COMPOSITIONS AND METHODS FOR PROTEIN DETECTION

Abstract

The invention relates generally to peptide biomarkers with specific ionization characteristics to directly quantify one or more target HPPD proteins in biological samples, including crop plant samples, by liquid chromatography coupled tandem mass spectrometry multiple reaction monitoring (MRM). The peptide biomarkers in combination with MRM-based methods may be used to quantify a single target protein or multiple target proteins within a crop plant, such as maize, utilizing selected peptide biomarkers either alone or in combination. The present disclosure allows for broad based, reliable quantitation in different biological matrices, including plant matrices. Also provided are different peptide biomarker combinations that can be used to perform the methods of the invention.

Claims

1. A labeled surrogate peptide that functions in a mass spectrometry assay to selectively detect or quantitate a p-hydroxyphenylpyurvate dioxygenase (HPPD) protein in a mixture of proteins in one or more biological samples from one or more crop plants, the surrogate peptide comprising a label and an amino acid sequence selected from the group consisting of GNFSELFK (SEQ ID NO:1) and GNFSQLFK (SEQ ID NO:2).

2. The labeled surrogate peptide of claim 1, wherein the peptide is labeled by incorporation of a stable isotope labeled (SIL) amino acid.

3. The labeled surrogate peptide of claim 2, wherein the SIL amino acid is lysine, isoleucine, valine or arginine.

4. The labeled surrogate peptide of claim 1, wherein said plant is barley, rice, soybean, wheat, oat or maize.

5. The surrogate peptide of claim 4, wherein said plant is barley, rice, soybean, wheat or rice and the surrogate peptide comprises a label and the amino acid sequence of SEQ ID NO:1.

6. The surrogate peptide of claim 4, wherein said plant is maize and the surrogate peptide comprises a label and the amino acid sequence of SEQ ID NO:2.

7. An assay cassette comprising at least two labeled surrogate peptides of claim 1.

8. A method of simultaneously detecting or quantitating one or more target HPPD proteins in a complex biological sample from a crop plant comprising a mixture of the target protein and non-target proteins, the method comprising: a. obtaining a biological sample from a crop plant; b. extracting proteins from the biological sample, resulting in an extract comprising a mixture of proteins; c. reducing the amount of insoluble proteins in the extract of step b, resulting in an extract of concentrated soluble proteins; d. digesting the soluble proteins in the extract of step c, resulting in an extract comprising peptide fragments, wherein the peptide fragments include at least one surrogate peptide specific for a target protein; e. concentrating the peptide fragments in the extract of step d, f. adding one or more labeled surrogate peptides of claim 1, wherein each labeled surrogate peptide has the same amino acid sequence as each surrogate peptide of the target protein, and wherein the number of labeled surrogate peptides that are added is equal to the number of target proteins in the mixture; g. concentrating the surrogate peptides and the labeled surrogate peptides by reducing the amount of non-surrogate peptides in the mixture; h. resolving the peptide fragment mixture from step g via liquid chromatography; i. analyzing the peptide fragment mixture resulting from step h via mass spectrometry, wherein detection of a transition ion fragment of a labeled surrogate peptide is indicative of the presence of a target protein from which the surrogate peptide is derived; and optionally, j. calculating an amount of a target protein in the biological sample by comparing mass spectrometry signals generated from the transition ion fragment of step i with mass spectrometry signals generated by a transition

9. The method of claim 8, wherein said crop plant is barley, rice, soybean, wheat or rice and the surrogate peptide comprises a label and the amino acid sequence of SEQ ID NO:1.

10. The method of claim 8, wherein said crop plant is maize and the surrogate peptide comprises a label and the amino acid sequence of SEQ ID NO:2.

11. The method of claim 9, wherein the peptide is labeled by incorporation of a stable isotope labeled (SIL) amino acid.

12. The method of claim 11, wherein the SIL amino acid is lysine, isoleucine, valine or arginine.

Description

EXAMPLES

[0054] While the invention has been described in connection with specific embodiments thereof, it will be understood that the inventive device is capable of further modifications. This patent application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features herein before set forth and as follows in scope of the appended claims.

[0055] All publications and patent applications mentioned in this specification are indicative of the level of skill of those skilled in the art that this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Example 1. Validation for the Quantitation of Endogenous p-Hydroxyphenylpyruvate Dioxygenase in Commodity Crop Articles of Commerce Using a Mass Spectrometry Assay

[0056] The purpose of this study was to validate the mass spectrometry (MS)-based method for the quantification of p-hydroxyphenylpyruvate dioxygenase (HPPD) protein in various commodity crops (barley, maize, rice, soybean, and wheat seed, and, barley, maize, oat, soybean and wheat forage) using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Surrogate peptides that are unique to the HPPD protein were used to determine the relative concentration. Prior to implementing a quantitative method in studies, the method was validated for the intended use in accordance to Good Laboratory Practice Standards (GLPS). Commodity crop samples were used to evaluate method performance parameters including specificity, linearity, limits of quantitation, carryover, precision and accuracy, extraction efficiency and stability.

[0057] Evaluation of specificity showed no significant interference at the retention time of the non-labeled peptides (<30.0% difference in the average ratio of the two transitions between the blank and buffer) and stable isotopic-labeled (SIL) peptides (≤5.0% of SIL signal of QCO (endogenous)) in any of the commodity crop samples that were tested. All specificity parameters met acceptance criteria.

[0058] Lower limits of quantitation (LLOQ) for each signature peptide used as surrogates for the target HPPD protein were determined. The limit of quantitation was 0.209 μg/g dry weight (DW) for barley seed, 0.122 μg/g DW for maize seed, 0.083 μg/g DW for rice seed, 0.686 μg/g DW for soybean seed, 0.301 μg/g DW for wheat seed, 0.524 μg/g DW for barley forage, 0.326 μg/g DW for maize forage, 0.660 μg/g DW for oat forage, 1.001 μg/g DW for soybean forage and 0.640 μg/g DW for wheat forage.

[0059] The validated quantitative range (LLOQ and upper limit of quantitation (ULOQ)) of HPPD for each commodity crop is summarized in

Table 1

[0060]

TABLE-US-00001 TABLE 1 Quantitative Ranges Quantitative Quantitative Plant Species/ Surrogate Range Range Matrix Peptide (fmol/mg DW) (μg/gDW) Barley Seed GNFSELFK  4.520 to 271.200  0.209 to 12.567 Rice Seed  1.776 to 106.543 0.083 to 5.001 Soybean Seed 14.054 to 843.231  0.686 to 41.161 Wheat Seed  6.457 to 387.429  0.301 to 18.060 Barley Forage 11.300 to 678.000  0.524 to 31.418 Soybean Forage  20.501 to 1230.086  1.001 to 60.045 Wheat Forage 13.721 to 823.286  0.640 to 38.378 Oat Forage 14.044 to 842.657  0.660 to 39.602 Maize Seed GNFSQLFK  2.585 to 155.077 0.122 to 7.289 Maize Forage  6.941 to 416.486  0.326 to 19.576

[0061] Intra- and inter-assay CVs were ≤25.0% for the QCO samples and ≤20.0% for the quality control (QC) samples at three concentrations (low, mid and high) showing good method precision. Similarly, the intra- and inter-assay % bias was within ±20.0% for the low, mid and high QC samples showing good method accuracy. Therefore, all method precision and accuracy parameters met acceptance criteria. The intra- and inter-assay precision and accuracy of the method are summarized in

Table 2

[0062]

TABLE-US-00002 TABLE 2 Intra- and Inter-Assay Precision and Accuracy Range for HPPD in Commodity Crops Intra-Assay Inter-Assay Plant Species/ Precision Accuracy Precision Accuracy Matrix (% CV) (% bias) (% CV) (% bias) Barley Seed 0.8 to 5.5 −8.4 to 1.5 2.3 to 5.0 −6.2 to −3.2 Maize Seed 0.5 to 6.7 −19.5 to −0.3 4.9 to 8.6 −9.9 to −3.8 Rice Seed 0.2 to 2.8  −6.3 to −0.4 1.3 to 2.4 −5.7 to −1.7 Soybean Seed 0.5 to 4.8  −8.9 to −2.9 2.5 to 3.4 −6.4 to −5.1 Wheat Seed 0.8 to 3.7 −10.1 to −1.5 1.5 to 4.4 −7.6 to −6.5 Barley Forage 0.5 to 5.8 −18.9 to −4.0 2.8 to 5.4 −16.6 to −5.3  Maize Forage 0.9 to 4.9 −15.6 to −2.1 5.3 to 7.0 −10.5 to −5.2  Oat Forage 0.4 to 8.6 −10.7 to 0.9  1.5 to 5.5 −7.6 to −2.8 Soybean Forage 0.6 to 5.1 −11.6 to −2.3 1.6 to 4.9 −6.5 to −5.6 Wheat Forage 0.9 to 6.2 −10.1 to −0.7 2.8 to 6.0 −8.2 to −4.6

[0063] A linear equation with a data weighting of 1/× was used to represent the concentration/detector response relationship. Therefore, all of the established data fell within the acceptance criteria and were found to be suitable for the linearity assessment. The efficiency of the protein extraction method was 59.9% for barley seed, 69.8% for maize seed, 73.9% for rice seed, 64.9% for soybean seed, 54.3% for wheat seed, 69.8% for barley forage, 76.3% for maize forage, 78.4% for oat forage, 65.4% for soybean forage and 77.2% for wheat forage. The CV of the first round of extraction was below 20.0% for all commodity crops except for wheat seed which was 27.5% CV. However the Precision and Accuracy results (QCO) of wheat seed coming from a single extraction demonstrate that a precision ≤20.0% was achieved.

[0064] The processed stability (dry extract) was evaluated for 6 days at −20° C. The stability assessment met acceptance criteria. The CV was ≤25.0% and the % difference of peak area ratios between stability and Day 0 QCs were within ±25.0% for all commodity crops.

[0065] All performance parameters evaluated met the defined acceptance criteria except for the % of the final extraction of barley and wheat seed which was 8.2 and 6.2% respectively as well as the precision of the first round of extraction for wheat seed which was at 27.5% CV. Since the concentration of HPPD in samples analysis will be determined from a single extraction (first round) and adjusted for % extraction efficiency and a precision of ≤20.0% was achieved for wheat seed in the precision and accuracy runs there is no impact on the outcome of the study.

[0066] Based on the results of this study, the mass spectrometry-based method has been confirmed to be suitable for quantification of HPPD protein in commodity crops in accordance with GLPS.

[0067] The purpose of this study was to validate the mass spectrometry (MS)-based method for the quantification of p-hydroxyphenylpyruvate dioxygenase (HPPD) protein in various commodity crops (barley, maize, rice, soybean, and wheat seed, and, barley, maize, oat, soybean and wheat forage) using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) analysis. Surrogate peptides that are unique to the HPPD protein were used to determine the relative concentration in the different plant species/matrices (Table 3). Prior to implementing a quantitative method in studies, the method was validated for the intended use in accordance to Good Laboratory Practice Standards (GLPS). Commodity crop samples were used to evaluate method performance parameters including specificity, linearity, limits of quantitation, carryover, precision and accuracy, extraction efficiency and stability.

TABLE-US-00003 TABLE 3 HPPD Surrogate Peptides Plant Species Matrix Surrogate Peptide rice, soybean, wheat, barley seed GNFSELFK (SEQ ID NO: 1) oat, soybean, wheat, barley forage maize seed GNFSQLFK (SEQ ID NO: 2) maize forage

[0068] The commodity crops material for this study are matrices from various plant species which were used to prepare linearity samples and quality control (QC) samples. Table 4 identifies the source of the matrix materials. These samples were provided by the Sponsor and were stored at a nominal temperature of −80° C.±10° C. until use.

TABLE-US-00004 TABLE 4 Commodity Crops Material Samples Description Material ID Commodity Non-transgenic barley seed MWF00450113-C Crops Non-transgenic maize seed MWF00450097-C Non-transgenic rice seed MWF00450103 Non-transgenic soybean seed MWF00450091-C Non-transgenic wheat seed MWF00450094-C Non-transgenic barley forage UR123450002-C Non-transgenic maize forage UR123450013-C Non-transgenic oat forage UR123450021-C Non-transgenic soybean forage UR123450041-C2 Non-transgenic wheat forage UR123450053-C

Standards and QC Samples

[0069] For the linearity assessment reverse curves were generated. A set of eight non-zero standards (STDs) were prepared using commodity crop extracts fortified with SIL peptides at different concentrations including both the LLOQ (STD 1) and ULOQ (STD 8) STDs. QC samples were prepared using the commodity crop extracts fortified with non-labeled peptides at three different concentrations (low, mid and high). Table 5 and Table 6 present the nominal concentrations.

TABLE-US-00005 TABLE 5 Concentrations of Standards in Commodity Crops (Nominal) Concentration (fmol/mg DW.sup.a) Plant Species/ STD 1 STD 8 Matrix (LLOQ) STD 2 STD 3 STD 4 STD 5 STD 6 STD 7 (ULOQ) Barley Seed 4.520 9.040 22.600 45.200 90.400 180.800 226.000 271.200 Maize Seed 2.585 5.169 12.923 25.846 51.692 103.385 129.231 155.077 Rice Seed 1.776 3.551 8.879 17.757 35.514 71.029 88.786 106.543 Soybean Seed 14.054 28.108 70.269 140.538 281.077 562.154 702.692 843.231 Wheat Seed 6.457 12.914 32.286 64.571 129.143 258.286 322.857 387.429 Barley Forage 11.300 22.600 56.500 113.000 226.000 452.000 565.000 678.000 Maize Forage 6.941 13.883 34.707 69.414 138.829 277.657 347.071 416.486 Oat Forage 14.044 28.089 70.221 140.443 280.886 561.771 702.214 842.657 Soybean Forage 20.501 41.003 102.507 205.014 410.029 820.057 1025.071 1230.086 Wheat Forage 13.721 27.443 68.607 137.214 274.429 548.857 686.071 823.286 .sup.aDW—dry weight

TABLE-US-00006 TABLE 6 Concentrations of QC Samples in Commodity Crops (Nominal.sup.a) Concentration (fmol/mg DW) Plant Species/ QC 1 QC 2 QC 3 Matrix (Low) (Mid) (High) Barley Seed 13.559 67.794 180.785 Maize Seed 7.754 38.771 103.389 Rice Seed 5.327 26.634 71.023 Soybean Seed 42.158 210.790 562.108 Wheat Seed 19.370 96.849 258.265 Barley Forage 33.897 169.486 451.963 Maize Forage 20.825 104.126 277.668 Oat Forage 42.129 210.647 561.725 Soybean Forage 61.499 307.496 819.990 Wheat Forage 41.161 205.805 548.812 .sup.aNominal = Nominal concentrations prior to adjustment with QC0 (endogenous level of non-labeled peptide)

Synthetic Peptides

[0070] The purified and quantified SIL and non-labeled synthetic peptides used in this study are listed in Table 7. The synthetic peptides were supplied by JPT Peptide Technologies GmbH and were stored at a nominal temperature of −20° C. until use.

TABLE-US-00007 TABLE 7 List of Synthetic Peptides Molecular Weight Type Name (g/mol) Batch No. Purity (%) Stable GNFSELF (SEQ ID NO: 1) 948.99 151018BB11 96.8 isotopic- [C13N15-HeavyK] labeled GNFSQLF (SEQ ID NO: 2) 948.01 030918SV2-38 97.4 [C13N15-HeavyK] Non- GNFSELFK (SEQ ID NO: 1) 941.05 151018BB10 97.4 labeled GNFSQLFK (SEQ ID NO: 2) 940.07 030918SV2-41 98.1

Analytical Method

[0071] The following experimental and data evaluation steps were involved in the validation process for the LC-MS/MS-based method to determine the quantity of HPPD protein in commodity crops. In brief, the LC-MS/MS method for identifying and quantifying surrogate peptides of HPPD in a complex biological matrix comprises: (i) weighing lyophilized commodity crops; (ii) homogenizing/extracting proteins from plant species/matrix samples in a lysis buffer; (iii) centrifugation of samples to separate soluble and insoluble proteins to enrich for protein of interest and reduce the sample complexity; (iv) digestion of soluble protein samples with trypsin; (v) centrifugation of samples; (vi) adding SIL peptides (fixed or variable depending on the assessment); (vii) desalting by solid-phase extraction utilizing cation exchange to minimize matrix effects or interferences and reduce ion suppression; and (viii) analysis of the sample by LC-MS/MS. The surrogate peptides of interest and corresponding SIL peptides that are unique to the HPPD protein for each commodity crop was measured by LC-MS/MS. Data were analyzed using MultiQuant™ software, version 3.0.2, where the chromatographic peak area of each surrogate peptide (non-labeled) and each corresponding SIL peptide was integrated for each sample.

[0072] For the reverse curve, the peak area of SIL peptide was determined for each surrogate peptide. Then, for each surrogate peptide, the peak area SIL peptide for each standard sample was plotted on the y-axis as a function of protein concentration (x-axis) to create the reverse curve.

[0073] For the QC samples, the peak area ratio (peak area of non-labeled peptide/peak area of corresponding SIL peptide) was determined. The non-labeled peptide concentration of the QC samples was calculated as follows:

[00001]$\mathrm{Concentration}\left(f\mathrm{mol}/\mathrm{mg}\mathrm{DW}\right)=\frac{\mathrm{Peak}\mathrm{Area}\mathrm{Non}‐\mathrm{labeled}\mathrm{peptide}}{\mathrm{Peak}\mathrm{Area}\mathrm{SIL}\mathrm{peptide}}\times \mathrm{Concentration}\mathrm{SIL}\left(f\mathrm{mol}/\mathrm{mg}\mathrm{DW}\right)$

Sample Processing

[0074] Between 10 and 18 mg of each commodity crops was weighed and added to tubes containing Matrix A lysing beads (MP Biomedicals). The lysis buffer (0.1% RapiGest™ (Waters) in phosphate-buffered saline (PBS)) was then added to each sample tube and homogenized using FastPrep®-24 Homogenizer (MP Biomedicals). Samples were then centrifuged at 4° C. to remove insoluble material. The supernatants were transferred; pooled and diluted accordingly in 0.1% RapiGest in PBS as described in

[0075] Table 8. These diluted commodity crops were fortified either with SIL peptides resulting in standards or with non-labeled peptides resulting in QC samples at various concentrations.

TABLE-US-00008 TABLE 8 Matrix Dilution Factor Plant Species/Matrix Dilution Factor Barley Seed 2.8 Maize Seed 1.6 Rice Seed 1.1 Soybean Seed 8.7 Wheat Seed 4.0 Barley Forage 7.0 Maize Forage 4.3 Oat Forage 8.7 Soybean Forage 12.7 Wheat Forage 8.5

[0076] For each standard and QC sample that was processed an equal volume of 2,2,2-trifluoroethanol (TFE) was added to denature the proteins, followed by a dilution of TFE to 10% with 100 mM ammonium bicarbonate and digestion using 0.1 μg/μL trypsin with incubation at 37° C. for 14 to 18 hours. After digestion, samples were acidified with a final formic acid (FA) concentration of 5% and SIL peptides were added to each sample at variable or fixed concentrations depending on the validation assessment except for blanks and carry-over blanks. Samples were then desalted by solid-phase extraction using mixed-mode cation exchange (MCX) μElution plates. The eluents were collected and transferred to two MS plates which were evaporated to dryness and stored at −20° C. (nominal) until MS analysis.

[0077] The processed samples were resolubilized with 11 μL of 92.5/7.5 water/acetonitrile (ACN)+0.2% FA, followed by sonication, vortexing and centrifugation. Eight microliters of material was injected per sample onto a NanoAcquity ultra-performance liquid chromatography (UPLC)® (Waters) coupled to a QTRAP 6500 mass spectrometer (AB Sciex). Peptide separation was achieved using a HALO peptide ES-C18 50mm×0.5mm, 2.7 μm column (Canadian Life Science). The LC gradient used is shown in

[0078] Table 9 below. The flow rate was 28.000 μL/min. Analytes were measured in positive ion mode using a Turbo V MS source. Data acquisition was performed using Analyst® version 1.6 (AB Sciex).

TABLE-US-00009 TABLE 9 LC Gradient of the LC-MS/MS Assay Time (97/3) Water/ (97/3) ACN/ (min) DMSO.sup.a + 0.2% FA DMSO.sup.a + 0.2% FA Initial 92.5 7.5 0.10 92.5 7.5 7.10 83.0 17.0 7.30 25.0 75.0 7.50 25.0 75.0 7.60 92.5 7.5 8.00 25.0 75.0 8.60 25.0 75.0 8.80 92.5 7.5 .sup.aDMSO—dimethyl sulfoxide

[0079] The surrogate peptides and corresponding SIL peptides are unique to the HPPD protein. The chromatographic peak area of each surrogate peptide (non-labeled) and each corresponding SIL peptide was integrated for each sample using MultiQuant version 3.0.2 (AB Sciex).

[0080] For the reverse curve, the peak area of SIL peptide was determined for each surrogate peptide. The peak area SIL peptide for each standard sample was plotted on the y-axis as a function of protein concentration (x-axis) to create the reverse curve.

[0081] For the QC samples, the peak area ratio (peak area of non-labeled peptide/peak area of corresponding SIL peptide) was determined. The non-labeled peptide concentration of the QC samples was calculated as described above.

[0082] Mean, standard deviation (SD), and coefficient of variation (CV) calculations were performed using Microsoft Office Excel® software. Unrounded values were used in calculations of the means, SDs, and CVs, and were then rounded appropriately in summary tables. Specificity

[0083] Specificity is determined by the ability of a method to measure and differentiate the surrogate peptides in the presence of various plant matrix components in a sample. The specificity is measured by determining the presence or absence of each unique surrogate peptide to the HPPD protein by LC-MS/MS.

[0084] The assay specificity was assessed for the non-labeled peptides using the quantifier and qualifier transitions and for the SIL peptides using only the quantifier transition in all commodity crop extracts as described below.

Non-Labeled Peptides

[0085] The following analysis was performed:

[0086] The assay specificity was evaluated by comparing the average ratio of the two transitions monitored (quantifier/qualifier) in digested bovine serum albumin (BSA) buffer (n=3) fortified with non-labeled peptide versus blank (n=3). Blank is considered matrix with detectable amounts of endogenous HPPD protein processed without the addition of SIL or non-labeled peptides.

[0087] The % difference was calculated using the following formula:

[00002]$\frac{\mathrm{Average}\mathrm{Ratio}\mathrm{Blank}-\mathrm{Average}\mathrm{Ratio}\mathrm{Buffer}}{\mathrm{Average}\mathrm{Ratio}\mathrm{Buffer}}\times 100$

[0088] The following acceptance criteria were used to confirm suitability of specificity assessment for the non-labeled peptide: The % difference between the blank and buffer must be within 30.0%.

SIL Peptides

[0089] The following analysis was performed:

[0090] The assay specificity was evaluated by determining the peak area of the SIL peptide (quantifier transition) in QCO (endogenous, n=3) versus blank (n=3). Blank is considered matrix with detectable amounts of endogenous HPPD protein processed without addition of SIL or non-labeled peptides.

[0091] The % of QCO (endogenous) was calculated using the following formula:

[00003]$\frac{\mathrm{Average}\mathrm{Peak}\mathrm{Area}\mathrm{Blank}}{\mathrm{Average}\mathrm{Peak}\mathrm{Area}\mathrm{Buffer}}\times 100$

[0092] The following acceptance criteria were used to confirm suitability of specificity assessment for the SIL peptide: The average SIL peptide peak area in the blank samples must be ≤5.0% of the average peak area of the SIL peptide in the QC0 (endogenous) samples.

Linearity

[0093] Linearity is the ability of a method to elicit results that are defined mathematically by the amount of analyte in the sample and the response. The linearity was evaluated based on the accuracy of the method. For HPPD in each plant species/matrix, the simplest regression model that defined the reverse curve was used, i.e. a linear curve fit. The model was applied based on quality of fit using the coefficient of correlation (R value).

[0094] A data weighting of 1/× was applied for all peptides. The same regression model and the same data weighting were applied for all assay runs of each plant species/matrix.

[0095] The following run acceptance criteria were used to confirm suitability of the linearity assessment: (1) At least 75.0% non-zero standards must be valid and must not deviate by more than 20.0% of nominal concentration, except at LLOQ where the deviation must not be more than 25.0%; (2) Interpolated curve must have R≥0.9900.

Limits of Quantitation

[0096] The LLOQ and ULOQ are the minimum and maximum concentration at which the response of a surrogate peptide can be determined within acceptable accuracy limits. The LLOQ and ULOQ were determined for a surrogate peptide in each plant species/matrix using the reverse curves as described.

[0097] The following acceptance criteria were used to confirm suitability of the LLOQ and ULOQ assessments: The LLOQ and ULOQ standards must meet the accuracy criteria defined above.

[0098] The quantitative range for HPPD is the interval between the upper and lower concentration for which it has been demonstrated that the analytical procedure had a suitable level of accuracy and linearity (refer to Table 5 for concentration of standards). The quantitative range was determined for HPPD in each plant species/matrix using the data obtained from the linearity evaluation of this method. Determining accuracy effectively validated the high and low concentrations tested as the quantitative range for the procedure.

[0099] Carryover is when an analyte is present in the subsequent injection. In this study, carryover is determined during the linearity assessment by evaluating two blank samples injected after each ULOQ standard. They must be free of interference. The following run acceptance criteria were applied to assess carry-over to all linearity runs. The first carryover blank sample injected after the ULOQ standard was assessed. The second carryover blank was assessed but was not part of the acceptance criteria. At least 50% of the first carryover blank samples injected after the ULOQ standard must be within acceptable interference as described below at the retention time of: The SIL peptide: peak area must be ≤20.0% of the mean peak area of the SIL peptide of the LLOQ standard(s). Furthermore, in the precision and accuracy as well as stability assessments, resolubilization buffer (RSB) samples were analyzed to assess carryover following injection of high QC samples. The sequence to assess carry-over was: High QC followed by two RSB samples.

Run Acceptance Criteria

[0100] As part of the validation, the precision and accuracy as well as stability runs included QC samples to demonstrate run acceptance. The following criteria must be met for the aforementioned runs to be considered valid. Each plant species/matrix was treated independently for acceptance criteria.

QC Samples

[0101] The QC samples provide the basis for accepting or rejecting a run. QC samples are prepared by fortifying the sample matrix with known concentrations of non-labeled peptides. The following acceptance criteria were used to confirm suitability of the QC samples using the low QC (QC1), midrange QC (QC2), high QC (QC3): (1) At least 50% of QC samples at each concentration low, mid and high must be within ±20.0% bias; (2) At least 67% of QC samples across low, mid and high concentrations must be within ±20.0% bias of their nominal values.

Precision and Accuracy

[0102] Precision is the degree of agreement among individual test results when the procedure is applied repeatedly to multiple samplings of a homogenous sample. Accuracy is the degree of agreement between the value found and an accepted reference value when the procedure is applied repeatedly to multiple samplings of a homogenous sample. In this study the precision and accuracy of the HPPD protein in each plant species/matrix for the LC-MS/MS assay was determined by assessing the assay-to-assay, and analyst-to-analyst variability.

[0103] Method precision and accuracy was evaluated using the QC samples. The precision and accuracy assays were performed with QC samples at three concentrations (low, mid and high) (Table 5 and Table 6). The QC samples were prepared in commodity crop extracts and fortified with non-labeled peptides.

[0104] Precision (CV) and accuracy (bias) were evaluated across three independent assay runs with two different analysts on three separate days.

[0105] Each precision and accuracy run consisted of three replicates per each QC concentration. QCO (endogenous) was also included and analyzed in triplicate.

[0106] The % bias was calculated using the following formula:

[00004]$\frac{\begin{array}{c}\mathrm{Measured}\mathrm{Concentration}\mathrm{of}\\ \mathrm{Fortified}\mathrm{sample}\left(f\mathrm{mol}/\mathrm{mg}\mathrm{DW}\right)-\\ \mathrm{Nominal}\mathrm{Protein}\mathrm{Concentration}\left(f\mathrm{mol}/\mathrm{mg}\mathrm{DW}\right)\end{array}}{\mathrm{Nominal}\mathrm{Protein}\mathrm{Concentration}\left(f\mathrm{mol}/\mathrm{mg}\mathrm{DW}\right)}\times 100$

[0107] The precision and accuracy runs that met run acceptance criteria stated in section 0 were used to evaluate intra-assay precision and accuracy. The precision and accuracy runs meeting the intra-assay criteria were then used to evaluate the inter-assay precision and accuracy. The following acceptance criteria were used to confirm suitability of precision and accuracy assessment for intra- and inter-assay runs: (1) The CV for the QCO samples must be ≤25.0%; (2) The CV for the low, mid, and high concentration QC samples must be ≤20.0% and within ±20.0% bias.

[0108] In addition, the maximum length of injection time of an assay run for study sample analysis was established by looking at the batch size of the precision and accuracy runs. The precision and accuracy run with the largest batch size was used for setting the maximum length of injection time for study sample analysis. Furthermore, a trend analysis of the QC0 (endogenous) samples was performed.

[0109] The extraction efficiency is the amount of protein of interest (i.e. HPPD) recovered from a matrix. The extraction efficiency was determined by consecutive sequential extractions. The extraction recovery is considered final if not more than 5.0% of the total protein is recovered in the last round. The efficiency of the protein extraction method was evaluated using commodity crops through iterative extractions of HPPD.

[0110] One analyst extracted three replicates of each commodity crop. The insoluble material was collected and extracted three more times, with each supernatant being retained for analysis.

[0111] The extraction efficiency for each sample was calculated using the following formula:

[00005]$\frac{\begin{array}{c}\mathrm{Peak}\mathrm{Area}\mathrm{Ratio}\mathrm{of}\mathrm{Protein}\\ \mathrm{in}\mathrm{first}\mathrm{extraction}\end{array}}{\begin{array}{c}\mathrm{Peak}\mathrm{Area}\mathrm{Ratio}\mathrm{of}\mathrm{Protein}\mathrm{in}\\ \mathrm{all}\mathrm{extractions}\mathrm{summed}\end{array}}\times 100$

[0112] The following acceptance criteria were used to confirm the suitability of extraction efficiency for each protein: The sequential extractions will be considered completed when the final extraction results were not more than 5.0% of the total recovered material for each individual protein from all combined extractions:

[00006]$\frac{\begin{array}{c}\mathrm{Peak}\mathrm{Area}\mathrm{Ratio}\mathrm{of}\mathrm{Protein}\\ \mathrm{in}\mathrm{last}\mathrm{extraction}\end{array}}{\begin{array}{c}\mathrm{Peak}\mathrm{Area}\mathrm{Ratio}\mathrm{of}\mathrm{Protein}\mathrm{in}\\ \mathrm{all}\mathrm{extractions}\mathrm{summed}\end{array}}\times 100\mathrm{is}\mathrm{less}\mathrm{than}5.\%$

The extraction efficiency (average of replicates of the first iteration) is expected to be ≥60.0% recovery and the precision must be ≤20.0% for the first round of extraction.

Stability

[0113] The stability of the HPPD protein in a given plant species/matrix under specific conditions for a given time interval was assessed. Stability was determined for the HPPD protein in each plant species/matrix, for the surrogate peptides in processed samples.

Processed Samples Stability

[0114] The processed samples stability of dry extracts was analyzed at two different concentrations (low and high) with three replicates per concentration. The freshly prepared and processed QC samples were analyzed by LC-MS/MS (considered Day 0). The dry stability samples were not immediately analyzed by LC-MS/MS but were stored for a pre-determined time period.

[0115] Dry stability samples were stored at nominal temperature of −20° C. for 6 days (146 hours 16 minutes), then re-solubilized and analyzed by LC-MS/MS.

[0116] The following acceptance criteria were used to confirm the stability of surrogate peptides in processed samples: (1) Overall mean peak area ratio of the processed Day 0 and stability samples must be ≤25.0% CV; (2) The percentage difference of peak area ratios between stability and Day 0 QCs (processed on the same day of injection) must be within ±25.0%.

[00007]$\%\mathrm{Difference}=\frac{\begin{array}{c}(\mathrm{Mean}\mathrm{Peak}\mathrm{Ratio}\mathrm{of}\mathrm{Stability}\mathrm{samples}-\\ \mathrm{Mean}\mathrm{Peak}\mathrm{Ratio}\mathrm{of}\mathrm{Day}0\mathrm{samples})\end{array}}{\mathrm{Mean}\mathrm{Peak}\mathrm{Ratio}\mathrm{of}\mathrm{Day}0\mathrm{samples}}\times 100$

[0117] As per the validation protocol, the carryover assessment is appropriately outlined in the general description where it is stated that peak area is used for the carryover evaluation however due to oversight the description found in the acceptance criteria states peak area ratio. Peak area is the correct way of performing the evaluation therefore in this study interference was assessed using peak areas. Therefore, there is no impact on data quality and integrity since the suitable approach for evaluating interference in the carry-over blanks was applied (i.e. peak areas).

[0118] As per the validation protocol, Peak Area ratio (SIL/non-labeled) for each peptide of the quantifier transition is used for plotting calibration curve data on a linear scale. However Peak Area for each peptide of the quantifier transition was used instead for plotting. Peak area ratio cannot be used for linearity assessment due to contribution to the non-labeled signal from the stable isotope labeled peptide at high spiking concentrations. There is no impact on the data quality and integrity since a linearity assessment was performed.

[0119] As per the validation protocol, the extraction efficiency evaluation is performed using 4 sequential extractions (rounds). For two matrices (i.e. barley and wheat seed) the extraction efficiency results did not meet acceptance criteria as outlined below.

Barley seed—Final extraction (4th round) result was 8.2% (Acceptance Criteria: <5.0%)
Wheat seed—Final extraction (4th round) result was 6.2% (Acceptance Criteria: <5.0%).
Precision of the 1st round of extraction was 27.5% CV (Acceptance criteria: ≤20.0%).

[0120] However, there is no impact on the outcome of the study since: (1) The final extraction results for barley and wheat seed show that the extraction of HPPD protein is near completion after four extraction rounds. Furthermore, the concentration of HPPD in samples analysis will be determined from a single extraction (first round) and adjusted for % extraction efficiency; and (2) For wheat seed, the precision of the first round of extraction (27.5% CV) exceeds the 20.0% CV criteria, however the Precision and Accuracy results for the QCO (endogenous) from three validation runs (Run 4 to 6) coming from a single extraction demonstrate that a precision ≤20.0% was achieved.

[0121] As per the validation protocol, for each precision and accuracy runs, two (2) RSB samples are injected after the high QC sample at the end of each matrix. However for one matrix (i.e. wheat seed), the RSB samples injected after the high QC sample (QC3 replicate 3) were acquired using the MRM method for peptide GNFSQLFK (SEQ ID NO:2) rather than peptide GNFSELFK (SEQ ID NO:1) due to oversight. Therefore the RSB carryover assessment was not performed for wheat seed.

[0122] However, there is no impact on the outcome of the study since: (1) Carryover of peptide GNFSELFK (SEQ ID NO:1) was not observed for any of the other matrices (including wheat forage), therefore the overall conclusion is that peptide GNFSELFK (SEQ ID NO:1) did not display any propensity for carryover and it can be inferred that carry over of peptide GNFSELFK for wheat seed matrix is highly improbable; and (2) As a consequence, the available dataset allows for establishing RSB carryover acceptance criteria (i.e. ≤5.0% at RT of non-labeled peptide peak area vs. QCO peak area) to be used in sample analysis for all matrices (including wheat seed) with regard to peptide GNFSELFK(SEQ ID NO:1) as well as GNFSQLFK (SEQ ID NO:2).

[0123] There were also minor SOP deviations which had no impact on the study. These are documented in the study file. No other circumstances occurred during the conduct of this study that would have adversely affected the quality or integrity of the data generated.

Specificity

[0124] The assay specificity was assessed for the non-labeled and SIL peptides in all commodity crop extracts. The evaluation showed some minor interference at the retention times of the surrogate peptides and corresponding SIL peptides in the commodity crop samples that were tested. For the non-labeled peptides, the percentage difference in the average ratio of the two transitions between the blank and buffer sample was below 30.0% in all plant species/matrices tested and all interferences were ≤5.0% of the mean peak area of the SIL peptides in QCO (endogenous) samples, meeting the specificity acceptance criteria.

Linearity

[0125] The linearity was determined for HPPD protein in each plant species/matrix using reverse curves as described in section 3.4 and 0. The simplest regression model that defined the reverse curve was used i.e. a linear regression. A data weighting of 1/× was used for all plant species/matrices. Table 10 summarizes the standard curve parameters (slope, intercept and R value) for the linearity assessment. The coefficient of correlation (R) for the standard curves for HPPD protein in each plant species/matrix was ≥0.9900. All of the established data fell within the acceptance criteria as described in section 0 and were found to be suitable for the linearity assessment.

TABLE-US-00010 TABLE 10 Reverse Curve Parameters in Commodity Crops for Linear Equation with a Weighting Factor of 1/x Plant Species/ Matrix Slope Intercept R Value Barley Seed 4411.65175 1324.06523 0.99926 Maize Seed 11316.54172 −1089.93977 0.99875 Rice Seed 11555.29853 −1882.67744 0.99918 Soybean Seed 1487.10444 −2985.15028 0.99920 Wheat Seed 3370.40265 −64.67755 0.99946 Barley Forage 1808.14443 1142.86508 0.99920 Maize Forage 4003.01356 −2528.34723 0.99921 Oat Forage 1420.89325 39.29666 0.99926 Soybean Forage 1046.53458 −3246.28194 0.99927 Wheat Forage 1506.99030 −1060.27312 0.99952

[0126] The back-calculated reverse curve standard concentrations in each plant species/matrix are provided in Table 11.

TABLE-US-00011 TABLE 11 Back-Calculated Reverse Curve Standard Concentrations in Commodity Crops Reverse Curve Standard Concentrations (fmol/mg DW) Plant STD 1 STD 8 Species/Matrix (LLOQ) STD 2 STD 3 STD 4 STD 5 STD 6 STD 7 (ULOQ) Barley Nominal 4.520 9.040 22.600 45.200 90.400 180.800 226.000 271.200 Seed Mean 4.846 8.977 21.563 44.481 89.938 177.504 227.040 275.412 % CV 4.6 5.3 0.8 1.2 2.1 0.4 7.6 2.8 % bias 7.2 −0.7 −4.6 −1.6 −0.5 −1.8 0.5 1.6 Maize Seed Nominal 2.585 5.169 12.923 25.846 51.692 103.385 129.231 155.077 Mean 2.712 5.090 12.045 26.226 52.152 105.102 133.364 149.219 % CV 7.2 5.1 1.3 3.5 4.7 5.4 3.1 5.7 % bias 4.9 −1.5 −6.8 1.5 0.9 1.7 3.2 −3.8 Rice Nominal 1.776 3.551 8.879 17.757 35.514 71.029 88.786 106.543 Seed Mean 1.852 3.510 8.552 17.076 37.601 70.535 87.819 106.892 % CV 5.3 3.1 3.7 3.3 5.6 7.0 0.8 1.7 % bias 4.3 −1.2 −3.7 −3.8 5.9 −0.7 −1.1 0.3 Soybean Nominal 14.054 28.108 70.269 140.538 281.077 562.154 702.692 843.231 Seed Mean 14.776 27.013 69.163 144.660 276.891 549.382 679.999 880.241 % CV 2.5 4.7 3.2 1.8 4.0 1.2 0.8 1.9 % bias 5.1 −3.9 −1.6 2.9 −1.5 −2.3 −3.2 4.4 Wheat Nominal 6.457 12.914 32.286 64.571 129.143 258.286 322.857 387.429 Seed Mean 6.586 12.578 32.427 65.641 125.242 265.315 320.769 385.387 % CV 3.6 5.9 6.5 5.2 4.6 3.4 2.4 2.7 % bias 2.0 −2.6 0.4 1.7 −3.0 2.7 −0.6 −0.5 Barley Nominal 11.300 22.600 56.500 113.000 226.000 452.000 565.000 678.000 Forage Mean 11.951 22.879 53.533 110.325 229.285 444.169 549.348 702.912 % CV 9.3 0.9 1.1 4.8 3.6 0.7 4.8 1.2 % bias 5.8 1.2 −5.3 −2.4 1.5 −1.7 −2.8 3.7 Maize Nominal 6.941 13.883 34.707 69.414 138.829 277.657 347.071 416.486 Forage Mean 7.390 13.976 32.974 67.648 138.373 277.929 344.462 422.237 % CV 4.0 3.5 0.6 5.2 1.7 7.2 1.6 5.0 % bias 6.5 0.7 −5.0 −2.5 −0.3 0.1 −0.8 1.4 Oat Nominal 14.044 28.089 70.221 140.443 280.886 561.771 702.214 842.657 Forage Mean 13.936 28.387 68.116 144.296 284.993 559.663 674.546 866.389 % CV 1.8 0.8 1.9 3.5 4.1 4.2 1.2 2.8 % bias 48 1.1 −3.0 2.7 1.5 −0.4 −3.9 2.8 Soybean Nominal 20.501 41.003 102.507 205.014 410.029 820.057 1025.071 1230.086 Forage Mean 22.248 40.651 100.303 195.691 403.086 815.038 997.191 1280.062 % CV 4.8 0.2 0.7 2.2 1.7 3.0 3.4 0.7 % bias 8.5 −0.9 −2.2 −4.5 −1.7 −0.6 −2.7 4.1 Wheat Nominal 13.721 27.443 68.607 137.214 274.429 548.857 686.071 823.286 Forage Mean 13.954 26.922 67.581 139.675 270.208 571.268 673.942 816.079 % CV 4.5 2.0 0.5 0.9 4.5 0.3 3.5 0.6 % bias 1.7 −1.9 −1.5 1.8 −1.5 4.1 −1.8 −0.9 N = 2 for each standard of each plant species/matrix

Limits of Quantitation

[0127] In the linearity assessment, the accuracy (bias) was within ±25.0% and ±20.0% for the LLOQ and ULOQ samples respectively (Table 11), therefore the limits of quantitation were set at the concentration of the lowest and highest non-zero standard. Table 12 summarizes the lower and upper limits of quantitation for HPPD in each plant species/matrix.

TABLE-US-00012 TABLE 12 Limits of Quantitation for HPPD in Commodity Crops LLOQ ULOQ Plant Species/ fmol/mg μg/g fmol/mg μg/g Matrix DW DW DW DW Barley Seed 4.520 0.209 271.200 12.567 Maize Seed 2.585 0.122 155.077 7.289 Rice Seed 1.776 0.083 106.543 5.001 Soybean Seed 14.054 0.686 843.231 41.161 Wheat Seed 6.457 0.301 387.429 18.060 Barley Forage 11.300 0.524 678.000 31.418 Maize Forage 6.941 0.326 416.486 19.576 Oat Forage 14.044 0.660 842.657 39.602 Soybean Forage 20.501 1.001 1230.086 60.045 Wheat Forage 13.721 0.640 823.286 38.378

[0128] The quantitative range for HPPD in each plant species/matrix is the interval between the lower (LLOQ) and upper (ULOQ) concentrations for which it has been demonstrated that the analytical procedure has a suitable level of accuracy. The LLOQ and ULOQ samples met the accuracy criteria for HPPD in each plant species/matrix. The quantitative range of the method was set for each plant species/matrix (Table 13).

TABLE-US-00013 TABLE 13 Quantitative Ranges of HPPD in Commodity Crops Plant Species/ Quantitative Range Quantitative Range Matrix (fmol/mg DW) (μg/g DW) Barley Seed  4.520 to 271.200  0.209 to 12.567 Maize Seed  2.585 to 155.077 0.122 to 7.289 Rice Seed  1.776 to 106.543 0.083 to 5.001 Soybean Seed 14.054 to 843.231  0.686 to 41.161 Wheat Seed  6.457 to 387.429  0.301 to 18.060 Barley Forage 11.300 to 678.000  0.524 to 31.418 Maize Forage  6.941 to 416.486  0.326 to 19.576 Oat Forage 14.044 to 842.657  0.660 to 39.602 Soybean Forage  20.501 to 1230.086  1.001 to 60.045 Wheat Forage 13.721 to 823.286  0.640 to 38.378

Carryover

[0129] Carry-over was determined in the linearity evaluation by assessing blank samples injected after the ULOQ standard for the commodity crop samples that were tested. The evaluation showed no interference at the retention times of the SIL peptide. The SIL peptide peak area ratio was ≤20.0% of the mean peak area ratio of the SIL peptide of the LLOQ standard(s) in at least 50% of the first carryover blank samples injected after the ULOQ standard, meeting the carryover acceptance criteria.

[0130] Furthermore carryover was evaluated during precision and accuracy as well as stability runs with the use of RSB samples following injection of high QC samples. Overall the evaluation showed no carry-over in the blank samples. The RSB blank carryover acceptance criteria for study sample analysis will be ≤5.0% of the mean peak area of the non-labeled peptides in QCO (endogenous) samples.

Precision and Accuracy

[0131] The precision and accuracy of the HPPD method for commodity crops was evaluated using the QC samples described herein. There were three precision and accuracy runs. All met the run acceptance criteria. Precision (CV) and accuracy (bias) data for intra- and inter-assay runs are summarized in Table 14 to

[0132] Table 23 (one table per plant species/matrix).

[0133] For both intra- and inter-assay, the CV was less than 25.0% for the QCO samples and less than 20.0% for the low, mid and high QC samples, therefore, the method precision assessment was suitable.

[0134] For both intra- and inter-assay, the bias was within ±20.0% for the low, mid and high QC samples; therefore the method accuracy assessment was suitable.

[0135] The longest injection time of a precision and accuracy batch was approximately 36 hours 58 minutes (batch size of 187 injections) therefore this was established as the maximum length of injection time of an assay for study sample analysis.

[0136] A trend analysis of the QCO (endogenous) samples from the precision and accuracy runs was performed. The QCO (endogenous) sample was also analyzed for samples analysis in order to extend the trend analysis.

TABLE-US-00014 TABLE 14 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Barley Seed QC Sample Plant Concentration (fmol/mg DW) Species/ QC 0 Matrix Run (endo) QC 1 QC 2 QC 3 Barley Nominal — 35.165 89.400 202.391 Seed 4 Mean 21.606 34.357 90.749 192.645 % CV 4.7 0.8 3.4 1.8 % bias N/Ap −2.3 1.5 −4.8 Nominal — 35.925 90.160 203.151 5 Mean 22.366 35.232 82.585 191.400 % CV 1.9 5.5 2.1 2.5 % bias N/Ap −1.9 −8.4 −5.8 Nominal — 35.007 89.242 202.233 6 Mean 21.448 33.163 84.298 186.075 % CV 1.5 1.5 2.8 1.1 % bias N/Ap −5.3 −5.5 −8.0 Overall Mean 21.806 34.250 85.877 190.040 % CV 3.3 4.0 5.0 2.3 % bias N/Ap −3.2 −4.1 −6.2 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00015 TABLE 15 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Maize Seed Plant QC Sample Concentration Species/ (fmol/mg DW) Matrix Run QC 0 (endo) QC 1 QC 2 QC 3 Maize Nominal — 17.153 48.170 112.788 Seed 4 Mean 9.399 16.581 45.943 109.282 % CV 2.8 1.3 0.7 0.5 % bias N/Ap −3.3 −4.6 −3.1 Nominal — 17.264 48.281 112.899 5 Mean 9.510 17.204 44.058 104.704 % CV 6.7 2.0 1.1 3.4 % bias N/Ap −0.3 −8.7 −7.3 Nominal — 16.664 47.681 112.299 6 Mean 8.910 15.390 41.133 90.452 % CV 4.6 3.1 1.0 0.5 % bias N/Ap −7.6 −13.7 −19.5 Overall Mean 9.273 16.392 43.711 101.479 % CV 5.2 5.2 4.9 8.6 % bias N/Ap −3.8 −9.0 −9.9 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00016 TABLE 16 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Rice Seed Plant QC Sample Concentration Species/ (fmol/mg DW) Matrix Run QC 0 (endo) QC 1 QC 2 QC 3 Rice Nominal — 18.316 39.623 84.012 Seed 4 Mean 12.989 18.246 39.261 80.176 % CV 2.0 0.2 1.2 1.6 % bias N/Ap −0.4 −0.9 −4.6 Nominal — 18.770 40.077 84.466 5 Mean 13.443 18.313 37.925 79.321 % CV 1.0 2.6 1.6 0.3 % bias N/Ap −2.4 −5.4 −6.1 6 Mean — 18.199 39.506 83.895 % CV 12.872 17.776 37.534 78.577 % bias 1.5 2.8 1.6 0.9 Overall Mean 13.102 18.112 38.240 79.358 % CV 2.4 2.4 2.4 1.3 % bias N/Ap −1.7 −3.8 −5.7 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00017 TABLE 17 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Soybean Seed Plant QC Sample Concentration Species/ (fmol/mg DW) Matrix Run QC 0 (endo) QC 1 QC 2 QC 3 Soybean Nominal — 69.443 238.075 589.393 Seed 4 Mean 27.285 66.423 231.098 564.305 % CV 4.8 1.3 4.1 2.9 % bias N/Ap −4.3 −2.9 −4.3 Nominal — 70.057 238.689 590.007 5 Mean 27.899 65.957 221.397 554.994 % CV 1.9 1.6 3.0 0.5 % bias N/Ap −5.9 −7.2 −5.9 Nominal — 69.542 238.174 589.492 6 Mean 27.384 63.345 222.298 558.821 % CV 2.9 0.7 1.5 4.0 % bias N/Ap −8.9 −6.7 −5.2 Overall Mean 27.523 65.242 224.931 559.373 % CV 3.1 2.5 3.4 2.6 % bias N/Ap −6.4 −5.6 −5.1 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00018 TABLE 18 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Wheat Seed Plant QC Sample Concentration Species/ (fmol/mg DW) Matrix Run QC 0 (endo) QC 1 QC 2 QC 3 Wheat Nominal — 29.025 106.504 267.920 Seed 4 Mean 9.655 27.583 104.898 249.407 % CV 3.3 3.7 2.3 1.9 % bias N/Ap −5.0 −1.5 −6.9 Nominal — 29.356 106.835 268.251 5 Mean 9.986 26.971 96.079 248.314 % CV 3.5 0.8 1.4 1.9 % bias N/Ap −8.1 −10.1 −7.4 Nominal — 28.888 106.367 267.783 6 Mean 9.518 26.072 98.070 247.141 % CV 2.7 2.0 2.1 0.8 % bias N/Ap −9.7 −7.8 −7.7 Overall Mean 9.720 26.875 99.682 248.287 % CV 3.5 3.3 4.4 1.5 % bias N/Ap −7.6 −6.5 −7.4 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00019 TABLE 19 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Barley Forage Plant QC Sample Concentration Species/ (fmol/mg DW) Matrix Run QC 0 (endo) QC 1 QC 2 QC 3 Barley Nominal — 81.820 217.409 499.886 Forage 4 Mean 47.923 78.550 193.554 405.369 % CV 4.1 0.5 2.9 2.6 % bias N/Ap −4.0 −11.0 −18.9 Nominal — 85.186 220.775 503.252 5 Mean 51.289 80.505 191.912 437.244 % CV 5.8 3.7 2.2 5.4 % bias N/Ap −5.5 −13.1 −13.1 Nominal — 81.988 217.577 500.054 6 Mean 48.091 76.829 184.943 410.701 % CV 4.7 1.0 1.8 4.2 % bias N/Ap −6.3 −15.0 −17.9 Overall Mean 49.101 78.628 190.136 417.771 % CV 5.4 2.8 2.9 5.1 % bias N/Ap −5.3 −13.0 −16.6 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00020 TABLE 20 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Maize Forage Plant QC Sample Concentration Species/ (fmol/mg DW) Matrix Run QC 0 (endo) QC 1 QC 2 QC 3 Maize Nominal — 39.271 122.572 296.114 Forage 4 Mean 18.446 38.431 116.655 278.998 % CV 1.8 1.1 1.0 1.1 % bias N/Ap −2.1 −4.8 −5.8 Nominal — 40.864 124.165 297.707 5 Mean 20.039 38.792 110.403 271.007 % CV 1.4 1.4 4.9 3.0 % bias N/Ap −5.1 −11.1 −9.0 Nominal — 37.976 121.277 294.819 6 Mean 17.151 34.744 102.368 251.701 % CV 3.1 0.9 4.0 4.8 % bias N/Ap −8.5 −15.6 −14.6 Overall Mean 18.545 37.322 109.809 267.235 % CV 7.0 5.3 6.4 5.3 % bias N/Ap −5.2 −10.5 −9.8 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00021 TABLE 21 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Oat Forage QC Sample Concentration Plant (fmol/mg DW) Species/ QC 0 Matrix Run (endo) QC 1 QC 2 QC 3 Oat Nominal — 89.741 258.259 609.337 Forage 4 Mean 47.612 90.569 254.083 560.642 % CV 2.2 1.7 1.1 0.4 % bias N/Ap 0.9 −1.6 −8.0 Nominal — 91.916 260.434 611.512 5 Mean 49.787 87.243 232.532 562.473 % CV 8.6 2.1 1.7 1.3 % bias N/Ap −5.1 −10.7 −8.0 Nominal — 89.184 257.702 608.780 6 Mean 47.055 85.524 237.272 568.318 % CV 3.3 0.6 2.1 2.5 % bias N/Ap −4.1 −7.9 −6.6 Overall Mean 48.151 87.779 241.296 563.811 % CV 5.5 2.9 4.3 1.5 % bias N/Ap −2.8 −6.8 −7.6 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00022 TABLE 22 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Soybean Forage Plant QC Sample Concentration Species/ (fmol/mg DW) Matrix Run QC 0 (endo) QC 1 QC 2 QC 3 Soybean Nominal — 81.488 327.485 839.979 Forage 4 Mean 19.989 79.634 317.915 781.981 % CV 5.1 4.4 1.5 0.7 % bias N/Ap −2.3 −2.9 −6.9 Nominal — 80.962 326.959 839.453 5 Mean 19.463 75.541 289.104 781.906 % CV 2.4 3.1 2.7 1.1 % bias N/Ap −6.7 −11.6 −6.9 Nominal — 79.889 325.886 838.380 6 Mean 18.390 73.556 309.219 795.280 % CV 0.9 0.6 4.0 2.5 % bias N/Ap −7.9 −5.1 −5.1 Overall Mean 19.280 76.244 305.413 786.389 % CV 4.7 4.5 4.9 1.6 % bias N/Ap −5.6 −6.5 −6.3 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

TABLE-US-00023 TABLE 23 Intra- and Inter-Assay Precision and Accuracy Results for HPPD in Wheat Forage Plant QC Sample Concentration Species/ (fmol/mg DW) Matrix Run QC 0 (endo) QC 1 QC 2 QC 3 Wheat Nominal — 79.853 244.497 587.504 Forage 4 Mean 38.692 78.642 242.896 556.087 % CV 1.6 1.5 1.9 2.3 % bias N/Ap −1.5 −0.7 −5.3 Nominal — 82.721 247.365 590.372 5 Mean 41.560 76.780 226.970 530.906 % CV 6.2 1.7 0.9 4.8 % bias N/Ap −7.2 −8.2 −10.1 Nominal — 78.362 243.006 586.013 6 Mean 37.201 74.375 223.243 533.051 % CV 1.6 1.9 2.8 1.6 % bias N/Ap −5.1 −8.1 −9.0 Overall Mean 39.151 76.599 231.036 540.015 % CV 6.0 2.8 4.3 3.6 % bias N/Ap −4.6 −5.7 −8.2 Nominal = Actual concentrations used for calculations N = 3 for each QC in each run N/Ap = not applicable

Extraction Efficiency

[0137] Table 24 summarizes the efficiency of the protein extraction method from commodity crops. All plant species/matrices for HPPD reached acceptable extraction efficiency at a single iteration. The mean extraction efficiencies of HPPD from barley seed (59.9%), maize seed (69.8%), rice seed (73.9%), soybean seed (64.9%), wheat seed (54.3%), barley forage (69.8%), maize forage (76.3%), oat forage (78.4%), soybean forage (65.4%) and wheat forage (77.2%) demonstrate that the method meets an acceptable extraction efficiency assessment. Moreover, the CV value was below 20.0% for HPPD in all plant species/matrices and the amount in the final extraction was below 5.0% for all commodity crops except for barley and wheat seed.

TABLE-US-00024 TABLE 24 Extraction Efficiency of HPPD from Commodity Crops Mean Extraction Plant Species/ Efficiency % Mean of the Final Matrix of Protein (%) CV Extraction (%) Barley Seed 59.9 3.4 Maize Seed 69.8 9.6 4.7 Rice Seed 73.9 10.7 2.5 Soybean Seed 64.9 4.8 4.7 Wheat Seed 54.3 Barley Forage 69.8 3.2 2.3 Maize Forage 76.3 2.2 1.9 Oat Forage 78.4 7.7 1.4 Soybean Forage 65.4 8.6 4.0 Wheat Forage 77.2 1.4 1.7 N = 4 extraction iterations and three replicates per iteration Extraction efficiency was performed in run 3 See Appendix A, Table A14 for details Values in italic and bold are outside acceptance criteria, refer to section 5.1.3

[0138] Table 25 summarizes the dry extract stability of surrogate peptides at a nominal temperature of −20° C. for 6 days (146 hours 16 minutes). The mean peak response ratio of the stability samples was ≤25.0% CV and the % difference of the stability samples when compared to the Day 0 QC samples was within ±25.0% for the dry processed samples stability assessment.

TABLE-US-00025 TABLE 25 Stability of Commodity Crop Dry Extracts at a Nominal Temperature of −20° C. for 6 Days (146 Hours 16 Minutes) Peak Area Ratio of QC Samples Plant Species/ Day 0 Stability Matrix QC 1 QC 3 QC 1 QC 3 Barley Seed Mean 1.5202 8.5241 1.5545 8.7697 % CV 0.8 1.8 2.8 3.3 % Difference.sup.a N/Ap 2.3 2.9 Maize Seed Mean 1.2830 8.4564 1.2975 8.0179 % CV 1.3 0.5 3.8 1.6 % Difference.sup.a N/Ap 1.1 −5.2 Rice Seed Mean 2.0550 9.0298 2.0270 8.7436 % CV 0.2 1.6 3.2 2.0 % Difference.sup.a N/Ap −1.4 −3.2 Soybean Seed Mean 0.9453 8.0306 0.9219 7.6973 % CV 1.3 2.9 4.6 1.0 % Difference.sup.a N/Ap −2.5 −4.2 Wheat Seed Mean 0.8543 7.7249 0.8889 8.1248 % CV 3.7 1.9 3.0 0.5 % Difference.sup.a N/Ap 4.0 5.2 Barley Forage Mean 1.3903 7.1747 1.6767 8.2002 % CV 0.5 2.6 5.2 1.5 % Difference.sup.a N/Ap 20.6 14.3 Maize Forage Mean 1.1073 8.0387 1.0890 7.7595 % CV 1.1 1.1 2.1 1.0 % Difference.sup.a N/Ap −1.7 −3.5 Oat Forage Mean 1.2898 7.9840 1.2859 8.4485 % CV 1.7 0.4 3.5 3.6 % Difference.sup.a N/Ap −0.3 5.8 Soybean Forage Mean 0.7769 7.6286 0.7813 7.9080 % CV 4.4 0.7 10.6 2.8 % Difference.sup.a N/Ap 0.6 3.7 Wheat Forage Mean 1.1463 8.1054 1.1414 8.5251 % CV 1.5 2.3 4.5 4.3 % Difference.sup.a N/Ap −0.4 5.2 N = 3 for all QC; N/Ap = not applicable .sup.a% Difference − (Stability QC − Day 0 QC )/Day 0 QC × 100 Dry stability was performed in run 7 Refer to Appendix A, Table A15 for details

[0139] The purpose of this study was to validate the MS-based method for quantification of p-hydroxyphenylpyruvate dioxygenase (HPPD) protein in various commodity crops (barley, maize, rice, soybean, and wheat seed, and, barley, maize, oat, soybean and wheat forage) using LC-MS/MS. Surrogate peptides that are unique to the HPPD protein were used to determine the relative concentration. Commodity crop samples were used to evaluate method performance parameters including specificity, linearity, limits of quantitation, carryover, precision and accuracy, extraction efficiency and stability.

[0140] Evaluation of specificity showed no significant interference at the retention time of the non-labeled peptides (<30.0% difference in the average ratio of the two transitions between the blank and buffer) and SIL peptides (≤5.0% of SIL signal of QCO (endogenous)) in any of the commodity crop samples that were tested. All specificity parameters met acceptance criteria.

[0141] The lower limit of quantitation and the quantitative range in fmol/mg DW and μg/g DW for HPPD in the commodity crops are shown in Table 26.

TABLE-US-00026 TABLE 26 List of Commodity Crops, Surrogate Peptides, Lower Limit of Quantitation and Quantitative Range Plant Species/ Surrogate Lower Limit of Quantitation Quantitative Range Matrix Peptide fmol/mg DW μg/g DW fmol/mg DW μg/g DW Barley Seed SEQ ID NO: 1 4.520 0.209  4.520 to 271.200 0.209 to 12.567 Maize Seed SEQ ID NO: 12 2.585 0.122  2.585 to 155.077 0.122 to 7.289  Rice Seed SEQ ID NO: 1 1.776 0.083  1.776 to 106.543 0.083 to 5.001  Soybean Seed SEQ ID NO: 1 14.054 0.686 14.054 to 843.231 0.686 to 41.161 Wheat Seed SEQ ID NO: 1 6.457 0.301  6.457 to 387.429 0.301 to 18.060 Barley Forage SEQ ID NO: 1 11.300 0.524 11.300 to 678.000 0.524 to 31.418 Maize Forage SEQ ID NO: 2 6.941 0.326  6.941 to 416.486 0.326 to 19.576 Oat Forage SEQ ID NO: 1 14.044 0.660 14.044 to 842.657 0.660 to 39.602 Soybean Forage SEQ ID NO: 1 20.501 1.001  20.501 to 1230.086 1.001 to 60.045 Wheat Forage SEQ ID NO: 1 13.721 0.640 13.721 to 823.286 0.640 to 38.378
The intra- and inter-assay precision and accuracy of the method are summarized in Table 27.

TABLE-US-00027 TABLE 27 Intra- and Inter-Assay Precision and Accuracy Range for HPPD in Commodity Crops Intra-Assay Inter-Assay Plant species/ Precision Accuracy Precision Accuracy Matrix (% CV) (% bias) (% CV) (% bias) Barley Seed 0.8 to 5.5 −8.4 to 1.5 2.3 to 5.0 −6.2 to −3.2 Maize Seed 0.5 to 6.7 −19.5 to −0.3 4.9 to 8.6 −9.9 to −3.8 Rice Seed 0.2 to 2.8  −6.3 to −0.4 1.3 to 2.4 −5.7 to −1.7 Soybean Seed 0.5 to 4.8  −8.9 to −2.9 2.5 to 3.4 −6.4 to −5.1 Wheat Seed 0.8 to 3.7 −10.1 to −1.5 1.5 to 4.4 −7.6 to −6.5 Barley Forage 0.5 to 5.8 −18.9 to −4.0 2.8 to 5.4 −16.6 to −5.3  Maize Forage 0.9 to 4.9 −15.6 to −2.1 5.3 to 7.0 −10.5 to −5.2  Oat Forage 0.4 to 8.6 −10.7 to 0.9   1.5 to 5.5 −7.6 to −2.8 Soybean Forage 0.6 to 5.1 −11.6 to −2.3 1.6 to 4.9 −6.5 to −5.6 Wheat Forage 0.9 to 6.2 −10.1 to −0.7 2.8 to 6.0 −8.2 to −4.6

[0142] A linear equation was determined to adequately represent the concentration/detector response relationship for HPPD in all commodity crops. A data weighting of 1/× was used for all commodity crops.

[0143] The efficiency of the protein extraction method was 59.9% for barley seed, 69.8% for maize seed, 73.9% for rice seed, 64.9% for soybean seed, 54.3% for wheat seed, 69.8% for barley forage, 76.3% for maize forage, 78.4% for oat forage, 65.4% for soybean forage and 77.2% for wheat forage. The CV of the first round of extraction was below 20.0% for all commodity crops except for wheat seed which was 27.5% CV. However the Precision and Accuracy results of QCO (endogenous) for wheat seed coming from a single extraction demonstrate that a precision ≤20.0% was achieved.

[0144] The processed stability (dry extract) was evaluated for 6 days at −20° C. The stability assessment met acceptance criteria. The CV was ≤25.0% and the % difference of peak area ratios between stability and Day 0 QCs were within ±25.0% for all commodity crops.

[0145] All performance parameters evaluated met the defined acceptance criteria except for the % of the final extraction of barley and wheat seed which was 8.2 and 6.2% respectively as well as the precision of the first round of extraction for wheat seed which was at 27.5% CV. Since the concentration of HPPD in samples analysis will be determined from a single extraction (first round) and adjusted for % extraction efficiency and a precision of ≤20.0% was achieved for wheat seed in the precision and accuracy runs there is no impact on the outcome of the study. Based on the results of this study, the mass spectrometry-based method has been confirmed to be suitable for quantification of HPPD protein for the list of commodity crops evaluated in this study in accordance with GLPS.

[0146] While the invention has been described in connection with specific embodiments thereof, it will be understood that the inventive device is capable of further modifications. This patent application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features herein before set forth and as follows in scope of the appended claims.

[0147] All publications and patent applications mentioned in this specification are indicative of the level of skill of those skilled in the art that this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.