Development of an SPE-LC/MS/MS Assay for the Simultaneous Quantification of Amyloid Beta Peptides in Cerebrospinal Fluid in Support of Alzheimer s Research Dr. Erin E. Chambers Waters Corporation Presented by Dr. Diego Rodriguez Cabaleiro Waters Europe 211 Waters Corporation 1
Background: Amyloid β Peptides Clinical significance of amyloid β peptides Formation of aggregates/plaques in the brain is a critical event in Alzheimer s Disease Drug development strategies aimed at lowering production of these peptides or enhancing their clearance o Inhibition/modulation of beta and gamma secretase enzyme Current analytical methodologies ELISA- based assays Immunoprecipitation (IP) followed by LCMSMS 211 Waters Corporation 2
Amyloid β Peptides for Quantification in CSF Amyloid β 1-38 DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGG MW 4132, pi 5.2, HPLC index 96 Amyloid β 1-4 DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV MW 433, pi 5.2, HPLC index 13 Amyloid β 1-42 DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA MW 4516, pi 5.2, HPLC index 117 Internal standards are N15 labeled versions of 1-38, 1-4, and 1-42 211 Waters Corporation 3
Waters Regulated Bioanalysis System Solution Sample Preparation Solutions Best in class ACQUITY UPLC I-Class The fastest and most resolving LC without compromise in robustness ACQUITY UPLC Columns Different choices for best performance TQ-S Most sensitive MS UNIFI Compliant, Interactive workflow-driven data platform Service Installation, maintenance & training Compliance services 211 Waters Corporation 4
Outline Introduction Mass Spectrometry Liquid Chromatography Choice of Standard Curve Matrix Solid Phase Extraction Partial Validation 211 Waters Corporation 5
Why LCMSMS? Why an LCMSMS based assay? ELISA assays not practical for discovery, no antibodies available yet Challenges with ELISA assays o time consuming, expensive to develop o require separate assay for each peptide o limited linear dynamic range o Possible cross reactivity Benefits of LC/MS/MS for peptides LCMSMS provides single assay for multiple amyloid peptides Broad linear dynamic range Accurate, precise Universal Faster, cheaper method development 211 Waters Corporation 6
Specific Challenges in Developing an LCMSMS Assay for Amyloid β Peptides Extremely hydrophobic Very poor peptide solubility High level of aggregation High level of non-specific binding (NSB) Low MS sensitivity Very large and hydrophobic Form many low abundance fragments Specificity in matrix 211 Waters Corporation 7
ESI- MSMS Spectra for Amyloid β 1-42 1 1126.76 M-4H 4- Daughters of 1127ES- 1.55e5 -H 2 O 1122.33 1117.78 Non-specific water loss 5 55 6 65 7 75 8 85 9 95 1 15 11 115 12 125 13 135 14 145 m/z 211 Waters Corporation 8
ESI+ MSMS Spectra for Amyloid β 1-42 1 b39 153.3 b4 178.52 Daughters of 1129ES+ 1.62e4 M+H 4+ b38 b41 116.86 b32 b34 1256.5 b33 b35 914.52 942.73 975.36 128.67 b36 12.8 b35 b38 b39 b4 1371.29 13.38 144.12 1437.73 b34 1.65 5 55 6 65 7 75 8 85 9 95 1 15 11 115 12 125 13 135 14 145 m/z 4+ fragments 3+ fragments 211 Waters Corporation 9
Amyloid β Peptide 1-42: Identification of Fragments with BioLynx In Silico Fragmentation Model Fragment choice is 4+ b 4 ion 211 Waters Corporation 1
Positive Ion versus Negative Ion Detection: Specificity 1-42 in Human CSF 25pgmL_hCSF_3291_2x 2.1 2: MRM of 3 Channels ES- 91.2 > 897.6 (a Beta 1-42) 7.5e4 2.12 Amyloid β 1-42 ESI- 6.4 1.12 2.7 5.54 2.21 5.66 3.88 4.6 4.27 4.39 4.89 5.5 5.95 25pgmL_hCSF_3291_2x 1: MRM of 3 Channels ES+ 6.39 1129 > 178.5 (a Beta 1-42) 1.2e4 Amyloid β 1-42 6.58 6.62 7.7 ESI+ 1 1.21 3.82 6.6 6.2 6.43 7.18 6.92 6.5 7.19 Time 211 Waters Corporation 11
Positive Ion versus Negative Ion Detection: Specificity 1-38 in Human Plasma Amyloid β 1-38 6.45 2: MRM of 3 Channels ES- 825 > 821.3 (a Beta 1-38) 3.35e5 5.2 7.3 ESI- 2.12 5.93 6.7 4.61 4.91 5.11 5.23 5.69 6.69 1: MRM of 3 Channels ES+ 5.93 133.5 > 1.3 (a beta 1-38) 2.99e4 Amyloid β 1-38 5.94 ESI+ 5.99 6.67 4.96 6. 5.1 5.81 4.83 6.65 2.18 4.22 4.6 5.41 7.17 6.95 7.28 7.57 7.39 7.94 Time 211 Waters Corporation 12
Effect of Using Higher m/z Precursor/Fragment: plasma 4- Precursor/fragment 2.48 MRM of 2 Channels ESa Beta 1-38 3.2e4 3.36.5 1. 1.5 2. 2.5 3. 3.5 MRM of 2 Channels ES- 2.48 a Beta 1-38 3.26e4 5- Precursor/fragment 1.22 1.63 1.67 1.96 2.49.5 1. 1.5 2. 2.5 3. 3.5 Time 211 Waters Corporation 13
Xevo TQ-S MSMS Conditions Xevo TQ-S MS operated in ESI+ mode MRM Transitions: Peptide Name Precursor Ion 4+ Product Ion 4+ Product Ion ID Cone voltage (V) Collision energy (ev) Amyloid β 1-38 133.5 1.3 b 36 33 23 Amyloid β 1-38 N15 IS 146 112.5 3 22 Amyloid β 1-4 183 153.6 b 39 33 25 Amyloid β 1-4 N15 IS 196 166.5 35 22 Amyloid β 1-42 1129 178.5 b 4 28 3 Amyloid β 1-42 N15 IS 1142.5 191.5 35 28 211 Waters Corporation 14
Impact of MS Platform Change Solvent Standard Comparison: Area counts for 5 pg/ml standard Xevo TQ Xevo TQ-S amyloid β 1-38 18 1468 amyloid β 1-4 133 1741 amyloid β 1-42 54 1589 211 Waters Corporation 15
Xevo TQ-S LOD: 12.5 pg/ml solvent standard in 5/5 elution solvent/water 12pt5pgmL_abetas_7261_1 Sm (SG, 3x5) 1 5.81 125. MRM of 3 Channels ES+ 1129.5 > 178.9 (Amyloid Beta 1-42) 5.58e3 Area Amyloid β 1-42 Peak Area 125 3. 3.5 4. 4.5 5. 5.5 6. 6.5 7. 7.5 12pt5pgmL_abetas_7261_1 Sm (SG, 3x5) MRM of 3 Channels ES+ 1 183.3 > 154 (Amyloid Beta 1-4) 5.58e3 Area 5.62 98. Amyloid β 1-4 Peak Area 98 3. 3.5 4. 4.5 5. 5.5 6. 6.5 7. 7.5 12pt5pgmL_abetas_7261_1 Sm (SG, 3x5) MRM of 3 Channels ES+ 1 5.39;129.9 133.75 > 1.75 (Amyloid Beta 1-38) 5.58e3 Area Amyloid β 1-38 Peak Area 13 3. 3.5 4. 4.5 5. 5.5 6. 6.5 7. 7.5 Time 1µL injection 211 Waters Corporation 18
Outline Introduction Mass Spectrometry Liquid Chromatography Choice of Standard Curve Matrix Solid Phase Extraction Partial Validation 211 Waters Corporation 19
UPLC Conditions: Final Method Column: 2.1 X 15mm, ACQUITY BEH C18 3Å, 1.7μm Mobile phase A:.3 NH 4 OH by volume, or.1 absolute Mobile Phase B: 9/1 ACN/mobile phase A Temperature: 5 C SNW: 65/25/1 ACN/water/NH 4 OH SNW volume: 6 µl WNW: 9/1 water/acn +.3 NH 4 OH WNW volume: 6 µl Flow rate:.2 ml/min Injection mode: partial loop Injection Volume: 1 µl Injection Solvent for standards: SPE elution solvent diluted with water; SPE elution solvent = 75 ACN, 15 water, 1 NH 4 OH Gradient Table 211 Waters Corporation 2
Representative Chromatogram: Extracted Spiked Artificial CSF Amyloid β 1-4 5.85 4.6e4 5.6 Amyloid β 1-42 Amyloid β 1-38 6.3 6.87 7.65 4.89 5.3 6.31 7.97 2 Time 211 Waters Corporation 21
Representative Chromatography: Extracted Human CSF Sample Basal Levels in Human CSF hcsf_pool1_basal_421_1 1-42 N15 IS 6.2 6.1 6.6 MRM of 6 Channels ES+ 1142.5 > 191.5 (a Beta 1-42 N15) 2.77e4 6.53 6.76 7.47 7.69 hcsf_pool1_basal_421_1 MRM of 6 Channels ES+ 6.3 1129 > 178.5 (a Beta 1-42) 6.1 6.5 8.54e3 1.25 1.85 5.88 6.47 4.9 5.42 6.61 7.77.18 7.67 6.18 7.817.91 1 hcsf_pool1_basal_421_1 MRM of 6 Channels ES+ 5.85 196 > 166.5 (a Beta 1-4 N15) 5.87 6.29e4 5.89 4.8 6.37 6.58 hcsf_pool1_basal_421_1 MRM of 6 Channels ES+ 5.85 183 > 153.6 (a Beta 1-4) 1-4 1.16e5 5.88 5.52 hcsf_pool1_basal_421_1 MRM of 6 Channels ES+ 5.61 146 > 112.5 (a Beta 1-38 N15) 5.62 4.5e4 5.67 5.36 6.46 6.67 7.7 hcsf_pool1_basal_421_1 MRM of 6 Channels ES+ 5.61 133.5 > 1.3 (a beta 1-38) 2.31e4 5.63 1.19 1-42 1-4 N15 IS 1-38 N15 IS 1-38 211 Waters Corporation 22 5.27 5.67 5.9 6.39 6.75 7.2 7.98 Time
Outline Introduction Mass Spectrometry Liquid Chromatography Choice of Standard Curve Matrix Solid Phase Extraction Partial Validation 211 Waters Corporation 23
Average Basal Levels in Human CSF: Comparison of Results with Different Standard Curve Preparations Standard curves prepared from either artificial CSF or by over-spiking human CSF Conc.(ng/mL) Source 1 Conc. (ng/ml) Source 2 Amyloid β 1-38 Conc from curve in art CSF.82.826 Conc from curve in human CSF.679 n/a Conc.(ng/mL) Source 1 Conc. (ng/ml) Source 2 Amyloid β 1-4 Conc from curve in art CSF 3.713 3.136 Conc from curve in human CSF 4.335 n/a average.75 std deviation.1 RSD 13.32 average 4.24 std deviation.44 RSD 1.93 Conc.(ng/mL) Source 1 Conc. (ng/ml) Source 2 Amyloid β 1-42 Conc from curve in art CSF 1.15.763 Conc from curve in human CSF 1.189.84 average 1.147.784 std deviation.59.29 RSD 5.178 3.7 *Human CSF corrected for basal level 211 Waters Corporation 24
Outline Introduction Mass Spectrometry Liquid Chromatography Choice of Standard Curve Matrix Solid Phase Extraction Partial Validation 211 Waters Corporation 25
Sample Extraction: Pretreatment Sample Pretreatment Spike human or artificial CSF + 5 rat plasma samples, mix Equilibrate samples at room temperature for 3 minutes Remove 5 µl spiked artificial CSF (to which 5 rat plasma was added) for standard curves, or human/monkey CSF (basal level or over-spike QC s) Add 5µL 5M guanidine HCl Shake samples at room temperature for 45 minutes Add 5µL 4 H 3 PO 4 in water, mix Note: 4X less sample is used than TQ MS method: 5 µl instead of 2 µl 211 Waters Corporation 26
Sample Extraction: Final Method Oasis MCX μelution Plate Condition: 2 µl MeOH Equilibrate: 2 µl 4 H 3 PO 4 Amyloid β Peptide SPE Recovery 1-38 94 1-4 92 1-42 9 Load: 15 μl diluted sample (pretreated sample: 5 µl human CSF, 5µL 5M guanidine HCl, 5µL 4 H 3 PO 4 in water) Wash 1: 2 µl 4 H 3 PO 4 Wash 2: 2 µl 1 ACN in water (by volume) Elute: 2 X 25 µl 75/1/15 ACN/conc. NH 4 OH/water (by volume) Dilute: 25 µl water Inject: 1 µl 211 Waters Corporation 27
Key Attributes for High Extraction Recovery Wash with no more than 1 ACN Removes polar interferences Does not impact recovery of 1-38 (earliest eluting/least hydrophobic of these 3 amyloid β peptides) Elute with no less than 75 ACN Provides required elutropic strength for 1-4 and 1-42 (the more hydrophobic of these 3 peptides) Elute with no less than 1 NH 4 OH Provides required solubility to fully elute 1-42 (least soluble/most hydrophobic of these 3 peptides) Addition of rat plasma to artificial CSF to eliminate nonspecific binding increases SPE recovery in this matrix from 6 on average to >9 Guanidine HCl denaturation Improves reproducibility of method; eliminates aggregation and protein binding 211 Waters Corporation 28
Impact of MS Platform: Standard Curve and QC Range Comparison 2 µl sample 5 µl sample Xevo TQ Xevo TQ-S Standard Curve Range.1 to 1 ng/ml.25 or.5 to 1 ng/ml QC Range.2 to 6 ng/ml.4 to 6 ng/ml 211 Waters Corporation 3
Outline Introduction Mass Spectrometry Liquid Chromatography Choice of Standard Curve Matrix Solid Phase Extraction Partial Validation 211 Waters Corporation 31
Summary of Samples Extracted Standard curves prepared in artificial CSF + 5 Rat plasma Calibration points are.25,.5,.1,.25,.35,.5,.75, 1, 5, 7.5, and 1 ng/ml Basal levels in human CSF 3 individual sources pooled human CSF samples, 1 source cynomalgous monkey 6 replicates from each source QC samples Prepared in each of the human CSF matrices 7 concentrations:.4,.75,.15,.2,.8, 2 and 6 ng/ml over-spike N=3 for each concentration, from each source of CSF 211 Waters Corporation 32
Representative Chromatogram: Basal Levels of Amyloid β 1-38 in Human and Monkey CSF hcsf_pool1_basal_421_1 Basal Level Amyloid β 1-38 5.61 MRM of 6 Channels ES+ 133.5 > 1.3 (a beta 1-38) 2.31e4 Human CSF, pooled sample 1 5.27 1.19 6.75 5.79 5.9 6.39 7.2 7.98 hcsf_pool2_basal_421_1 MRM of 6 Channels ES+ 5.61 133.5 > 1.3 (a beta 1-38) 5.6 2.96e4 Human CSF, pooled sample 2 5.63 5.64 5.66 1.12 2.12 5.26 5.91 6.23 6.546.74 7.13 hcsf_pool3_basal_421_1 MRM of 6 Channels ES+ 5.61 133.5 > 1.3 (a beta 1-38) 1.33e4 Human CSF, pooled sample 3 6.5 6.74 2.12 3.99 5.94 1.22 6.21 6.96 7.62 7.86 1 cyno_csf_pool_basal_421_1 MRM of 6 Channels ES+ 5.62 133.5 > 1.3 (a beta 1-38) 2.43e4 Monkey CSF, pooled sample 1 5.6 5.59 5.65 2.12 5.4 5.23 5.74 6.18 1.11.29 6.36 6.79 6.96 7.71 7.82 Time 211 Waters Corporation 33
Representative Chromatogram: Basal Levels of Amyloid β 1-4 in Human and Monkey CSF Basal Level Amyloid β 1-4 hcsf_pool1_basal_421_1 Human CSF, pooled sample 1 5.85 5.88 MRM of 6 Channels ES+ 183 > 153.6 (a Beta 1-4) 1.16e5 5.52 hcsf_pool2_basal_421_1 MRM of 6 Channels ES+ 5.85 183 > 153.6 (a Beta 1-4) 1.47e5 Human CSF, pooled sample 2 hcsf_pool3_basal_421_1 MRM of 6 Channels ES+ 5.86 183 > 153.6 (a Beta 1-4) 8.91e4 Human CSF, pooled sample 3 cyno_csf_pool_basal_421_1 MRM of 6 Channels ES+ 5.86 183 > 153.6 (a Beta 1-4) 1.37e5 Monkey CSF, pooled sample 1 6.57 Time 211 Waters Corporation 34
Representative Chromatogram: Basal Levels of Amyloid β 1-42 in Human and Monkey CSF Basal Level Amyloid β 1-42 hcsf_pool1_basal_421_1 Human CSF, pooled sample 1 6.3 MRM of 6 Channels ES+ 1129 > 178.5 (a Beta 1-42) 6.61e3 1.25 1.85 5.93 5.42 5.71 6.47 7.18 6.59 7.717.817.91 hcsf_pool2_basal_421_1 MRM of 6 Channels ES+ 6.4 1129 > 178.5 (a Beta 1-42) 8.77e3 Human CSF, pooled sample 2 1 1.85 3.91 4.98 hcsf_pool3_basal_421_1 MRM of 6 Channels ES+ 6.4 1129 > 178.5 (a Beta 1-42) 4.87e3 Human CSF, pooled sample 3 5.74 5.91 6.3 6.41 6.64 7.88 6.87 2 99 1.1 1.22 1.89 5.16 5.9 6.1 6.42 6.74 6.92 7.48 cyno_csf_pool_basal_421_1 MRM of 6 Channels ES+ 1.86 6.4 1129 > 178.5 (a Beta 1-42) 8.13e3 Monkey CSF, pooled sample 1 7.93-1 1.16 2.9 4.76 4.91 5.94 6.36 6.47 7.86 6.88 7.5 7.24 Time 211 Waters Corporation 35
Baseline Levels of Amyloid β in Pooled Human and Monkey CSF Amyloid Beta 1-38 Human CSF Pool 1 ng/ml Human CSF Pool 3 ng/ml Human CSF Replicate # Pool 2 ng/ml 1 1.585 2.354 1.14 1.713 2 1.65 2.13 1.371 1.65 3 1.614 2.464.95 1.947 4 1.657 1.939 1.68 1.541 5 1.82 2.158 1.471 1.675 6 1.486 1.995 1.167 1.644 Mean 1.635 2.169 1.264 1.688 Std. Deviation.11.24.262.14 CV 6.7 9.4 2.7 8.3 Cyno CSF Pool 1 ng/ml Amyloid Beta 1-42 Human CSF Pool 1 ng/ml Human CSF Pool 3 ng/ml Human CSF Replicate # Pool 2 ng/ml 1.519.616.421.675 2.421.656.481.621 3.542.644.534.623 4.471.567.348.659 5.476.573.487.7 6.561.713.51.688 Mean.498.628.463.661 Std. Deviation.52.55.68.33 CV 1.4 8.7 14.7 5.1 Cyno CSF Pool 1 ng/ml Amyloid Beta 1-4 Human CSF Pool 1 ng/ml Human CSF Pool 3 ng/ml Human CSF Replicate # Pool 2 ng/ml 1 3.83 4.31 2.541 3.699 2 3.391 3.776 2.593 3.989 3 3.292 3.598 2.58 3.525 4 2.884 3.533 2.612 3.956 5 3.131 3.23 2.58 3.284 6 3.656 3.619 2.49 3.595 Mean 3.24 3.631 2.554 3.675 Std. Deviation.269.266.49.268 CV 8.3 7.3 1.9 7.3 Cyno CSF Pool 1 ng/ml 211 Waters Corporation 36
Response Residual Representative Standard Curve: Amyloid β 1-42 Compound name: Amyloid Beta 1-42 Correlation coefficient: r =.998799, r^2 =.9976 Calibration curve:.887923 * x +.13161 Response type: Internal Std ( Ref 2 ), Area * ( IS Conc. / IS Area ) Curve type: Linear, Origin: Exclude, Weighting: 1/x, Axis trans: None 1.. -1. Conc 5.. Conc. 2. 4. 6. 8. 1. 211 Waters Corporation 37
Representative Standard Curve: Amyloid β 1-42 Name Type Std. Conc RT Area IS Area Response Conc. Dev blank artificial CSF 5.73 19.7 7. 5 pg/ml artificial CSF Standard.5 5.71 23.4 362.5.64.57 14 1 pg/ml artificial CSF Standard.1 5.71 39.8 3585.1.19.18 8.1 25 pg/ml artificial CSF Standard.25 5.71 778.3 3737.3.28.22-12 35 pg/ml artificial CSF Standard.35 5.71 1267.3 3693.8.343.372 6.2 5 pg/ml artificial CSF Standard.5 5.71 1494.7 3566.8.419.457-8.5 75 pg/ml artificial CSF Standard.75 5.71 2733.5 4152..658.727-3.1 1 ng/ml artificial CSF Standard 1 5.71 3166.8 3792.5.835.926-7.4 5 ng/ml artificial CSF Standard 5 5.72 14773.9 3148.3 4.693 5.27 5.4 7.5 ng/ml artificial CSF Standard 7.5 5.72 24576.9 3877. 6.339 7.125-5 1 ng/ml artificial CSF Standard 1 5.72 33343.3 3662.5 9.14 1.238 2.4 211 Waters Corporation 38
Average Deviation Values for all Overspike QC Samples QC.4 ng/ml QC.75 ng/ml QC.15 ng/ml QC.2 ng/ml QC.8ng/mL QC 2 ng/ml QC 6 ng/ml Amyloid β 1-38 Human CSF 1 and 2 2.3 5.8-3.2 7.3 14.8 5.1 13.1 Amyloid β 1-4 Human CSF 1 and 2 -.8-3.2-1.9 2.5-2.6-4.2-3.8 Amyloid β 1-42 Human CSF 1 and 2 1.3 13.4-3.6 5.6 2. -.6 -.2 211 Waters Corporation 4
Conclusions Single flexible LC/MS/MS platform developed for simultaneous quantification of multiple amyloid peptides Highly selective sample preparation based on mixed-mode SPE Improved MS selectivity using positive ion mode and sequence ion fragments High sensitivity using new MS platform Highly reproducible, accurate, and precise Sample pretreatment and choice of SPE and LC solutions eliminate handling (NSB, losses, etc.) problems One method for multiple Aβ peptides, advantage over ELISA which requires individual assays for each peptide Fast, simple sample prep 211 Waters Corporation 42
Total Solution for Regulated Bioanalysis - Bioanalysis of Peptides Sample Prep Kits and protocols µelution plate No evaporation & reconstitution 15x concentration UNIFI IntelliStart and BioLynx functionalities Multiple charge precursor ions ACQUITY UPLC I Class & Columns Lower dispersion Dedicated PST columns Longer columns if needed Lowest carryover Xevo TQ-S Stepwave Mass range Minimal dwell time RADAR PIC SERVICE Application support and troubleshooting 211 Waters Corporation 43
Acknowledgements Mary E. Lame, Neuroscience Research Unit, Pfizer Global R&D 211 Waters Corporation 44