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 § 112(b)
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 1-20 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.
Claims 1-20 recite “matching a first peak of the reference compound to a first peak of the sample compound by defining a predetermined window of time after the sample compound was injected into the MS apparatus based on a mass-to-charge ratio of the first peak of the reference compound, the predetermined window of time encompassing a group of candidate peaks in the sample compound, and automatically selecting a peak from the group of candidate peak”. It is unclear how defining a time window relates to mapping or grouping of mass peaks, since any mass peak could theoretically occur at any time. It will be assumed for the purposes of examination that the ”pre-defined time window” is translated to a mass window based on the timing of different mass ejections. In that case
Claim Rejections - 35 USC § 103
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.
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) 1-20 is/are rejected under 35 U.S.C. 103 as obvious over ‘Waters Quattro micro API Mass Spectrometer Operator’s Guide’ (the guide).
Regarding claim 1, the guide discloses a method comprising:
receiving an analysis of a sample compound from a mass spectrometry (MS) apparatus, the analysis associated with a plurality of mass peaks (‘A mass spectrum of a reference compound (a calibration file) is acquired’ p. 5-2);
receiving a set of mass peaks of a reference compound (‘a table of the expected masses of the peaks in the reference compound which are stored as a reference file.’ P. 5-2);
mapping a subset of the plurality of mass peaks of the sample compound to a corresponding subset of peaks of the reference compound (‘A mass spectrum of a reference compound (a calibration file) is acquired and matched against a table of the expected masses of the peaks in the reference compound’ p. 5-2), by defining a predetermined window of time after the sample compound was injected into the MS apparatus based on a mass-to-charge ratio of the first peak of the reference compound, the predetermined window of time encompassing a group of candidate peaks in the sample compound, and automatically selecting a peak from the group of candidate peak (“The Peak Match parameters determine the limits within which the acquired data must lie for the software to recognise the calibration masses and result in a successful calibration. The default values are shown.” P. 5-3);
presenting a group of candidate peaks on a display (‘An expanded region can be displayed by clicking and dragging with the left mouse button.’ p. 5-21);
overriding the mapping by performing at least one of: matching the first peak of the reference compound to a second peak of the sample compound, or matching the first peak of the reference compound to no peak in the sample compound (‘If an incorrect peak has been matched in the calibration process, this peak can be excluded manually from within the on-screen calibration report. … If the true reference peak is present, this can be included in the calibration by the same procedure:’ P. 5-24);
and defining a scaling factor based on the mapping to define a calibrating adjustment, the scaling factor scaling the peaks as a function of at least one of a mass value, a charge value, an intensity value, or a time value (‘The mass differences between the reference peaks and calibration peaks are the calibration points. A calibration curve is fitted through the calibration points.’ p. 5-2).
The guide does disclose limiting the display of candidate peaks or overriding options to the specific group of candidate peaks in the predetermined window of time on the display or limiting. It would have been obvious to a person having ordinary skill in the art at the time the application was filed to modify the method to limit the display and editing of the peak matching to this predefined mass window to ensure the user does not degrade the quality of the calibration by adding clearly erroneous matches.
The guide does not disclose that the analysis received is from a mass spectrometry (MS) apparatus having a drift tube with an effective length of at least 20 cm that allows molecules to travel in a cyclic pattern and to be selectively ejected to a detector during each cycle. However, the form of the mass separator used to form the mass spectrum has does not appear to have any effect on the method, since only the detected masses are received and manipulated. Therefore, this is considered non-limiting.
Alternatively, mass spectrometry (MS) apparatuses having a drift tube with an effective length of at least 20 cm that allows molecules to travel in a cyclic pattern and to be selectively ejected to a detector during each cycle are known in the art, and it would have been obvious to a person having ordinary skill in the art at the time the application was filed to apply the method of the guide to a mass spectrum received from such an apparatus in order to calibrate the spectrum.
Regarding claim 2, the guide discloses the claimed invention except for the MS apparatus being an ion mobility apparatus. However, as discussed above, the form of the ion separator used to form the mass spectrum has does not appear to have any effect on the method. Therefore, this is considered non-limiting.
Alternatively, ion mobility mass spectrometers are well known in the art, and it would have been obvious to a person having ordinary skill in the art at the time the application was filed to apply the method to mass spectra obtained using such an apparatus because calibration will be required of all mass spectrometers, including ion mobility mass spectrometers.
Regarding claim 3, the guide discloses the method of claim 1, wherein the reference compound is a custom reference compound received from a user (‘Selecting the appropriate reference file for the reference sample to be used.’ p. 5-4).
Regarding claim 4, the guide discloses the method of claim 1, further comprising:
displaying the corresponding subset of peaks of the reference compound in a reference compound interface on a display (‘The calibration report contains four displays: … the reference spectrum’ p. 5-21);
receiving a selection of the first peak of the reference compound (‘An expanded region can be displayed by clicking and dragging with the left mouse button.’ p. 5-21); and
displaying, in a sample compound interface on the display, a plurality of peaks of the sample compound that fall within a predefined window of masses around the first peak of the reference compound, the plurality of peaks comprising the first peak of the sample compound and the second peak of the sample compound (‘An expanded region can be displayed by clicking and dragging with the left mouse button.’ p. 5-21).
Regarding claim 5, the guide discloses the method of claim 4, wherein overriding the mapping comprises receiving a selection of the second peak of the sample compound in the sample compound interface (‘If the true reference peak is present, this can be included in the calibration by the same procedure: Place the cursor over the required peak and click with the right mouse button. The peak is matched with the closest peak in the reference spectrum.’ p. 5-24).
Regarding claim 6, the guide discloses the method of claim 1, further comprising:
for each of the plurality of mass peaks of the sample compound mapped to corresponding peaks of the reference compound, calculating a residual value by calculating a difference between each mapped pair of peaks (‘The vertical distance of each calibration point from the curve is calculated. This distance represents the remaining (or residual) mass difference after calibration.’ p. 5-2);
displaying the residual values in a residual interface on the display (‘The calibration report contains four displays: … a plot of residual against mass’ p. 5-21);
receiving a selection of one of the residual values, the selected residual value corresponding to a pair of matched peaks from the reference compound and the sample compound (‘An expanded region can be displayed by clicking and dragging with the left mouse button. In this way, the less intense peaks in the spectrum can be examined to check that the correct peaks have been matched.’ p. 5-21);
removing the mapping between the pair of matched peaks (‘If an incorrect peak has been matched in the calibration process, this peak can be excluded manually from within the on-screen calibration report.’ p. 5-24); and
recalculating the calibrating adjustment (inherent, the calibrating adjustment is based on the matching and changing the matching will change the points being fitting to the curve).
Regarding claim 7, the guide discloses the method of claim 1, wherein the calibrating adjustment is based on a plurality of points fitted with a regression line, and further comprising:
displaying the plurality of points and the regression line in a model fit interface on the display (‘The calibration report contains four displays: … a plot of mass difference against mass (the calibration curve)’ p. 5-21);
receiving a selection of one of the points, the selected point corresponding to a pair of matched peaks from the reference compound and the sample compound (‘An expanded region can be displayed by clicking and dragging with the left mouse button.’ p. 5-21);
removing the mapping between the pair of matched peaks (‘If an incorrect peak has been matched in the calibration process, this peak can be excluded manually from within the on-screen calibration report. … If the true reference peak is present, this can be included in the calibration by the same procedure:’ p. 5-24); and
recalculating the calibrating adjustment with the selected point removed from the plurality of points (inherent, the calibrating adjustment is based on the matching and removing the matching will change the points being fitting to the curve).
Regarding claim 8, the guide discloses a non-transitory computer-readable storage medium, the computer-readable storage medium including instructions that when executed by a computer (‘The MassLynx™ software’ p. 1-3), cause the computer to:
receive an analysis of a sample compound from a mass spectrometry (MS) apparatus the analysis associated with a plurality of mass peaks (‘A mass spectrum of a reference compound (a calibration file) is acquired’ p. 5-2);
receive a set of mass peaks of a reference compound (‘a table of the expected masses of the peaks in the reference compound which are stored as a reference file.’ p. 5-2);
map a subset of the plurality of mass peaks of the sample compound to a corresponding subset of peaks of the reference compound, the mapping matching a first peak of the reference compound to a first peak of the sample compound (‘A mass spectrum of a reference compound (a calibration file) is acquired and matched against a table of the expected masses of the peaks in the reference compound’ p. 5-2) by defining a predetermined window of time after the sample compound was injected into the MS apparatus based on a mass-to-charge ratio of the first peak of the reference compound, the predetermined window of time encompassing a group of candidate peaks in the sample compound, and automatically selecting a peak from the group of candidate peak (“The Peak Match parameters determine the limits within which the acquired data must lie for the software to recognise the calibration masses and result in a successful calibration. The default values are shown.” P. 5-3);
present a group of candidate peaks on a display (‘An expanded region can be displayed by clicking and dragging with the left mouse button.’ p. 5-21);
override the mapping by performing at least one of: match the first peak of the reference compound to a second peak of the sample compound, or match the first peak of the reference compound to no peak in the sample compound (‘If an incorrect peak has been matched in the calibration process, this peak can be excluded manually from within the on-screen calibration report. … If the true reference peak is present, this can be included in the calibration by the same procedure:’ P. 5-24); and
define a scaling factor based on the mapping to define a calibrating adjustment, the scaling factor scaling the peaks as a function of at least one of a mass value, a charge value, an intensity value, or a time value (‘The mass differences between the reference peaks and calibration peaks are the calibration points. A calibration curve is fitted through the calibration points.’ p. 5-2).
The guide does disclose limiting the display of candidate peaks or overriding options to the specific group of candidate peaks in the predetermined window of time on the display or limiting. It would have been obvious to a person having ordinary skill in the art at the time the application was filed to modify the software to limit the display and editing of the peak matching to this predefined mass window to ensure the user does not degrade the quality of the calibration by adding clearly erroneous matches.
The guide does not disclose that the analysis received is from a mass spectrometry (MS) apparatus having a drift tube with an effective length of at least 20 cm that allows molecules to travel in a cyclic pattern and to be selectively ejected to a detector during each cycle. However, the form of the mass separator used to form the mass spectrum has does not appear to have any effect on the instructions, since only the detected masses are received and manipulated. Therefore, this is considered non-limiting.
Alternatively, mass spectrometry (MS) apparatuses having a drift tube with an effective length of at least 20 cm that allows molecules to travel in a cyclic pattern and to be selectively ejected to a detector during each cycle are known in the art, and it would have been obvious to a person having ordinary skill in the art at the time the application was filed to apply the method of the guide to a mass spectrum received from such an apparatus in order to calibrate the spectrum.
Regarding claims 9-14, see analysis of claims 2-7.
Regarding claim 15, the guide discloses a computing apparatus comprising:
a processor (‘host computer’); and
a memory storing instructions that (‘The MassLynx™ software’ p. 1-3), when executed by the processor, configure the apparatus to:
receive an analysis of a sample compound from a mass spectrometry (MS) apparatus the analysis associated with a plurality of mass peaks (‘A mass spectrum of a reference compound (a calibration file) is acquired’ p. 5-2);
receive a set of mass peaks of a reference compound (‘a table of the expected masses of the peaks in the reference compound which are stored as a reference file.’ p. 5-2);
map a subset of the plurality of mass peaks of the sample compound to a corresponding subset of peaks of the reference compound, the mapping matching a first peak of the reference compound to a first peak of the sample compound (‘A mass spectrum of a reference compound (a calibration file) is acquired and matched against a table of the expected masses of the peaks in the reference compound’ p. 5-2) by defining a predetermined window of time after the sample compound was injected into the MS apparatus based on a mass-to-charge ratio of the first peak of the reference compound, the predetermined window of time encompassing a group of candidate peaks in the sample compound, and automatically selecting a peak from the group of candidate peak (“The Peak Match parameters determine the limits within which the acquired data must lie for the software to recognise the calibration masses and result in a successful calibration. The default values are shown.” P. 5-3);
present a group of candidate peaks on a display (‘An expanded region can be displayed by clicking and dragging with the left mouse button.’ p. 5-21)
override the mapping by performing at least one of: match the first peak of the reference compound to a second peak of the sample compound, or match the first peak of the reference compound to no peak in the sample compound (‘If an incorrect peak has been matched in the calibration process, this peak can be excluded manually from within the on-screen calibration report. … If the true reference peak is present, this can be included in the calibration by the same procedure:’ P. 5-24); and
define a scaling factor based on the mapping to define a calibrating adjustment, the scaling factor scaling the peaks as a function of at least one of a mass value, a charge value, an intensity value, or a time value (‘The mass differences between the reference peaks and calibration peaks are the calibration points. A calibration curve is fitted through the calibration points.’ p. 5-2).
The guide does disclose limiting the display of candidate peaks or overriding options to the specific group of candidate peaks in the predetermined window of time on the display or limiting. It would have been obvious to a person having ordinary skill in the art at the time the application was filed to modify the software to limit the display and editing of the peak matching to this predefined mass window to ensure the user does not degrade the quality of the calibration by adding clearly erroneous matches.
The guide does not disclose that the analysis received is from a mass spectrometry (MS) apparatus having a drift tube with an effective length of at least 20 cm that allows molecules to travel in a cyclic pattern and to be selectively ejected to a detector during each cycle. However, the form of the mass separator used to form the mass spectrum has does not appear to have any effect on the instructions, since only the detected masses are received and manipulated. Therefore, this is considered non-limiting.
Alternatively, mass spectrometry (MS) apparatuses having a drift tube with an effective length of at least 20 cm that allows molecules to travel in a cyclic pattern and to be selectively ejected to a detector during each cycle are known in the art, and it would have been obvious to a person having ordinary skill in the art at the time the application was filed to apply the method of the guide to a mass spectrum received from such an apparatus in order to calibrate the spectrum.
Regarding claims 16-20, see analysis of claims 2 and 4-7.
Response to Arguments
Applicant’s arguments with respect to claim(s) have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIZA W OSENBAUGH-STEWART whose telephone number is (571)270-5782. The examiner can normally be reached 10am - 6pm Pacific Time M-F.
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.
/ELIZA W OSENBAUGH-STEWART/Primary Examiner, Art Unit 2881