DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 1-20 are under examination.
Claim Rejections - 35 USC § 101
2. 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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Claims 1-20 are directed to method and apparatus for predicting a collision cross-section value and assigning an error or variance to the predicted CCS value. As described in Alice Corp. Pty. Ltd. V. CLS Bank Int’l, 573 U.S._, 134 S. Cr. 2347, 110 U.S.P.Q.2d 1976 (2014), a two-step analysis is required in considering the patent eligibility of the claimed subject matter. The first step requires determining if the claimed subject matter is directed to a judicial exception. The instant claims require the steps of calculating one or more molecular properties for the chemical compound; predicting a collision cross-section (CCS) value for the chemical compound; using the one or more calculated molecular properties to assign an error or variance to the predicted CCS value. These steps are drawn to mental steps or a mathematical algorithm. Dependent claims 2-7, 9-14, and 16-20 are drawn to additional mental or mathematical steps or the data used in the algorithm. The courts have found mathematical algorithms to be drawn to the judicial exception of an abstract idea (In re Grams, 888 F.2d 835, 12 U.S.P.Q.2d 1824 (Fed. Cir. 1989)). Thus, the instant claims are drawn to a judicial exception.
This judicial exception is not integrated into a practical application. The instant claims do not recite an element that reflects an improvement in the functioning of a computer or other technology, an element that applies the judicial exception to effect a particular treatment, an element that implements the judicial exception with a particular machine, or an element that effects a transformation of a particular article to a different state or thing. The instant claims recite a step of receiving a description of a chemical compound. Receiving data is an extra solution data gathering step, which does not in integrate the judicial exception into a practical application. The instant claims also recite the elements of a non-transitory computer-readable medium, instructions, processor, and apparatus. The instant claims do not recite structural limitations of these elements and do not recite a particular machine. The instant claims do not integrate the judicial exception into a practical application.
The second part of the analysis requires determining if the claims include additional elements that are sufficient to amount to significantly more than the judicial exception. The instant claims recite the step of receiving a description of a chemical compound. However, this steps is a well-understood, conventional, and routine data gathering step (Specification, pages 10-11). The instant claims also recite the elements of non-transitory computer-readable medium, instructions, processor, and apparatus. However, these elements are well-understood, conventional, and routine (Specification, pages 6-9). Reciting such well-understood, routine, and conventional elements and data gathering steps do not transform a judicial exception into patent eligible subject matter. In addition, the recitation of the specific types of data, to be used in the judicial exception, does not transform the abstract idea into a non-abstract idea. (See buySAFE, Inc. v Google, Inc. 765 F.3d 1350, 112 U.S.P.Q.2d 1093 (Fed.Cir.2014)). Furthermore, the elements taken as a combination are also well-understood, routine, and conventional, since the elements are merely specifying the types of data for a data gathering step and a general computer for implementing the judicial exception. Thus, the instant claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Claim Rejections - 35 USC § 102
3. In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 4, 8, 11 and 15 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lee et al. (“Structural Characterization of Small Molecular Ions by Ion Mobility Mass Spectrometry in Nitrogen Drift Gas: Improving the Accuracy of Trajectory Method Calculations”, Analyst (2008) Volume 143, no. 8, pages 1786-1796).
Regarding claims 1, 8, and 15, Lee et al. teach a computer implemented method (page 1788, right column, under “CCS calculations”) that includes the steps of receiving a description of a chemical compound (page 1788, right column, under “CCS calculations”), calculating one or more molecular properties for the chemical compound (page 1789, left column, first paragraph); predicting a collision cross-section (CCS) value for the chemical compound (page 1788, right column, under “CCS calculations”), using the one or more calculated molecular properties to assign an error or variance to the predicted CCS value (abstract; page 1790, right column, middle paragraph). Furthermore, Lee et al. teach implementing their method using MOBCAL code (page 1788, right column, under “CCS calculation”), which would require a computer with a hardware processor and non-transitory computer readable medium and instructions to perform the method.
Regarding claims 4 and 11, Lee et al.t each where the chemical compound is small molecule (page 1789, right column, under “Results and discussion”).
Claim Rejections - 35 USC § 103
4. In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 2, 3, 5-7, 9, 10, 12-14, and 16-20 are rejected under 35 U.S.C. 103 as being unpatentable over Lee et al. (“Structural Characterization of Small Molecular Ions by Ion Mobility Mass Spectrometry in Nitrogen Drift Gas: Improving the Accuracy of Trajectory Method Calculations”, Analyst (2008) Volume 143, no. 8, pages 1786-1796) as applied to claims 1, 4, 8, 11 and 15 above, and further in view of Mosier et al. (“Prediction of Peptide Ion Collision Cross Sections from Topological Molecular Structure and Amino Acid Parameters”, Anal. Chem. (2002) volume 74, pages 1360-1370).
Lee et al. is applied as above.
Lee et al. does not teach applying their method to a peptide.
Regarding claim 2, 9, and 16, Moiser et al. teach a method of predicting peptide ion collision cross sections that includes where the CCS value is an assignment of a charge to a particular location in the chemical compound (page 1361, left column)
Regarding claim 3, 10, and 17, Moiser et al. teach where the compound is a peptide (abstract). Lee et al. teach where the molecular property is a Van der Walls volume (abstract).
Regarding claims 5, 12, and 18, Moiser et al. teach where the molecular properties comprises structural flexibility (page 1367, right column, under “Sequence Isomer Discrimination”).
Regarding claims 6, 13, and 19, Moiser et al. teach where the compound is capable of exhibiting a plurality of CCS values indication a plurality of possible locations for a charge on the compound and building a model of the chemical compound (pages 1367-1368, section under “Sequence Isomer Discrimination”).
Regarding claims 7, 14, and 20, Moiser et al. teach where the CCS value is predicted using machine learning (abstract; page 1361, right column).
It would have been obvious for one of ordinary skill in the art, at the time of filing, to combine the teachings of Lee et al. and Moiser et al. to gain the benefit of applying the method of Lee et al. to peptides. Lee et al. teaches that IM-MS is an emerging tool in structural biology for a multi-dimensional analysis in complex samples (page 1786). One of ordinary skill in the art would seek to apply this method to biological compounds such as peptides. Moiser et al. teach a using this method for analyzing peptides. Thus, one of ordinary skill in the art would have been motivated to combine the teachings of Lee et al. and Moiser et al.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JERRY LIN whose telephone number is (571)272-2561. The examiner can normally be reached T-F 7am-5pm.
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/JERRY LIN/Primary Examiner, Art Unit 1685
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