Application of Differential Mobility Spectrometry Coupled with Multiple Ion Monitoring for Quantitation of Peptides Not Suited for MRM Analysis

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1 Application of Differential Mobility Spectrometry Coupled with Multiple Ion Monitoring for Quantitation of Peptides Not Suited for MRM Analysis Yuan-Qing Xia *1, Eugene Ciccimaro, Jr. 2, Naiyu Zheng 2, Mingshe Zhu 2 1 SCIEX; 2 Bristol-Myers Squibb Company 2015 ASMS, St. Louis, MO, June 4, 2015

2 Peptide quantitation by LC/MS in drug discovery and development Quantitation of peptides and signature peptides from protein digests by LC/MS has become highly demanding Bioanalysis of protein and peptide therapeutics Protein and peptide biomarkers Drug target proteins as well as CYP enzymes and transporter proteins Triple quadrupole-based MRM is the method of choice for peptide quantitation in the Pharma industry Excellent selectivity and sensitivity for a majority of peptide analytes Most bioanalytical labs have mainly used triple quad instruments so that no needs for new LC/MS instrument, training in operation, instrument qualification and software validation AB Sciex

3 MRM approach for bioanalytical quantitation of protein therapeutics 1) Sample prep 2) Enzyme digestion * Choice of surrogate peptide(s) for quantitation Protein LC/MS/MS analysis AB Sciex

4 Challenges in peptide quantitation by triple quad-based MRM approaches Sample preparation, selection of surrogate peptides/enzymes, develop/optimize LC-MS method, peptide stability, non-specific binding, accuracy/precision, etc. Some peptides have no suitable CID fragment ions for MRM Low CID fragmentation efficiency led to poor sensitivity (cyclic peptides) Only generate non-specific small fragments, resulted in poor MRM specificity If a peptide, especially cyclic peptide, is not suited for quantitation by MRM, what are the analytical alternatives? HRMS full scan MS AB Sciex

5 An example of human atrial natriuretic peptide (ANP) not suitable for MRM bioanalysis Ciccimaro et al. Anal Chem AB Sciex

6 Analysis of atrial natriuretic peptide by HR-SIM and HR- Survivor-SIM HR-SIM HR-Survivor-SIM Ciccimaro et al. Anal Chem AB Sciex

7 If a bioanalytical lab only has triple quadrupole MS without HRMS instrument, how to handle peptides not suitable for quantitation by MRM? Multiple ion monitoring (MIM, lack of selectivity?) DMS-MIM AB Sciex

8 Use of sunflower trypsin inhibitor (SFTI) as a model compound to assess DMS-MIM in cyclic peptide quantification SFTI is a 14 amino acid cyclic peptide which possesses exceptionally potent trypsin-inhibitory activity and has promise as a stable peptide-based drug template It combines a head-to-tail cyclized backbone and a disulfide bond Sample preparation was done by mixing plasma with methanol in a 1:1 ratio SCIEX QTRAP 6500 with SelexION TM DMS Shimadzu Prominence UHPLC system LC column was Atlantis dc18 (2x150 mm, 5 µ) Mobile phases were 0.1% formic acid in water and acetonitrile GRCTKSIPPICFPD AB Sciex

9 Product ion spectra of SFTI a) CE 21 ev c) CE 41 ev b) CE 31 ev d) CE 51 ev SFTI had no major MSMS fragment ions under these 4 different collision energies It was unable to develop a sensitive MRM method for the quantitation MIM of m/z 757>757 was selected for evaluation for bioanalysis AB Sciex

10 Qtrap-based MIM-EPI workflow for drug metabolite identification MIM Ion trap Precursor ion fixed Minimal Fragmentation Precursor ion fixed - MIM: Select precursor ion in Q1 and the same precursor ion in Q3 - MIM can trigger sensitive MS/MS acquisition - MS/MS dataset acquired by MIM can be processed for metabolite detection - M. Yao et al., JMS M. Yao et al., RCM, AB Sciex

11 Use of MIM only approach in analysis of SFTI in rat plasma a) ng/ml b) 5 ng/ml A high baseline was obtained using LC-MIM (m/z 757>757) approach in analysis of SFTI in rat plasma 5 ng/ml (b) could be consider as LLOQ with S/N equals AB Sciex

12 Differential mobility spectrometry DMS can eliminate matrix interference, reduce high chemical background and separate matrix/isobaric interference Consisted of a pair of planar electrodes Separate ions based on the difference of ion mobility in the gas phase between electrodes Located between ESI/APCI sprayer and MS orifice/operated in atmospheric pressure Short residence times (5 ms) and pause time (20 ms) Uniform conditions for the addition of chemical modifiers Transparent Mode Allows all ions to be transmitted by turning off voltages DMS Q3 Q1 Q AB Sciex

13 DMS-MIM method development MIM Optimize collision energy and declustering potential Optimize source parameters Gas 1&2 and curtain gas IonSpray voltage Source temperature DMS Separation voltage (SV) Separation voltage waveform Compensation voltage (COV) DC offset potential between two electrodes DMS resolution enhancement (DR) Flow rate of gas AB Sciex

14 Effect of separation voltage and DMS resolution enhancement (gas flow) on COV and analyte signal responses A) Effect of SV B) Effect of gas flow DMS resolution Blue: open Pink: off Red: low Green: medium SV: 2500 V SV: 3500 V COV shifted to more positive at higher separation voltage while the peak responses remain The lower the DMS gas flow, the higher the resolution AB Sciex

15 DMS method development - COV ramp at a fixed separation voltage via LC injection Optimize COV via LC injection has the advantage of using the exact same elution conditions to separate matrix endogenous interference and high baseline At fixed SV (3500 V), an optimized COV was obtained which provided the best sensitive and selective responses for the analyte AB Sciex

16 Comparison of MIM and DMS-MIM in quantitative bioanalysis of SFTI in rat plasma DMS-MIM achieved LLOQ ng/ml while MIM had LLOQ of 5 ng/ml Excellent accuracy and precision for the calibration curve AB Sciex

17 Proposed decision tree for quantitation of peptides using triple quadruple mass spectrometer Peptide molecule or signature peptides Acquire MS/MS spectral data of all of tested peptide(s) peptide(s) generate MS/MS fragment(s) suited for MRM peptide(s) have low fragmentation efficiency not suitable for developing MRM method Some peptide(s) have low fragmentation efficiency and some peptide(s) generate MS/MS fragment(s) suited for MRM LC-MRM method LC-DMS-MIM method Combined LC-MRM & LC-DMS-MIM AB Sciex

18 Acknowledgements Bristol-Myers Squibb Asoka Ranasinghe Li Ma Jianing Zeng Anne-Francoise Aubry Tim Olah Mark Arnold Sciex Suma Ramagiri Kelli Jonakin Tom Biesenthal Jeff Miller Anthony Romanelli Joseph Fox Elliott Jones AB Sciex

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