Zabrouskov in Bonner. One would have been motivated to do so in order to ensure product ion isolation corresponding to the precursor windows. Zabrouskov 13:35-49.
Regarding Claim 19:
The modified invention of claim 18 teaches the system of claim 18, wherein at least one of said ion transmission bandwidths of the first mass filter (Zabrouskov Fig. 2a (42a)) has a lower low m/z cutoff and a higher high m/z cutoff than a respective low m/z cutoff and high m/z cutoff of said at least one respective ion selection window of the second mass filter (Zabrouskov Fig. 2a corresponding window (44) in the middle of the (42a) scan region).
Regarding Claim 20:
The modified invention of claim 18 teaches the system of claim 18, wherein said at least one respective ion selection window of said second mass filter comprises at least two consecutive ion selection windows. Zabrouskov Fig. 2a (44) demonstrates a long series of consecutive windows.
Claims 12-13 are rejected under 35 U.S.C. 103 as being unpatentable over Bonner in view of US 2013/0228682 A1 [Yasuda].
Regarding Claim 12:
Bonner discloses the mass spectrometer of claim 1, but fails to specify that any of said first mass filter and said second mass filter comprises at least one set of rods arranged in a multipole configuration to at least one of which one or more RF voltages can be applied for providing radial confinement of the ions and to at least one of which a DC resolving voltage can be applied for generating said transmission bandwidth thereof, and wherein said multipole configuration optionally comprises a quadrupole configuration.
Yasuda demonstrates a MS2 system similar to that claimed. Abstract. Yasuda teaches the well-known quadrupole filter (See e.g., Fig. 2a (5)), which has one set of rods arranged in a multipole configuration to at least one of which one or more RF voltages can be applied for providing radial confinement of the ions and to at least one of which a DC resolving voltage can be applied for generating said transmission bandwidth thereof, and wherein said multipole configuration optionally comprises a quadrupole configuration. Fig. 2a, para 53.
It would have been obvious to one of ordinary skill in the art before the effective time of filing to use the quadrupole of Yasuda as a mass filter in the system of Bonner. One would have been motivated to do so since such quadrupoles are well known for their effective mass filtering, which is precisely what Yasuda uses it for.
Regarding Claim 13:
The modified invention of claim 12 teaches the mass spectrometer of claim 12, wherein said at least one set of rods comprises multiple sets of rods positioned in series, wherein each rod set comprises a plurality of rods arranged in a multipole configuration. Yasuda Fig. 2a (6, 12) correspond to the claims first and second filters, and are both quadrupoles.
It would have been obvious to one of ordinary skill in the art before the effective time of filing to use the quadrupoles of Yasuda as the mass filters in the system of Bonner. One would have been motivated to do so since such quadrupoles are well known for their effective mass filtering, which is precisely what Yasuda uses it for.
Response to Arguments
Applicant's arguments filed 5/11/26 have been fully considered but they are not persuasive.
The indefiniteness rejection of claim 5 is withdrawn in light of applicant’s amendments.
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Applicant argues that “Bonner does not include a mass filter having an m/z selection window.” This is not persuasive. Bonner clearly has a mass filter. See Annotated Fig. 4. Further, in that the first mass analyzer passes ions to the fragmentation chamber, it must have a transmission window. As such, Bonner does teach both a mass filter, and further, an m/z selection window associated with said mass filter.
Applicant argues that “Bonner does not include any disclosure of a first or second mass filter.” This is not persuasive. As anyone of ordinary skill in the art would recognize, the mass analyzers of Bonner are mass filters. Although the applicant is allowed to be his own lexicographer, there exists no known authority allowing the applicant to provide special definitions for terminology in a prior art document. Here, Bonner, and indeed every other reference in the prior art, recognizes that mass analyzers selecting ions by m/z are mass filters. Thus, irrespective of applicant’s assertion to the contrary, Bonner clearly discloses the claimed first and second mass filters.
Applicant argues that the combination of Bonner and Zabrouskov fails to teach the invention of claim 18. This is not persuasive. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Here, Bonner teaches all of the claimed structure, and Zabrouskov teaches the particular ion scanning processes described in claim 18. One of ordinary skill in the art would easily implement the process of Zabrouskov in Bonner, thus reaching the claimed invention.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to WYATT A STOFFA whose telephone number is (571)270-1782. The examiner can normally be reached M-F 0700-1600 EST.
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WYATT STOFFA
Primary Examiner
Art Unit 2881
/WYATT A STOFFA/Primary Examiner, Art Unit 2881
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