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 .
Information Disclosure Statement
The listing of references in the specification (e.g., page 14, U.S. Patent No. 6,630,662) is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Drawings
The drawings are objected to under 37 CFR 1.83(a). The drawings must show every feature of the invention specified in the claims. Therefore, the following must be shown or the feature(s) canceled from the claim(s):
Claim 8: obtaining a charge-reduced product ion mass spectra of each set of charge-reduced precursor ions prior to one or more portions of the respective set of charge-reduced precursor ions being selectively transmitted to the fragmentation device; identifying areas of the charge-reduced product ion mass spectra in which charge-reduced precursor ions are not present; and adjusting parameters for selectively transmitting the one or more portions of the set of charge-reduced precursor ions based on the identified areas
No new matter should be entered.
The use of the term Zeno®, which is a trade name or a mark used in commerce, has been noted in this application (FIG. 3). The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they do not include the following reference sign(s) mentioned in the description:
Q1;
602.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description:
FIGs. 2A, 3-6: IQ3
FIG. 5: 502
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). 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.
Specification
The use of the term SWATH®, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Applicant is advised that should claim 13 be found allowable, claim 14 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claim Rejections - 35 USC § 112
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.
Claim 8 is 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 claims 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.
An original claim may lack written description support when the claim defines the invention in functional language specifying a desired result but the disclosure fails to sufficiently identify how the function is performed or the result is achieved.
Claim 8 recites the achieved result “obtaining a charge-reduced product ion mass spectra of each set of charge-reduced precursor ions prior to one or more portions of the respective set of charge-reduced precursor ions being selectively transmitted to the fragmentation device” (emphasis added). Claim 8 further recites the functional limitations “identifying areas of the charge-reduced product ion mass spectra in which charge-reduced precursor ions are not present; and adjusting parameters for selectively transmitting the one or more portions of the set of charge-reduced precursor ions based on the identified areas.”
The specification as filed discloses that “mass spectra of each set of charge-reduced precursor ions are obtained prior to one or more portions of the respective set of charge-reduced precursor ions being selectively transmitted to the fragmentation device” (page 2, last paragraph, emphasis added). The specification further discloses that the phrase “product ions” refers to ions which have undergone fragmentation (page 10, paragraph beginning “The ions released…”). Therefore, the disclosure fails to sufficiently identify how a product ion mass spectrum is obtained for each set of precursor ions prior to fragmentation of the precursor ions; the product ions are obtained through fragmentation of the precursor ions, not prior to fragmentation of the precursor ions.
Similarly, the specification fails to describe how areas of the product ion mass spectra in which charge-reduced precursor ions are not present are identified. The only disclosure of an identification of such areas is that “area[s] of the mass spectra [of each set of charge-reduced precursor ions] in which the charge-reduced precursor ions are not present are identified” (page 2, last paragraph).
Furthermore, the specification fails to sufficiently identify how parameters for selectively transmitting portions of the precursor ions are adjusted, or how said adjustments are related to the identified areas. The specification discloses only that “parameters for selectively transmitting the one or more portions of the set of charge-reduced ions are adjusted based on the identified areas” (page 2, last paragraph). There is no disclosure of any actual relationship between the identified areas and the selective transmission parameters, nor is there any disclosure of what these parameters might be or how they are adjusted.
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.
Claim 8 is 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 8 recites the limitations “obtaining a charge-reduced product ion mass spectra of each set of charge-reduced precursor ions prior to one or more portions of the respective set of charge-reduced precursor ions being selectively transmitted to the fragmentation device; identifying areas of the charge-reduced product ion mas spectra” (emphasis added). As discussed supra, the specification discloses that the phrase “product ions” refers to ions which have undergone fragmentation (page 10, paragraph beginning “The ions released…”). Therefore, the claim is indefinite because it is unclear how a product ion mass spectrum is obtained prior to fragmentation of the precursor ions.
For the purpose of compact prosecution, the Examiner has interpreted “obtaining a charge-reduced product ion mass spectra of each set of charge-reduced precursor ions…identifying areas of the charge-reduced product ion mas spectra” to mean “obtaining a charge-reduced precursor ion mass spectra of each set of charge-reduced precursor ions…identifying areas of the charge-reduced precursor ion mas spectra”.
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.
(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, 4-5, 11-12, and 15 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by McGee et al. (U.S. Patent Application Publication No. 2017/0205424 A1), hereinafter McGee.
Regarding claim 1, McGee discloses a method for analyzing ions, comprising:
filtering a plurality of ions to sequentially transmit a plurality of precursor ion subsets (FIG. 3B, step 355; paragraph 0090: the precursor ion subsets are “the choice of m/z ranges of original ions that are isolated”) to a proton transfer reaction device (FIG. 3B, step 357);
for each precursor ion subset, performing a charge reduction reaction within the proton transfer reaction device to generate a set of charge-reduced precursor ions associated with one of the precursor ion subsets (FIG. 3B, step 357);
selectively transmitting one or more portions of the set of charge-reduced precursor ions associated with each respective precursor ion subset (FIG. 3B, step 359) to a fragmentation device (FIG. 3B, step 363);
fragmenting the charge-reduced precursor ions as each of the one or more portions are received by the fragmentation device to generate a set of fragment ions associated with each respective precursor ion subset (FIG. 3B, step 363); and
obtaining one or more mass spectra of the set of fragment ions (FIG. 3B, step 365), and
associating the one or more mass spectra of the set of fragment ions with each respective precursor ion subset (FIG. 3B, step 367; paragraph 0096).
Regarding claim 2, McGee as applied to claim 1 discloses the method of claim 1.
In addition, McGee discloses that a mass filter is configured to transmit the plurality of precursor ion subsets (paragraph 0071; mass filter transmits the precursor ion subsets through C-trap 210, which transfers ions to element 216) to the proton transfer reaction device (paragraph 0075: the proton reaction device 217b within element 216), wherein ions within each precursor ion subset are within a different m/z window established by the mass filter (paragraph 0071, lines 1-4).
Regarding claim 4, McGee as applied to claim 1 discloses the method of claim 1.
In addition, McGee discloses that the one or more portions of the set of charge-reduced precursor ions associated with each respective precursor ion subset are selectively transmitted to the fragmentation device based on their m/z (paragraph 0091 discloses that step 359 corresponds to step 314 in FIG. 3A; paragraph 0087, lines 2-3 discloses that selective transmission is performed according to m/z in step 314).
Regarding claim 5, McGee as applied to claim 4 discloses the method of claim 4.
In addition, McGee discloses that the charge-reduced precursor ions are mass selectively scanned from the proton transfer reaction device to the fragmentation device (FIG. 3B shows that step 359 immediately follows the proton transfer reaction in step 357; paragraph 0091 discloses that step 359 corresponds to step 314 in FIG. 3A; paragraph 0087, lines 2-3 discloses that selective transmission is performed according to m/z in step 314).
Regarding claim 11, McGee as applied to claim 1 discloses the method of claim 1.
In addition, McGee discloses that the fragmentation devices comprises a collision cell (FIG. 3B, step 363: the fragmentation is HCD, or Higher collisional Energy Dissociation).
Regarding claim 12, McGee as applied to claim 11 discloses the method of claim 11.
In addition, McGee discloses that fragmenting the charge-reduced precursor ions comprises performing collision induced dissociation in the collision cell (FIG. 3B, step 363: the fragmentation is HCD, or Higher collisional Energy Dissociation).
Regarding claim 15, McGee discloses a system for analyzing ions, comprising:
an ion filtering device (FIG. 2, element 208);
a proton reaction device (FIG. 2, element 217a);
a fragmentation device (FIG. 2, element 214);
a mass analyzer (FIG. 2, element 212); and
a controller comprising a processor (FIG. 1, element 160) and configured to:
cause the ion filtering device to sequentially transmit a plurality of precursor ion subsets (FIG. 3B, step 355; paragraph 0090: the precursor ion subsets are “the choice of m/z ranges of original ions that are isolated”) to a proton reaction device (FIG. 3B, step 357);
cause the proton reaction device to perform a charge reduction reaction so as to generate a set of charge-reduced precursor ions associated with each precursor ion subset (FIG. 3B, step 357);
cause one or more portions of the set of charge-reduced precursor ions associated with each respective precursor ion subset (FIG. 3B, step 359) to be selectively transmitted to the fragmentation device (FIG. 3B, step 363);
cause the fragmentation device to fragment the charge-reduced precursor ions as each of the one or more portions are received by the fragmentation device to generate a set of fragment ions associated with each respective precursor ion subset (FIG. 3B, step 363); and
cause the mass analyzer to obtain a mass spectra of the set of fragment ions (FIG. 3B, step 365) associated with each respective precursor ion subset (FIG. 3B, step 367; paragraph 0096).
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.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over McGee in view of Campbell et al. (U.S. Patent Application Publication No. 2014/0357502 A1), hereinafter Campbell.
Regarding claim 3, McGee as applied to claim 1 discloses the method of claim 1.
McGee fails to disclose that a mobility device is configured to transmit the plurality of precursor ion subsets to the proton transfer reaction device, wherein ions within each precursor ion subset are within a different ion mobility window established by the mobility device.
However, Campbell discloses that a mobility device (FIG. 11, mobility cell 210) is configured to transmit the plurality of precursor ion subsets (paragraph 0064, lines 7-12) to the charge reduction device (FIG. 11, charge reduction device 160), wherein ions within each precursor ion subset are within a different ion mobility window established by the mobility device (paragraph 0064, lines 7-8).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified McGee to include that a mobility device is configured to transmit the plurality of precursor ion subsets to the proton transfer reaction device, wherein ions within each precursor ion subset are within a different ion mobility window established by the mobility device, based on the teachings of Campbell that this improves the selectivity of the precursor ion subsets which are charge reduced (Campbell, paragraph 0078).
Claims 6-7, 9-10, and 13-14 are rejected under 35 U.S.C. 103 as being unpatentable over McGee in view of Brown et al. (U.S. Patent No. 8,283,626 B2), hereinafter Brown.
Regarding claim 6, McGee as applied to claim 4 discloses the method of claim 4.
McGee fails to disclose that the charge-reduced precursor ions are trapped in an ion trap disposed between the proton transfer reaction device and the fragmentation device prior to being selectively transmitted to the fragmentation device.
However, Brown discloses that the charge-reduced precursor ions are trapped in an ion trap (column 35, lines 55-57 discloses that element 26 may be operated as an ion guide; column 39, lines 63-66 discloses that ions may be trapped within the ion guide; therefore, element 26 in FIG. 10 is an ion trap) disposed between the proton transfer reaction device (FIG. 10, PTR device 25) and the fragmentation device prior to being selectively transmitted to the fragmentation device (FIG. 10, fragmentation device 27).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified McGee to include that the charge-reduced precursor ions are trapped in an ion trap disposed between the proton transfer reaction device and the fragmentation device prior to being selectively transmitted to the fragmentation device, based on the teachings of Brown that the ion trapping provides greater control over the degree of fragmentation (Brown, column 39, line 63 to column 40, line 15).
Regarding claim 7, McGee in view of Brown as applied to claim 6 discloses the method of claim 6.
In addition, Brown discloses that the charge-reduced precursor ions are ejected from the proton transfer reaction device into the ion trap upon being charge-reduced (FIG. 10 shows that ion trap 26 immediately follows proton transfer reaction device 25; therefore, the ions traveling from left to right as represented by the arrows in the Figure are sent into ion trap 26 upon being charge-reduced in PTR device 25).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified McGee in view of Brown to include that the charge-reduced precursor ions are ejected from the proton transfer reaction device into the ion trap upon being charge-reduced, based on the additional teachings of Brown that the ion trapping provides greater control over the degree of fragmentation in the subsequent fragmentation device following the ion trap (Brown, column 39, line 63 to column 40, line 15).
Regarding claim 9, McGee as applied to claim 1 discloses the method of claim 1.
McGee fails to disclose that the one or more portions of the set of charge-reduced precursor ions associated with each respective precursor ion subset are selectively transmitted to the fragmentation device based on their ion mobility.
However, Brown discloses that the one or more portions of the set of charge-reduced precursor ions associated with each respective precursor ion subset (column 40, line 65) are selectively transmitted to the fragmentation device (FIG. 10, fragmentation device 27) based on their ion mobility (column 40, lines 65-66).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified McGee to include that the one or more portions of the set of charge-reduced precursor ions associated with each respective precursor ion subset are selectively transmitted to the fragmentation device based on their ion mobility, based on the teachings of Brown that separating the precursor ions based on their ion mobility improves the sensitivity and duty cycle of the ion analysis (Brown, column 28, lines 46-58).
Regarding claim 10, McGee in view of Brown as applied to claim 9 discloses the method of claim 9.
In addition, Brown discloses that the charge-reduced precursor ions are trapped in an ion trap (column 35, lines 55-57 discloses that element 26 may be operated as an ion guide; column 39, lines 63-66 discloses that ions may be trapped within the ion guide; therefore, element 26 in FIG. 10 is an ion trap) disposed between the proton transfer reaction device (FIG. 10, PTR device 25) and the fragmentation device prior to being selectively transmitted to the fragmentation device (FIG. 10, fragmentation device 27).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified McGee in view of Brown to include that the charge-reduced precursor ions are trapped in an ion trap disposed between the proton transfer reaction device and the fragmentation device prior to being selectively transmitted to the fragmentation device, based on the additional teachings of Brown that the ion trapping provides greater control over the degree of fragmentation (Brown, column 39, line 63 to column 40, line 15).
Regarding claims 13 and 14, McGee as applied to claim 1 discloses the method of claim 1.
McGee fails to disclose that obtaining one or more mass spectra comprises using a time-of-flight mass analyzer.
However, Brown discloses that obtaining one or more mass spectra comprises using a time-of-flight mass analyzer (column 36, lines 14-17).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified McGee to include that obtaining one or more mass spectra comprises using a time-of-flight mass analyzer, based on the teachings of Brown that the output of the time-of-flight mass analyzer can be used to optimize the reaction conditions in the fragmentation device (Brown, column 36, lines 18-21).
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over McGee in view of Brown as applied to claim 6 above, and further in view of Bonner et al. (U.S. Patent No. 9,269,553 B2), hereinafter Bonner.
Regarding claim 8, McGee in view of Brown as applied to claim 6 discloses the method of claim 6, including generating the sets of charge-reduced precursor ions (McGee, FIG. 3B, step 357).
McGee in view of Brown fails to disclose obtaining a charge-reduced product ion mass spectra of each set of charge-reduced precursor ions prior to one or more portions of the respective set of charge-reduced precursor ions being selectively transmitted to the fragmentation device; identifying areas of the charge-reduced product ion mass spectra in which charge-reduced precursor ions are not present; and adjusting parameters for selectively transmitting the one or more portions of the set of charge-reduced precursor ions based on the identified areas.
However, Bonner discloses obtaining a precursor ion mass spectra of each set of precursor ions prior to one or more portions of the respective set of precursor ions being selectively transmitted to the fragmentation device (column 5, lines 12-17 discloses that windowed regions are identified from the mass spectra; column 5, lines 53-55 disclose “fragmentation of windowed regions”, i.e., the windowed regions are identified from the mass spectra prior to fragmentation);
identifying areas of the product ion mass spectra in which charge-reduced precursor ions are not present (column 5, lines 53-55, “windowed regions that do not appear to have a precursor ion present”); and
adjusting parameters for selectively transmitting the one or more portions of the set of charge-reduced precursor ions based on the identified areas (column 5, lines 48-57).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified McGee in view of Brown to include obtaining a charge-reduced product ion mass spectra of each set of charge-reduced precursor ions prior to one or more portions of the respective set of charge-reduced precursor ions being selectively transmitted to the fragmentation device; identifying areas of the charge-reduced product ion mass spectra in which charge-reduced precursor ions are not present; and adjusting parameters for selectively transmitting the one or more portions of the set of charge-reduced precursor ions based on the identified areas, based on the teachings of Bonner that this mitigates matrix suppression effects and other undesirable complications (Bonner, column 5, lines 48-57).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Frey et al. (U.S. Patent Application Publication No. 2007/0102634 A1), hereinafter Frey, teaches a system for analyzing ions, comprising: a proton reaction device; a fragmentation device; and a mass analyzer.
Bonner et al. (U.S. Patent Application Publication No. 2013/0206979 A1), hereinafter Bonner (2013), teaches a method for data independent acquisition mass spectrometry.
Chen et al. (U.S. Patent Application Publication No. 2011/0114835 A1), hereinafter Chen, teaches a mobility device configured to transmit a plurality of ions to a proton transfer reaction device.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALINA R KALISZEWSKI whose telephone number is (703)756-5581. The examiner can normally be reached Monday - Friday 8:00am - 5:00pm EST.
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/A.K./Examiner, Art Unit 2881
/WYATT A STOFFA/Primary Examiner, Art Unit 2881
