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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 Objections
Claims 1-15 are objected to because of the following informalities: “a plurality of a measured image-charge/current signals” is grammatically unclear. Appropriate correction is required.
Claim 1 is objected to because of the following informalities: “…a given charge state (Q)” … “the charge state (Q)…”. Appropriate correction is required.
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 1-15 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 and 12 recite the limitation “the integer charge value (|Q^i|)”. There is no clear definition for (|Q^i|) and can be interpreted as ([Q]) and ([Qi]). For the purpose of a compact prosecution, we have interpreted the limitation, “(|Qi^)” to mean the integer charge value achieving the highest said score value, according to the specification (pg. 5).
Claim 2 recites the limitation "generating an integer charge value ([Q]) comprises generating a plurality of integer charge values ([Q])" in lines 2-3. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Specifically, representative Claim 1 recites:
“A method of processing data determined from an image- charge/current signal representative of ions of a given charge state (Q) undergoing oscillatory motion of a respective oscillation frequency (f) within an ion analyzer apparatus, the method comprising:
acquiring a data set comprising a measured signal frequency (fo) common to a plurality of a measured image-charge/current signals and a plurality of estimated ion charge values corresponding to respective amplitudes of each one of said plurality of measured image-charge/current signals;
generating an integer charge value ([Q]) corresponding to a said estimated ion charge value rounded to the nearest integer value; and,
(a) selecting said integer charge value ([Qi]) and therewith calculating a plurality of different candidate image-charge/current signal frequency values (f) according to said selected measured signal frequency (fo) and according to a corresponding one of one or more different candidate charge states of the ion and/or of ion isotope or isotopologue; then,
(b) comparing the calculated plurality of different candidate image- charge/current signal frequency values (f) to a plurality of different signal frequencies (f) of the measured image-charge/current signals and calculating a score value representing a degree of similarity therebetween according to the comparison;
determining the charge state (Q) of the ion undergoing oscillatory motion of said selected measured signal frequency (fo), to be equal to the integer charge value ([Q]) if said score value matches or exceeds a threshold score value.”
The claim limitations in the abstract idea have been highlighted in bold above; the remaining limitations are “additional element”.
Under the Step 1 of the eligibility analysis, we determine whether the claims are to a statutory category by considering whether the claimed subject matter falls within the four statutory categories of patentable subject matter identified by 35 U.S.C. 101: Process, machine, manufacture, or composition of matter. The above claim is considered to be in a statutory category (process).
Under the Step 2A, Prong One, we consider whether the claim recites a judicial exception (abstract idea). In the above claim, the highlighted portion constitutes an abstract idea because, under a broadest reasonable interpretation, it recites limitations that fall into/recite an abstract idea exceptions. Specifically, under the 2019 Revised Patent Subject matter Eligibility Guidance, it falls into the groupings of subject matter when recited as such in a claim limitation that covers mathematical concepts - mathematical relationships, mathematical formulas or equations, mathematical calculations and mental processes — concepts performed in the human mind including an observation, evaluation, judgement, and/or opinion.
For example, steps of “generating an integer charge value ([Q]) corresponding to a said estimated ion charge value rounded to the nearest integer value; and, (a) selecting said integer charge value ([Qi]) and therewith calculating a plurality of different candidate image-charge/current signal frequency values (f) according to said selected measured signal frequency (fo) and according to a corresponding one of one or more different candidate charge states of the ion and/or of ion isotope or isotopologue; then,(b) comparing the calculated plurality of different candidate image- charge/current signal frequency values (f) to a plurality of different signal frequencies (f) of the measured image-charge/current signals and calculating a score value representing a degree of similarity therebetween according to the comparison” are treated as belonging to mathematical process grouping while “determining the charge state (Q) of the ion undergoing oscillatory motion of said selected measured signal frequency (fo), to be equal to the integer charge value ([Q]) if said score value matches or exceeds a threshold score value” are treated as belonging to the mental process grouping. This mental step represents a process that, under its broadest reasonable interpretation, covers performance of the limitation in the mind. That is, nothing in the claim element precludes the step from practically being performed in the mind. In the context of this claim, it encompasses the user manually making a determination regarding score value matching or exceeding a threshold score value.
Similar limitations comprise the abstract ideas of Claim 11.
Next, under the Step 2A, Prong Two, we consider whether the claim that recites a judicial exception is integrated into a practical application.
In this step, we evaluate whether the claim recites additional elements that
integrate the exception into a practical application of that exception. This judicial exception is not integrated into a practical application because there is no improvement to another technology or technical field; improvements to the functioning of the computer itself; a particular machine; effecting a transformation or reduction of a particular article to a different state or thing. Examiner notes that since the claimed methods and system are not tied to a particular machine or apparatus, they do not represent an improvement to another technology or technical field. Similarly there are no other meaningful limitations linking the use to a particular technological environment. Finally, there is nothing in the claims that indicates an improvement to the functioning of the computer itself or transform a particular article to a new state.
Finally, under Step 2B, we consider whether the additional elements are sufficient to amount to significantly more than the abstract idea.
The above claims comprise the following additional elements:
Claim 1: A method of processing data determined from an image- charge/current signal representative of ions of a given charge state (Q) undergoing oscillatory motion of a respective oscillation frequency (f) within an ion analyzer apparatus, the method comprising: acquiring a data set comprising a measured signal frequency (fo) common to a plurality of a measured image-charge/current signals and a plurality of estimated ion charge values corresponding to respective amplitudes of each one of said plurality of measured image-charge/current signals.
Claim 11: An apparatus configured to processing data determined from an image-charge/current signal representative of ions of a given charge state (Q) undergoing oscillatory motion of a respective oscillation frequency (f) within an ion analyzer apparatus, comprising a processor module configured to: acquire a data set comprising a measured signal frequency (fo) common to a plurality of a measured image-charge/current signals and a plurality of estimated ion charge values corresponding to respective amplitudes of each one of said plurality of measured image-charge/current signals.
The above steps of “a method of processing data determined from an image- charge/current signal representative of ions of a given charge state (Q) undergoing oscillatory motion of a respective oscillation frequency (f) within an ion analyzer apparatus, the method comprising:” is generically recited, not meaningful, does not represent a particular machine and/or eligible transformation. It does not indicate a practical application. “Acquiring a data set comprising a measured signal frequency (fo) common to a plurality of a measured image-charge/current signals and a plurality of estimated ion charge values corresponding to respective amplitudes of each one of said plurality of measured image-charge/current signals” are generically recited are generically recited and represent mere data gathering steps (insignificant extra-solution activity) necessary to execute the abstract idea.
The independent claims, therefore, are not patent eligible.
With regards to the dependent claims, claims 2-10 and 12-15 provide additional features/steps which further limit the abstract idea of the independent claims without adding additional elements/steps that integrate the abstract limitations into a practical application.
101 computer program product
Claim 14 is rejected under 35 USC § 101 because it is directed to non-statutory subject matter.
The descriptions or expressions of the programs are not physical “things.” They are neither computer components nor statutory processes, as they are not “acts” being performed. Such claimed computer programs do not define any structural and functional interrelationships between the computer program and other claimed elements of a computer, which permit the computer program' s functionality to be realized. In contrast, a claimed a non-transitory computer-readable medium encoded with a computer program is a computer element which defines structural and functional interrelationships between the computer program and the rest of the computer which permit the computer program' s functionality to be realized, and is thus statutory. Accordingly, it is important to distinguish claims that define descriptive material per se from claims that define statutory inventions.
In order to overcome this rejection, the following language is suggested:
Claim 14. (Currently amended) A non-transitory computer readable medium encoded with a computer program product for …”
Claim 14. (currently amended) the non-transitory computer readable medium as in claim 1 further includes: …”
Non-transitory computer readable medium
Claim 15 is rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Claim 15 presents "a computer readable medium". The broadest reasonable interpretation of a claim drawn to a computer readable medium typically covers forms of non-transitory tangible media and transitory propagating signals per se in view of the ordinary and customary meaning of computer readable media, particularly when the specification is silent See MPEP 2111.01.
As currently claimed, the language a computer readable medium does not specify if the computer readable medium is "transitory" or "non-transitory" and therefore claim 15 is considered to be non-statutory under 35 U.S.C. 101 (See In re Nuijten, 500 F.3d 1346, 1356-57 (Fed. Cir. 2007) (transitory embodiments are not directed to statutory subject matter) and Interim Examination Instructions for Evaluating Subject Matter Eligibility Under 35 U.S.C. § 101, Aug. 24, 2009; p. 2).
In order to overcome this rejection, the following language is suggested:
Claim 15. (Currently amended) A non-transitory computer readable medium having computer-executable components …”
Claim 15. (currently amended) the non-transitory computer readable medium as in claim 14 wherein …”
Allowable Subject Matter
Examiner notes that the claims are not allowed due to the outstanding rejection of claim 1-15 under 35 U.S.C. 101.
Regarding Claims 1 and 11, Ding (US20140263992) discloses a method of processing data determined from an image-charge/current signal representative of ions of a given charge state (Q) undergoing oscillatory motion of a respective oscillation frequency (f) within an ion analyzer apparatus, the method comprising: acquiring a data set comprising a plurality of a measured image-charge/current signals and (In general, the frequency of oscillation of trapped ions in an ion trap is dependent on mass/charge ratio of the ions, since ions with large mass/charge ratios generally take longer to perform an oscillation compared with ions with small mass/charge ratios. Using an image charge/current detector, it is possible to obtain, non-destructively, an image charge/current signal representative of trapped ions undergoing oscillatory motion in the time domain [0006]); generating an integer charge value ([Q]) corresponding to a said estimated ion charge value rounded to the nearest integer value (The image charge or image current signals picked up by the pick-up electrodes, although being periodic according to the oscillation frequency of the ion, are in general not sinusoidal. Depend on the size and location of the pick-up electrodes, they form certain distinct waveform patterns, as shown in FIG. 4, in which [0245];Fig. 4); and, (a) a plurality of different candidate image-charge/current signal frequency values (ficand) according to said selected measured signal frequency (fo) (When a Fourier Transform is applied to these signals, even if the reference ions have the same mass/charge ratio (as depicted in FIG. 4), all frequency domain signals generally have same fundamental frequency component and same gaps between every higher order harmonic peaks. This is demonstrated by FIG. 5a and FIG. 5b, in which [0252]); then, (b) comparing the calculated plurality of different candidate image- charge/current signal frequency values (ficand) to a plurality of different signal frequencies (f) of the measured image-charge/current signals (Herein, a (e.g. "targeted" or "unwanted") harmonic component of the image charge/current signals within the linear combination may be viewed as being suppressed if, in the frequency domain, a ratio value calculated as the height of a peak belonging to the (e.g. "targeted" or "unwanted") harmonic component divided by the height of a corresponding peak belonging to another (e.g. "untargeted" or "wanted") harmonic component is smaller for the linear combination produced using the predetermined coefficients compared with the same ratio calculated for a simple sum up of each image charge/current signal. In this context, "corresponding" peaks means peaks caused by trapped ions having the same mass/charge ratio [0083]) and a degree of similarity therebetween (Preferably, applying the validity test to a peak in the image charge/current signal in the frequency domain includes determining whether a phase angle associated with the peak falls within a predetermined range, e.g. by determining whether a phase angle associated with the peak is equal to a predetermined value within a predetermined tolerance [0036]).
Regarding Claim 1 and 11, Thoeing discloses a method of processing data determined from an image-charge/current signal representative of ions of a given charge state (Q) undergoing oscillatory motion of a respective oscillation frequency (f) within an ion analyzer apparatus (In an embodiment of the inventive method for identification of the monoisotopic mass or a parameter correlated to the mass of the isotopes of the isotope distribution of at least one species of molecules contained in a sample and/or originated from a sample by at least an ionization process wherein in each of the fractions of at least one range of measured m/z values at least one isotope distribution of ions of one species of molecules having a specific charge z is detected [0018]), the method comprising: acquiring a data set comprising a measured signal frequency (fo) common to a plurality of a measured image-charge/current signals and a plurality of estimated ion charge values corresponding to respective amplitudes of each one of said plurality of measured image-charge/current signals (dividing at least one range of measured m/z values of the mass spectrum of the sample into fractions [0014]; Fig. 1); generating an integer charge value ([Q]) corresponding to a said estimated ion charge value rounded to the nearest integer value (Typically, the factor with which the evaluated maximum charge state is multiplied is in the range of 1.10 and 1.30, preferably in the range of 1.125 and 1.20. Preferably the so achieved is round up to the next natural number, i.e. positive integer [0084]); and,(a) selecting said integer charge value ([Qi]) and therewith calculating a plurality of different candidate image-charge/current signal frequency values (fand) according to said selected measured signal frequency (fo) and according to a corresponding one of one or more different candidate charge states of the ion and/or of ion isotope or isotopologue (Typically, the factor with which the evaluated maximum charge state is multiplied is in the range of 1.10 and 1.30, preferably in the range of 1.125 and 1.20. Preferably the so achieved is round up to the next natural number, i.e. positive integer [0084]); then, the measured image-charge/current signals and calculating a score value representing a degree of similarity therebetween according to the comparison (As already explained above the minimum resolution Δ(m/z) of a mass analyzer when measuring a peak has to be similar or below the expected difference Δ.sub.iso(z) of the m/z value of two neighboring isotopes, if their peaks are separated in the mass spectrum [0140]); determining the charge state (Q) of the ion undergoing oscillatory motion of said selected measured signal frequency (fo), to be equal to the integer charge value ([QL]) if said score value matches or exceeds a threshold score value (All of these fractions with the starting window width Δm/z.sub.start are investigated if they have a significant peak. Only fractions with such a peak are assigned to a processor which will then deduce an isotope distribution from the measured mass spectrum in the range of the fraction of the at least one range of measured m/z values. Mostly the investigation if a fraction with the starting window width Δm/z.sub.start has a significant peak is started at one boundary of the at least one range of measured m/z values which shall be divided, the highest m/z value or the lowest m/z value. A fraction has a significant peak if the peak of the highest intensity of the fraction has a signal to noise ratio S/N which is higher than a threshold value T [0063]).
Regarding Claims 1 and 11, Yip (US20190164735) discloses a method of processing data of ions of a given charge state (Q) within an ion analyzer apparatus, (In a simple data-dependent experiment shown in FIG. 1A, a detector continuously measures total current attributable to ions entering a mass spectrometer detector [0004]); generating a charge value ([Q]) corresponding to a said estimated ion charge value rounded to the nearest integer value (It is not uncommon for a single protein to generate greater than hundreds of resolved peaks (including both charge states and isotopes) per MS mass spectrum on high resolution/mass accuracy instruments [0012]); and, (a) selecting said charge value ([Qi]) and therewith calculating a one or more different candidate charge states of the ion and/or of ion isotope or isotopologue (There is thus a need in the art of mass spectrometry of biomolecules for improved methods of analysis that can efficiently differentiate signal from noise, correctly allocate related m/z values into proper isotopic clusters, correctly determine charge states and properly organize the various charge states into distribution envelopes [0013]); then,(b) comparing the calculated plurality of different candidate image- charge/current signal (FIGS. 21A and 21B are a table illustrating a comparison between theoretical and observed protein fragment ion masses obtained during long gradient LCMS analysis of an extract of the yeast Candida albicans [0056]); determining the charge state (Q) of the ion, value matches or exceeds a threshold score value (The present methods only take into consideration whether a centroid intensity is above a threshold or not. If the intensity value meets a user-settable criterion based on signal intensity or signal-to-noise ratio or both, then that intensity value assumes a Boolean “True” value, otherwise a value of “False” is assigned, regardless of the actual numerical value of the intensity [0073]).
Regarding Claims 1 and 11, Smirnov (US20190035615) discloses a method of processing data determined from an image- charge/current signal representative of ions of a given charge state (Q), the method comprising: acquiring a data set comprising a plurality of a measured image-charge/current signals (Using an image charge/current detector, it is possible to obtain, non-destructively, an image charge/current signal representative of trapped ions undergoing oscillatory motion in the time domain [0005]); then,(b) comparing the calculated plurality of different candidate image- charge/current signal frequency values (Application of an Orthogonal Projection Method to the selected basis signals results in improved calculation of the relative ion abundances from an FFT power spectrum compared with Reference [1], where the masses used to derive the basis signals are uniformly spaced along a mass range of interest [0144]); determining the charge state (Q) of the ion undergoing oscillatory motion of said selected measured signal frequency (fo), to be equal to charge value ([Q]) if said value matches or exceeds a threshold score value (Thus, in some embodiments, the method may include a further step of estimating relative abundances of ions corresponding to the candidate fundamental frequencies by mapping a subset of the basis signals to the image charge/current signal, wherein the subset of the basis signals excludes any basis signals that mapped to the image charge/current signal with an intensity that is deemed to be zero or close to zero (e.g. that is zero within a predetermined error threshold [0101]).
In regards to Claim 1, the closest prior art Ding, Thoeing, Yip, and Smirnov either singularly or in combination, fail to anticipate or render obvious, selecting said integer charge value ([Qi]) and therewith calculating a plurality of different candidate image-charge/current signal frequency values (ficand) according to said selected measured signal frequency (fo) and according to a corresponding one of one or more different candidate charge states of the ion and/or of ion isotope or isotopologue in combination with all other limitations in the claim as claimed and defined by applicant.
The Examiner notes that the references Ding and Thoeing included in the written opinion were used to reject the claims of the instant application. However, the examiner disagrees with this finding due to the fact that the references use m/z values instead of image-charge/current signal frequencies to calculate the score and was unable to locate a reference showing the correlation between m/z and image-current/current signals when calculating the score of an isotope.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Michael Senko (US20210210331) discloses an analyte ion is injected into an electrostatic trap, which has electrodes shaped and arranged to establish a trapping field that causes the analyte ion to undergo harmonic motion along a longitudinal axis.
Aleksandr Rusinov (US11011364) discloses an apparatus configured to produce an image charge/current signal representative of trapped ions undergoing oscillatory motion.
Yang Wang (US20080067352) discloses combined desorption and ionization sources provided to generate molecular ions form a sample disposed on a substrate surface and the combined desorption and ionization sources coupled by a vacuum interface to a mass spectrometer, where the sample molecule ions can be analyzed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHARAH ZAAB whose telephone number is (571)272-4973. The examiner can normally be reached Monday - Friday 7:00 am - 4:30 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Catherine Rastovski can be reached on 571-272-0349. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SHARAH ZAAB/Examiner, Art Unit 2857
/Catherine T. Rastovski/Supervisory Primary Examiner, Art Unit 2857
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