DETAILED ACTION
Election/Restrictions
Applicant's election with traverse of Group I in the reply filed on 21 July 2026 is acknowledged. The traversal is on the ground(s) that there is substantial overlap between at least groups I and II. This has not been found persuasive. Specifically, groups II and II only require DDA as intended use. This suggests groups II and III are much broader in scope allowing for significant additional prior art references to be applied. Moreover, the special technical feature of groups II and III can be seen and either a method of mass spectrometry (group II) or a computer program product to perform a method of mass spectrometry (group III). This is separate from the express requirement of a tandem MS system that requires a DDA experiment.
Lastly the arguments suggest no search burden has been established. Search burden is not required in a lack of unity requirement1. However, as demonstrated below numerous issues under 112 are raised in the elected invention, which would at least raise the burden in determining compliance of non-elected groups under 35 USC 112. Moreover, there would be considerable search burden as the broader claims would allow for numerous additional pieces of prior art to be searched using more generic CPC symbols and keywords, not applicable to the elected invention. The requirement is still deemed proper and is therefore made FINAL.
Drawings
Figures 2-9 should be designated by a legend such as --Prior Art-- because only that which is old is illustrated. See MPEP § 608.02(g). Corrected drawings in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. The replacement sheet(s) should be labeled “Replacement Sheet” in the page header (as per 37 CFR 1.84(c)) so as not to obstruct any portion of the drawing figures. If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
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 1-13 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 is rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention. The claim recites an apparatus and a method of its use in the same claim. A single claim which claims both an apparatus and the method steps of using the apparatus is indefinite under 35 U.S.C. 112(b). MPEP 2173.05(p) (II); and See In re Katz Interactive Call Processing Patent Litigation, 639 F.3d 1303 (Fed. Cir. 2011). Specifically, the claim recites the steps of “creates precursor ion peak list of an DDA experiment by transmitting a mass range of precursor ions from the ion beam, measuring a precursor ion mass spectrum for the mass range using the mass analyzer, and selecting one or more peaks of the mass spectrum for the peak list, and that for each precursor ion peak of the peak list, selects a peak mass range including the precursor ion peak, scans a precursor ion mass selection window with a width smaller than the peak mass range across the peak mass range in overlapping steps using the mass filter, producing a series of overlapping precursor ion mass selection windows across the peak mass range, fragments each overlapping precursor ion mass selection window of the series using the fragmentation device, and mass analyzes product ions produced from each overlapping precursor ion mass selection window of the series using the mass analyzer, producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak..” These limitation is a step because it recites active steps (i.e. creates, measuring, selecting, selects, scans, producing, mass analyzing and producing) that may be initiated by a user. These limitation makes the claim indefinite because the step claim language makes it unclear whether infringement occurs when one creates the system that allows for the step, or whether infringement occurs when the step actually occurs.
Claim 1 is vague and indefinite for reciting “a tandem mass spectrometer that includes a mass filter device, a fragmentation device, and a mass analyzer, that creates precursor ion peak list of an DDA experiment by transmitting a mass range of precursor ions from the ion beam”, specifically it is not clear whether the tandem mass spectrometer or one of its components or some unclaimed component creates the claimed peak list. It appears from the instant specification that it is the tandem mass spectrometer 1030 (see figure 10) that creates the peak list ( see paragraph [0119] of the originally filed specification). For the purposes of examination, it will be interpreted as the tandem MS that generates the peak list. It is noted that, a tandem mass spectrometer merely generates a spectrum. A processor would be required to take the spectrum and generate the peak list, this is supported in paragraph [00136] of the originally filed specification, however this is not what is claimed. Therefore, for the purposes of examination, any spectrum generated by a tandem MS is sufficient to meet the claimed “ion peak list of a DDA experiment”.
Claim 1 recites the limitation “selecting one or more peaks of the mass spectrum for the peak list” is vague and indefinite because the claim does not provide a discernable boundary on what performs the function. The recited function does not follow from the structure recited in the claim i.e. the tandem MS, the mass filter device, the fragmentation device or the mass analyzer, so it is unclear whether the function requires some other structure or is simply a result of operating the tandem MS, the mass filter device, the fragmentation device or the mass analyzer in a certain manner. Thus, one of ordinary skill in the art would not be able to draw a clear boundary between what is and is not covered by the claim. See MPEP 2173.05(g) for more information.
Claim 1 is also vague and indefinite for reciting “selects a peak mass range including the precursor ion peak” for the same reasons discussed in the above paragraph.
Claim 2 is vague and indefinite for reciting an apparatus and method in the same claim and is rejected for the same reasons as claim 1 above.
Claim 2 recites the limitation “receives the plurality of product ion spectra, for at least one product ion of the plurality of product ion spectra, calculates a function that describes how an intensity of the at least one product ion from the plurality of product ion spectra varies with precursor ion mass as the precursor ion mass selection window is stepped across a peak mass range, and identifies a precursor ion of the at least one product ion from the function” is vague and indefinite because the claim does not provide a discernable boundary on what performs the function. The recited function does not follow from the structure recited in the claim i.e. the tandem MS, the mass filter device, the fragmentation device or the mass analyzer or the processor, so it is unclear whether the function requires some other structure or is simply a result of operating the tandem MS, the mass filter device, the fragmentation device or the mass analyzer or processor in a certain manner. Thus, one of ordinary skill in the art would not be able to draw a clear boundary between what is and is not covered by the claim. See MPEP 2173.05(g) for more information.
Claim 11similarly requires an apparatus and method in the same claim and is rejected on the same basis as claim 1 above.
Additionally, claim 11 does not tie the steps to the processor, therefore it is unclear as to what performs the claimed steps.
All dependent claims are indefinite by virtue of their dependencies on rejected claim 1.
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.
Claim(s) 1-3 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tate (US pgPub 2020/0013609).
Regarding claim 1, Tate teaches a system (SWATH in a tandem mass spectrometry method requires a system [0006]) for performing a data-dependent acquisition (DDA) mass spectrometry experiment (intended use), comprising:
an ion source device ([0006], inherent to ionization) that ionizes one or more compounds of a sample (inherent to an ion source in a mass spectrometer), producing an ion beam (inherent to an ion source in a mass spectrometer);
a tandem mass spectrometer ([0006]/[0039] teaches fragmentation thus a tandem MS) that includes a mass filter device ([0037] teaches filtering thus requiring a mass filter), a fragmentation device ([0039] teaches fragmentation, thus requiring a fragmentation device), and a mass analyzer (necessary to acquire spectra of figure 5), that creates precursor ion peak list of an DDA experiment (fig. 5, precursors 311-314, note DDA is not defined in the claim to be distinguished over a scanning SWATH, therefore since the product ions are correlated with peaks in a selected mass range, it is interpreted as a data dependent analysis experiment (i.e. correlation between product and precursor ions is dependent on the data collected from precursor ions). Additionally, since the instant specification broadly defines the tandem mass analyzer sufficient to create a ion peak list of a DDA experiment (see 112(b) rejection above) and Tate teaches a tandem MS to create a spectrum of precursor peaks, the tandem MS of Tate that generates precursor ions 311-314 is sufficient to be the claimed peak list of a DDA experiment) by transmitting a mass range of precursor ions from the ion beam ([0037]), measuring a precursor ion mass spectrum for the mass range using the mass analyzer (as evident by spectrum 510/310), and selecting one or more peaks of the mass spectrum for the peak list (311-314 are selected for the overlapping window 521 as evident by the scans), and that for each precursor ion peak of the peak list, selects a peak mass range including the precursor ion peak (mass range 100-120 covered by window 521 in scan 1 includes peak 311),
scans a precursor ion mass selection window (521 from first to second to third scan) with a width smaller than the peak mass range across the peak mass range (width of 521 is 100-120 in first scan, thus smaller than 100-300 in figure 5) in overlapping steps using the mass filter ([0038], wherein paragraph [0043] teaches precursor ion that is filtered by overlapping precursor ion mass selection windows thus requiring the filter), producing a series of overlapping precursor ion mass selection windows across the peak mass range (best seen in figure 6, 645 or 640), fragments each overlapping precursor ion mass selection window of the series using the fragmentation device ([0038] teaches overlap between windows and fragmentation of precursor ion mass selection window thus requiring the fragmentation device), and mass analyzes product ions produced from each overlapping precursor ion mass selection window of the series using the mass analyzer (inherent to produce product ion spectra 531-533), producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak (each of 531-533).
Regarding claim 2, Tate teaches a processor (fig. 10, 1040) in communication with the mass filter, fragmentation device, and the mass analyzer ([0120]) that for each precursor ion peak of the peak list (fig. 5, 311-314), receives the plurality of product ion spectra (531-533), for at least one product ion of the plurality of product ion spectra, calculates a function that describes how an intensity of the at least one product ion from the plurality of product ion spectra varies with precursor ion mass as the precursor ion mass selection window is stepped across a peak mass range ([0036] teaches intensities of the product ions produced by the overlapping windows can be plotted as a function of the precursor ion m/z value, see figure 6), and identifies a precursor ion of the at least one product ion from the function ([0049] teaches leading and trailing edges of QIT can be used to determine the corresponding precursor ion of the selected product ion).
Regarding claim 3, Tate teaches wherein the processor further, for each precursor ion peak of the peak list, combines groups of product ion spectra from the plurality of product ion spectra to produce the function that has a shape that is non-constant with precursor mass (combined in function as seen in figure 6, [0046], wherein the shape is non-constant because there is a step. Further see QIT in figure 7 that shows a clearly non-constant shape).
Claim(s) 1-10 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bloomfield et al. (US pgPub 2016/0217988).
Regarding claim 1, Bloomfield teaches a system (fig. 8) for performing a data-dependent acquisition (DDA) mass spectrometry experiment (fig. 4, wherein 460 is dependent upon data obtained in 410), comprising:
an ion source device (inherent to the device of figure 8) that ionizes one or more compounds of a sample (inherent to an ion source in a mass spectrometer), producing an ion beam (inherent to an ion source in a mass spectrometer);
a tandem mass spectrometer (800) that includes a mass filter device (810), a fragmentation device (820), and a mass analyzer (830), that creates precursor ion peak list of an DDA experiment (peak list 410) by transmitting a mass range of precursor ions from the ion beam (necessary to obtain 420 from 410, note the DDA experiment is interpreted in light of the specification which merely in paragraph [0119] “tandem mass spectrometer 1030 creates precursor ion peak list of a DDA experiment”. Therefore, it is interpreted that any collected precursor mass spectrum from a tandem MS is a ion peak list. Alternatively, since the product ions are correlated to the precursor ions, the scanning swath is interpreted as data dependent (i.e. product spectra correlation is dependent upon precursor spectrum)), measuring a precursor ion mass spectrum for the mass range using the mass analyzer (as evident by spectrum 410), and selecting one or more peaks of the mass spectrum for the peak list (420), and that for each precursor ion peak of the peak list, selects a peak mass range including the precursor ion peak (mass range of 410),
scans a precursor ion mass selection window (fig. 440) with a width smaller than the peak mass range across the peak mass range ([0059] overlapping rectangular precursor ion transmission windows 440 are stepped across the mass range (i.e. of the precursor ion range) producing a plurality of product ion spectrum, thus smaller than the peak mass range) in overlapping steps using the mass filter ([0075]), producing a series of overlapping precursor ion mass selection windows across the peak mass range (440), fragments each overlapping precursor ion mass selection window of the series using the fragmentation device ([0059] wherein to produce product ions requires the fragmentation device), and mass analyzes product ions produced from each overlapping precursor ion mass selection window of the series using the mass analyzer (inherent to the device of fig. 8), producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak ([0064] teaches summing product ion spectra thus producing a product ion spectra for each overlap 440).
Regarding claim 2, Bloomfield teaches a processor (fig. 8, 840) in communication with the mass filter, fragmentation device, and the mass analyzer ([0074]) that for each precursor ion peak of the peak list (fig. 4, 420), receives the plurality of product ion spectra ([0059]), for at least one product ion of the plurality of product ion spectra (420, see [0059]), calculates a function that describes how an intensity of the at least one product ion from the plurality of product ion spectra varies with precursor ion mass ([0059]) as the precursor ion mass selection window is stepped across a peak mass range ([0059]).
Regarding claim 3, Bloomfield teaches wherein the processor further, for each precursor ion peak of the peak list, combines groups of product ion spectra from the plurality of product ion spectra to produce the function that has a shape that is non-constant with precursor mass ([0060]).
Regarding claim 4, Bloomfield teaches wherein the shape comprises a triangle (as seen in figure 4).
Regarding claim 5, Bloomfield teaches wherein the processor identifies a precursor ion of the at least one product ion from the function by calculating a parameter of a shape of the function ([0058] “a shape that is non-constant with precursor mass is created to more accurately determine the precursor mass… the apex or center of gravity of the function for each product ion points to the precursor ion mass.”).
Regarding claim 6, Bloomfield teaches wherein the parameter comprises a center of gravity of the shape ([0058]).
Regarding claim 7, Bloomfield teaches wherein the parameter comprises an apex of the shape ([0058]).
Regarding claim 8, Bloomfield teaches wherein the mass filter comprises a quadrupole ([0073] teaches “the mass filter, the fragmentation device, and the mass analyzer are shown as different stages of a quadrupole”).
Regarding claim 9, Bloomfield teaches wherein the mass analyzer comprises a quadrupole ([0073] teaches “the mass filter, the fragmentation device, and the mass analyzer are shown as different stages of a quadrupole”).
Regarding claim 10, Bloomfield teaches wherein the mass analyzer comprises a time-of-flight (TOF) mass analyzer ([0073] teaches “one of ordinary skill in the art can appreciate that the mass filter, the fragmentation device, and the mass analyzer can include, but are not limited to, one or more of an ion trap, orbitrap, an ion mobility device, or a time-of-flight (TOF) device”).
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.
Claim(s) 1-10 are rejected under 35 U.S.C. 103 as being unpatentable over Tate (second interpretation) in view of Bloomfield.
Regarding claim 1, Tate teaches a system (fig. 10) for performing a data-dependent acquisition (DDA) mass spectrometry experiment ([0139]), comprising:
an ion source device (1010) that ionizes one or more compounds of a sample (inherent to an ion source in a mass spectrometer), producing an ion beam (inherent to an ion source in a mass spectrometer);
a tandem mass spectrometer (1000) that includes a mass filter device (1021), a fragmentation device (1022), and a mass analyzer (1030), that creates precursor ion peak list of an DDA experiment ([0139]) by transmitting a mass range of precursor ions from the ion beam ([0010] teaches survey scan to generate ion peak list in IDS, paragraph [0139], wherein the survey scan inherently comprises a mass range), measuring a precursor ion mass spectrum for the mass range using the mass analyzer (inherent to generate peak list), and selecting one or more peaks of the mass spectrum for the peak list ([0139]), and that for each precursor ion peak of the peak list, selects a peak mass range including the precursor ion peak ([0139]).
While Tate teaches selecting each precursor ion of the list of precursor ions with the mass filter, fragmenting the precursor ions and analyzing the product ions oof each precursor ion and an overlapping scanning SWATH method for precursor ions.
Tate fails to expressly suggest scans a precursor ion mass selection window with a width smaller than the peak mass range across the peak mass range in overlapping steps using the mass filter, producing a series of overlapping precursor ion mass selection windows across the peak mass range, fragments each overlapping precursor ion mass selection window of the series using the fragmentation device, and mass analyzes product ions produced from each overlapping precursor ion mass selection window of the series using the mass analyzer, producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak.
However, Bloomfield teaches scans a precursor ion mass selection window (fig. 4, 440) with a width smaller than the peak mass range across the peak mass range ([0059] overlapping rectangular precursor ion transmission windows 440 are stepped across the mass range (i.e. of the precursor ion range) producing a plurality of product ion spectrum ) in overlapping steps using the mass filter ([0075]), producing a series of overlapping precursor ion mass selection windows across the peak mass range (440), fragments each overlapping precursor ion mass selection window of the series using the fragmentation device ([0059] wherein to produce product ions requires the fragmentation device), and mass analyzes product ions produced from each overlapping precursor ion mass selection window of the series using the mass analyzer (inherent to the device of fig. 8), producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak ([0064] teaches summing product ion spectra thus producing a product ion spectra for each overlap 440).
Bloomfield modifies Tate by suggesting a scanning swath method applied to the peak list of Tate.
Since both inventions are directed towards scanning swath type methods and correlating the product ions with precursor ions, it would have been obvious to one of ordinary skill in the art to apply the scanning swath method of Bloomsfield to Tate because “the accuracy of the correlation is improved by combing product ion spectra from successive groups of the overlapping rectangular precursor ion transmission windows. Product ion spectra from successive groups are combined by successively summing the intensities of the product ions in the product ion spectra.” ([0057] of Bloomsfield)
Regarding claim 2, Tate in view of Bloomfield2 teaches a processor (fig. 8, 840) in communication with the mass filter, fragmentation device, and the mass analyzer ([0074]) that for each precursor ion peak of the peak list (fig. 4, 420), receives the plurality of product ion spectra ([0059]), for at least one product ion of the plurality of product ion spectra (420, see [0059]), calculates a function that describes how an intensity of the at least one product ion from the plurality of product ion spectra varies with precursor ion mass ([0059]) as the precursor ion mass selection window is stepped across a peak mass range ([0059]).
Regarding claim 3, Tate in view of Bloomfield teaches wherein the processor further, for each precursor ion peak of the peak list, combines groups of product ion spectra from the plurality of product ion spectra to produce the function that has a shape that is non-constant with precursor mass ([0060]).
Regarding claim 4, Tate in view of Bloomfield teaches wherein the shape comprises a triangle (as seen in figure 4).
Regarding claim 5, Tate in view of Bloomfield teaches wherein the processor identifies a precursor ion of the at least one product ion from the function by calculating a parameter of a shape of the function ([0058] “a shape that is non-constant with precursor mass is created to more accurately determine the precursor mass… the apex or center of gravity of the function for each product ion points to the precursor ion mass.”).
Regarding claim 6, Tate in view of Bloomfield teaches wherein the parameter comprises a center of gravity of the shape ([0058]).
Regarding claim 7, Tate in view of Bloomfield teaches wherein the parameter comprises an apex of the shape ([0058]).
Regarding claim 8, Tate in view of Bloomfield teaches wherein the mass filter comprises a quadrupole ([0073] teaches “the mass filter, the fragmentation device, and the mass analyzer are shown as different stages of a quadrupole”).
Regarding claim 9, Tate in view of Bloomfield teaches wherein the mass analyzer comprises a quadrupole ([0073] teaches “the mass filter, the fragmentation device, and the mass analyzer are shown as different stages of a quadrupole”).
Regarding claim 10, Tate in view of Bloomfield teaches wherein the mass analyzer comprises a time-of-flight (TOF) mass analyzer ([0073] teaches “one of ordinary skill in the art can appreciate that the mass filter, the fragmentation device, and the mass analyzer can include, but are not limited to, one or more of an ion trap, orbitrap, an ion mobility device, or a time-of-flight (TOF) device”).
Claim(s) 11-13 are rejected under 35 U.S.C. 103 as being unpatentable over Bloomfield in view of Ivosev et al. (US pgPub 2019/0228957) or alternatively Tate in view of Bloomfield and further in view of Ivosev.
Regarding claim 11, Bloomsfield or Tate in view of Bloomsfield teaches a processor in communication with the mass filter, fragmentation device, and the mass analyzer that for each precursor ion peak of the peak list, receives the plurality of product ion spectra (see above citations in claim 2).
Bloomsfield fails to disclose the mass analyzer selects at least one product ion from the plurality of product ion spectra that has an intensity above a predetermined threshold, for the selected product ion, retrieves the intensities of the selected product ion from the plurality of product ion spectra for at least one scan of the precursor ion mass selection window across the peak mass range, producing a trace that describes how the intensity of the selected product ion varies with precursor ion mass-to-charge ratio (m/z) as the precursor ion mass selection window is scanned across the peak mass range, creates a matrix multiplication equation that describes how one or more precursor ions corresponds to the trace for the selected product ion, wherein the matrix multiplication equation includes a known n x m mass filter matrix multiplied by an unknown precursor ion column matrix of length m that equates to a selected ion trace column matrix of length n, and solves the matrix multiplication equation for the unknown precursor ion column matrix using a numerical method, producing intensities for one or more precursor ion m/z values corresponding to the selected product ion.
However, Ivosev et al. teaches selects at least one product ion from the plurality of product ion spectra that has an intensity above a predetermined threshold ([0022]), for the selected product ion, retrieves the intensities of the selected product ion from the plurality of product ion spectra for at least one scan of the precursor ion mass selection window across the peak mass range ([0022]), producing a trace that describes how the intensity of the selected product ion varies with precursor ion mass-to-charge ratio (m/z) as the precursor ion mass selection window is scanned across the peak mass range ([0022]), creates a matrix multiplication equation that describes how one or more precursor ions corresponds to the trace for the selected product ion, wherein the matrix multiplication equation includes a known n x m mass filter matrix multiplied by an unknown precursor ion column matrix of length m that equates to a selected ion trace column matrix of length n, and solves the matrix multiplication equation for the unknown precursor ion column matrix using a numerical method, producing intensities for one or more precursor ion m/z values corresponding to the selected product ion ([0023]).
Ivosev modifies Tate by suggesting a process for thresholding and using a numerical method (i.e. NNLS, see paragraph [0094]) in the identification process of Tate.
Since both inventions are directed towards correlating product and precursor ions, it would have been obvious to one of ordinary skill in the art to apply the threshold and trace method of Ivosev to the device of Tate because applying the NNLS method to a matrix multiplication equation provides a significant improvement over current methods, particularly in the case of multiple interfering precursor ions ([0103]).
Regarding claim 12, Bloomsfield (or Tate in view of Bloomsfield) in view of Ivosev teaches wherein the numerical method comprises non-negative least squares (NNLS) (Ivosev, [0094]).
Regarding claim 13, Bloomsfield (or Tate in view of Bloomsfield) in view of Ivosev teaches wherein rows, n, of the mass filter matrix are the locations of the precursor ion mass selection window across the peak mass range, the columns, m, of the mass filter matrix are the precursor ion m/z values across the peak mass range, and the elements of the mass filter matrix represent the transmission or non-transmission by the precursor ion mass selection window (Ivosev, [0087]), wherein rows, m, of the unknown precursor ion column matrix correspond to the columns of the mass filter matrix and are the precursor ion m/z values across the peak mass range (Ivosev, [0088]), and the elements of the unknown precursor ion column matrix are the intensities of the precursor ions corresponding to the selected product ion ([0088]), and wherein the rows, n, of the trace column matrix correspond to the rows of the mass filter matrix and are the locations of the precursor ion mass selection window across the peak mass range, and the elements of the trace column matrix are the intensities of the selected product ion at locations of the precursor ion mass selection window across the peak mass range ([0089]).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
WO2020240506 or US20220189754 would anticipate claim 1 for the same reasons as Tate and Bloomfield. See figure 3 and associated text.
US9,991,585 teaches a system (fig. 4b) for performing a data-dependent acquisition (DDA) mass spectrometry experiment (title), comprising:
an ion source device (fig. 4b, 312) that ionizes one or more compounds of a sample (inherent to an ion source in a mass spectrometer), producing an ion beam (inherent to an ion source in a mass spectrometer);
a tandem mass spectrometer (fig. 4b, includes a CID 309 thus capable of tandem MS) that includes a mass filter device (333), a fragmentation device (309), and a mass analyzer (340), that creates precursor ion peak list of an DDA experiment (col. 11, lines 66-67 through col. 12, liens 1-3 teaches a survey scan prior to the occurrence of each series of consecutive isolation window) by transmitting a mass range of precursor ions from the ion beam (col. 13, lines 8-18 teach beginning the m/z range of first generation ion species to be investigated (mass analyzed), figure 2a shows precursor ion survey scans 42a-42d and 46a-46d), measuring a precursor ion mass spectrum for the mass range using the mass analyzer (inherent to a precursor ion scan), and selecting one or more peaks of the mass spectrum for the peak list (col. 12, lines 27-29 teaches each survey scan is provided so as to identify possible precursor ions of interest, identifying precursor ions is via peak, see also col. 13, lines 20-25 which teaches assessing various spectral ..),
scans a precursor ion mass selection window with a width smaller than the peak mass range across the peak mass range in overlapping steps using the mass filter (44), producing a series of overlapping precursor ion mass selection windows across the peak mass range, fragments each overlapping precursor ion mass selection window of the series using the fragmentation device (44), and mass analyzes product ions produced from each overlapping precursor ion mass selection window of the series using the mass analyzer, producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak (necessary for MS).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHAEL J LOGIE whose telephone number is (571)270-1616. The examiner can normally be reached M-F: 7:00AM-3:00PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert Kim can be reached at (571)272-2293. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MICHAEL J LOGIE/ Primary Examiner, Art Unit 2881
1 MPEP 1893.03(d) recites When making a lack of unity requirement, the examiner must (1) list the different groups of claims and (2) explain why each group lacks unity with each other group (i.e., why there is no single general inventive concept) specifically describing the unique special technical feature in each group
2 Note all claims 2-10 cite Bloomsfield
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