Strategy to Improve the Quantitative LC-MS Analysis of Molecular

Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry ...
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Strategy to Improve the Quantitative LC-MS Analysis of Molecular Ions Resistant to Gas-Phase Collision Induced Dissociation: Application to Disulfide-Rich Cyclic Peptides. Eugene Ciccimaro, Asoka Ranasinghe, Celia D'arienzo, Carrie Xu, Joelle Onorato, Dieter M. Drexler, Jonathan L. Josephs, Michael A Poss, and Timothy Olah Anal. Chem., Just Accepted Manuscript • DOI: 10.1021/ac502678y • Publication Date (Web): 05 Nov 2014 Downloaded from http://pubs.acs.org on November 15, 2014

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Strategy to Improve the Quantitative LC-MS Analysis of Molecular Ions Resistant to Gas-Phase Collision Induced Dissociation: Application to Disulfide-Rich Cyclic Peptides Eugene Ciccimaro*, Asoka Ranasinghe, Celia D’Arienzo, Carrie Xu, Joelle Onorato, Dieter M. Drexler, Jonathan L. Josephs†, Michael Poss, Timothy Olah Bristol-Myers Squibb, Princeton, New Jersey 08543, United States

ABSTRACT: Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive LC-MS/MS assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte’s surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte’s unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma.

ground interferences of isobaric m/z (b+). In HRAM SIM analysis, selected ions containing both nominally isobaric background ions and target analyte are then detected (2a). In contrast, HRAM survivor-SIM (Scheme 1, Panel B) passes selected ions through a collision cell where unstable background ions are removed by CID fragmentation (2b) prior to HRAM detection of the surviving precursor ion (3b). Although this type of analysis has been described for small molecule analysis on TQMS8, to our knowledge survivor-SIM has not been described previously using HRAM analysis or for application to small peptides or biologics. Cyclic peptides are a class of molecules often resistant to CID, possibly due to their knotted tertiary structure and/or nonmobile proton(s). These peptides often produce low intensity and complex CID product ion spectra.9 Disulfide-rich cyclic peptides are found throughout various biological systems and show unique proteolytic stability.10 Due to their stability in blood and potential for oral dosing, this class of molecules is being explored as a potential drug modality.11-14 Although not head-to-tail cyclized, other bioactive peptides with inter-chain disulfide bonds can, in some cases, also be resistant to CID making them candidates for survivor-SIM analysis. To illustrate the concept of HRAM survivor-SIM bioanalysis, natriuretic peptides were selected as model compounds. Atrial natriuretic peptide (ANP) is a 27-AA peptide that forms a central loop through a disulfide bridge between residues 7-23, similar to closely related family members brain natriuretic peptide and C-type natriuretic peptide.15 Although structurally unique, ANP was found to behave identically to in-house engineered head-to-tail cyclized disulfide-rich peptides during survivorSIM analysis and is used as a tool peptide here to demonstrate the power of survivor-SIM analysis for enabling

Tandem mass spectrometry (MS/MS) employing collision induced dissociation (CID, referred to here as low energy fragmentation in a collision cell1) enables unit resolution mass spectrometers, such as triple-stage quadrupole (TQMS) and ion trap (IT) instruments, with the selectivity necessary to perform sensitive and specific LC-MS bioanalysis of molecules in complex matrices.2 However, various molecular ions derived from, for example, large disulfide containing peptides, sterols and fatty acids are not amenable to CID fragmentation, making development of sensitive and specific LC-MS/MS assays for these types of molecules very challenging.3 Fragmentation inefficiency, in simplest terms, is described by the loss of signal intensity between a precursor ion (measured prior to CID) and fragment ions (measured following CID).4 Elegant solutions have been devised for the analysis of these molecules by unit resolution LC-MS/MS and selected ion monitoring (SIM), but these approaches can be labor intensive, dependent on analytically unreliable adduct ions5 and, in the case of unit resolution SIM, can suffer from poor signal-tonoise (S/N). Offering an alternative to TQMS for analysis of molecular ions resistant to CID, high resolution accurate mass (HRAM) employing time-of-flight (ToF) or Orbitrap mass spectrometers affords selectivity without MS/MS due to the resolving power of the mass analyzer.6,7 The limit of trace level bioanalysis by HRAM, however, can be determined by the inability to resolve a target analyte from isobaric chemical interferences. In this report, we take advantage of an analyte’s resistance to CID fragmentation to perform HRAM SIM after the filtering of selected ions through a collision cell. Scheme 1 (Panel A) illustrates traditional HRAM SIM, where the majority of background ions (B+) emitted by the ESI plume are filtered by a quadrupole (1a) selecting only a narrow m/z region of interest containing the target analyte (A+) and back-

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SIM

(2a) HRAM Detection

(1a) Precursor Selection

+ESI

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B+ B+ B+ B+ b + B+ A+ + b B+ B+ B+

A+ b + b + A+ b+ + b +A+ b+ b

Survivor-SIM (1b) Precursor Selection +ESI

(2b) CID

B+ B+ B+ B+ b + B+ A + + B+ B+ b B+

A+ bx+ bx+ A+ bx + + bx b +A +bx + x

(3b) HRAM Detection A+ + A A+

Scheme 1: HRAM SIM and Survivor-SIM Showing Simplified Experimental Events. support of drug discovery PK experiments on CID resistant molecules. Using this unique technique, we have observed a 510 fold improvement in LLOQ compared to traditional HRAM SIM for CID-resistant peptides in plasma extracted samples. MATERIALS AND METHODS Sample Preparation. Human ANP (CAS No:91917-63-4) was acquired from Anaspec (Fremont, CA). Rat plasma was spiked with standard and a 12 point dilution series from 0.5 to 5000 ng/mL and QC samples in plasma were prepared without internal calibration in replicate. 50 µL plasma was then immediately protein precipitated 1:2 with methanol containing 1% formic acid and the supernatant was analyzed by LC-MS. Engineered disulfide-rich cyclic peptides were produced inhouse and prepared essentially as described for ANP. Instrumentation and Liquid Chromatography. TQMS experiments were performed on a Triple Quadrupole MS API6500 (AB Sciex, Framingham, MA). Ultra-high pressure liquid chromatography systems were used in-line with a quadrupole-Orbitrap (Q ExactiveTM, Thermo Fisher Scientific, San Jose, CA) fitted with a HESI source. Reversed phase chromatography was performed on a 2.1 x 50 mm charged surface hybrid (CSH C18, 1.7 µm) column (Waters corp., Milford, MA) heated to 60 °C. Aqueous mobile phase (water containing 0.1% formic acid) and organic mobile phase (acetonitrile containing 0.1% formic acid) were used for gradient elution at 600 µL/min from 5 to 45% organic in 5 min. Mass Spectrometry. MS on the Q Exactive was done in positive ionization mode using a spray voltage of 3000 V, probe temperature of 500 °C, capillary temperature of 300 °C, sheath gas of 60 (arb. units), auxiliary gas of 25 (arb. Units) and spare gas of 3 (arb. units). SIM analysis targeted the most sensitive charge species (determined from method development experiments) and applied an isolation width of 3 amu, an automatic gain control setting of 1e5, a maximum ion time setting of 150 ms, and a resolution setting of 35,000. Survivor-SIM analysis used identical settings to the SIM analysis with the exception

that higher-energy collision dissociation (HCD)-mode was employed at a normalized collision setting of 20 units (z = 4). Data Analysis. Qualitative and quantitative review of results was performed using vendor supplied software (Thermo Fisher Scientific). For quantification, an extracted ion chromatogram (EIC) was generated using the summation of signal from the monoisotopic (M0), M1, M2, and M3 isotopologues extracted using a ±10 ppm mass window. For generation of calibration curves, EIC area response was plotted versus expected concentration; curves were fitted with quadratic regression and a 1/X weighting. RESULTS AND DISCUSSION Resistance to CID. ANP showed similar LC-MS/MS behavior to engineered disulfide-rich cyclic molecules of similar size analyzed in our lab. By positive-mode ESI, the molecular ion of these molecules existed in multiple charge states (typically a distribution between [M+3H]+3 and [M+6H]+6 ) that were resistant to fragmentation. Figure 1 a-c shows an example of the MS properties of a cyclic peptide infused on a TQMS. The most intense precursor charge state ([M+4H]+4) was isolated for MS/MS and remained intact during CID up to ~ 25 eV CE, as observed in the spectra (Figure 1a) and represented graphically by signal intensity versus collision energy (Figure 1c). Further increasing the CE induced fragmentation that was both inefficient (as indicated by the observed ~ 100x loss of signal between the most intense fragment ion formed and the molecular ion, Figure 1c) and complex, as demonstrated by the multitude of low abundance, poorly resolved fragment ions formed following CID (Figure 1b). This lack of formation of an abundant fragment ion(s) prevented sensitive detection by tandem mass analysis. SIM and survivor-SIM on a TQMS were investigated, but in general resulted in unacceptable LLOQ (>100 nM) due to low S/N, which was likely the result of remaining nominally isobaric interferences. It has been shown that HCD on an Orbitrap platform produces similar fragmentation behavior for most molecules to beam-type TQMS CID (HCD is therefore

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Figure 1. Unique stability of disulfide containing cyclic peptide during CID on TQMS(a-c) and Orbitrap(d) systems

referred to as CID here for simplicity).16 Indeed, the unique CID resistance of these cyclic molecules was observed across MS platforms. This is illustrated in Figure 1d, which shows the MS/MS spectra of an engineered disulfide containing cyclic peptide compared to the spectra of a “normal” peptide on the Q Exactive. The co-isolation and fragmentation of both parent ions with no collision energy showed the normal peptide [M+4H]+4 ion at greater intensity to the cyclic peptide [M+4H]+4 ion. However, by 15 NCE, the normal peptide molecular ion was no longer detected within this m/z region (due to dissociation to fragment ions or charge stripping) while the cyclic peptide ion intensity was relatively unaltered. HRAM SIM. The required sensitivity and selectivity needed to support PK studies was unachievable due to CID inefficiency by traditional LC-MS/MS (on either a TQMS or HRAM platform). Failing sensitive LC-MS/MS method development for these cyclic molecules, precursor ion quantification using HRAM was explored. HRAM SIM of ANP was performed by focusing the analysis on a narrow mass window surrounding the [M+4H]+4 ion (Table 1). Using this SIM method, a LLOQ in extracted plasma samples of 5 ng/mL (1.6 nM) was achieved for ANP (Table 1, supplemental). Example EICs are shown in Figure 2 for HRAM SIM analysis of blank extracted plasma and 2 ng/mL ANP extracted plasma. As apparent from the apex spectra (Figure 2, apex spectra) only the M1 and M3 isotopologues of ANP were free of chemical interference at 2 ng/mL extracted from plasma. At the spectral level, nonbaseline resolved interferences resulted in a mass shift of analyte isotopes away from calculated in some scans (causing the analyte to fall out of the EIC window). While in other scans, such as the apex peak shown in Figure 2C, an incorporation of overlapping interference into the analyte isotope signal altered the observed isotopic abundance resulting in a large deviation from theoretical relative abundance. The analytical impact of these interferences was inaccuracy at the limit of detection as indicated by the calculated concentration at the 2 ng/mL level

approaching 70% deviation from expected (Table 2, supplemental). Although HRAM SIM showed significant improvement over LC-MS/MS results, sensitivity still did not meet the requirements to support a full PK time coarse, requiring the need for additional method refinement.

Table 1: Calculated m/z and Relative Isotopic Abundance for [M+4H]+4 ion of ANP Indicating Isotopologues Used for Quantification. LC PEAK 14000

Apex Spectra 100

(A)

10000

NL: 2.9e3 772.0895

(C)

12000

771.1852

serum blank

8000

50

RT: 1.74 AA: 1090

4000 2000 0

14000

(B)

RT: 1.75 AA: 10419

12000

2 ng/mL

10000

Relative Abundance (%)

6000

Signal Intensity

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0

771.1201

100

771.3737 770.8693

8000

NL: 5.3e3

(D) 772.0915

50

6000 4000 2000 0

1.2

1.4

1.6 1.8 2.0 Time (min)

2.2

0

770.5

771.0

771.5

772.0

772.5

m/z

Figure 2. HRAM SIM analysis of blank extracted plasma and 2 ng/mL ANP extracted from plasma showing EIC peak and corresponding apex spectra.

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ence. In such cases, where LLOQ is chemical noise limited, gaining additional selectivity using MS/MS through a traditional manner on a HRAM platform is analytically beneficial.18 Importantly, we demonstrate here that for ions that are resistant to CID, additional selectivity is still gained using MS/MS, but in a nontraditional manner, by removal of interfering ions and the noisefree detection of the surviving precursor ion of interest (termed HRAM survivor-SIM).

HRAM Survivor-SIM. The LLOQ using HRAM SIM was limited by chemical interference. To improve sensitivity, HRAM survivor-SIM was developed to eliminate noise from the analysis. Survivor-SIM of ANP showed a significant improvement (10-fold) in analytical performance, allowing for an LLOQ of 0.5 ng/mL (160 pM) and accurate quantification over four orders of dynamic range (Table 3, supplemental). As compared to the SIM result (inaccuracy at 0.5 ng/mL = ~200%) accuracy at 0.5 ng/mL was dramatically improved (less than 5% difference from theoretical). As demonstrated in the EIC and spectra shown in Figure 3, chemical interference across all isotopologues was eliminated in blank plasma (3A and 3C), resulting in accurate detection of the isotopic cluster at 2 ng/mL (Figure 3). Although the isotopic relative abundance for the M0 ion was not perfect in the single apex scan, observed ~40% rather than the expected ~60%, the cluster as a whole was dramatically more accurate than observed in SIM analysis. Spectral accuracy of isotopic abundance on the Orbitrap platform is proven.17 In our observation, accuracy improved with increased ion S/N, as apparent upon inspecting apex spectra from HRAM survivor-SIM at increasing ANP concentration (Figure 1, supplemental). In addition to improving the spectral results, the EIC of the 2 ng/mL sample, as compared to this level using SIM, showed symmetric LC peak shape without interfering shoulders. Analysis of engineered head-to-tail disulfide-rich cyclic peptides showed similar improvements in sensitivity and accuracy when compared to HRAM SIM. LC PEAK 14000

Improved Acquisition Speed. An additional benefit of eliminating chemical interference on the Orbitrap platform is that it allows for a reduced effective resolution setting enabling for faster acquisition speeds. For most survivor-SIM experiments, 35,000 resolution was found adequate to resolve any remaining isobaric interference, resulting in more scans across an LC peak (or more analytes measured per acquisition) than would be possible at a higher resolution setting. Although most interference was removed using survivor-SIM, remaining nominally isobaric interferences were still observed, suggesting unit resolution instruments (~1,0001,500 resolving power) will still be negatively impacted analytically by this remaining background. Alternatives. HRAM survivor-SIM is a simple and sensitive means to measure disulfide bond containing cyclic peptides. Although alternative approaches could be considered, they may suffer from important caveats. For example, MS methods incorporating electron-transfer dissociation (ETD) may be useful for the analysis of disulfide containing cyclic peptides by MS/MS.19 Extending ETD to a quantitative assay however may prove challenging due to longer MS/MS reaction times. Another possible alternative strategy is the reduction and alkylation of these molecules followed by MS/MS detection. Once reduced, these molecules may prove more amenable to CID. Essentially a derivatization step, this approach would add additional sample preparation time and possibly error, especially in cases where an authentic internal standard is not available. More importantly, for drug optimization purposes, reduction and alkylation may be precluded since measurement of the intact non-reduced molecule is necessary to indicate the structural integrity of the circulating species.

Apex Spectra 100

(A)

NL: 0

(C)

12000 10000

serum blank

8000

50 6000

Relative Abundance (%)

4000

Signal Intensity

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

2000 0

14000

RT: 1.76 AA: 12524

(B)

12000

0

770.8682

(D)

CONCLUSIONS

771.1185 z=4

2 ng/mL

10000

NL: 5.6e3

z=4

100

771.3721 z=4

8000

For compounds that fragment inefficiently by CID, precursor ion detection by HRAM offers superior sensitivity to TQMS approaches. We highlight further analytical improvement over traditional HRAM analysis for the quantification of disulfide-bond containing cyclic peptides using HRAM survivor-SIM. Cyclic peptides are analytically challenging molecules and are being explored within the biopharmaceutical industry as a potential drug modality due to their inherent plasma stability and potential for oral formulation and dosing. The utility of survivor-SIM, however, could potentially be applied to a wider range of molecules (any CID resistant molecular ion). For example, large peptides and small proteins containing disulfide bonds, especially those containing “cystine knot” motifs (growth factors such as nerve growth factor, transforming growth factor b2, and platelet derived growth factor)21 will likely show improved quantification using survivor-SIM. Using this approach, the target analyte is essentially selected from background based on the unique structural characteristic that affords it CID resistance. Further, one may consider the possibility that any given analyte, even if only marginally resistant to fragmentation compared to its chemical interferent, will benefit from survivor-SIM when applying finely tuned collision energy. Since detection of a molecular ion is inherently more sensitive (absolute signal) than detection of a fragment ion, this

50

770.6187

6000

z=4

4000

771.6162 z=4

2000 0

1.2

1.4

1.6 1.8 2.0 Time (min)

2.2

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0

770.5

771.0

771.5 m/z

772.0

772.5

Figure 3. HRAM survivor-SIM analysis of blank extracted plasma and 2 ng/mL ANP extracted from plasma showing EIC peak and corresponding apex spectra. Improved Selectivity. It should not be overlooked that a significant improvement in assay performance ~50-fold was realized by simply switching from TQMS based approaches to HRAM SIM on the Orbitrap. This platform not only provides high resolution, but accurate mass (~3 ppm) over several days. The combination of resolving power and stable accurate mass, allows accurate EIC of a precursor ion, achieving quantitative performance on par with SRM assays by TQMS.20 In complex matrices, even at high resolving power the SIM LLOQ may however be defined by chemical noise rather than analyte signal. For many biologics, extraction from tissue or plasma using organic solvents or other means (e.g. solid-phase extraction or affinity enrichment) will generally not produce a final sample completely free of isobaric interfer-

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mode of HRAM analysis could prove more sensitive (lower LLOQ) over MS/MS detection.

(11) Northfield, S. E.; Wang, C. K.; Schroeder, C. I.; Durek, T.; Kan, M. W.; Swedberg, J. E.; Craik, D. J. European journal of medicinal chemistry 2014, 77, 248-257. (12) Ji, Y.; Majumder, S.; Millard, M.; Borra, R.; Bi, T.; Elnagar, A. Y.; Neamati, N.; Shekhtman, A.; Camarero, J. A. Journal of the American Chemical Society 2013, 135, 11623-11633. (13) Craik, D. J.; Daly, N. L.; Waine, C. Toxicon : official journal of the International Society on Toxinology 2001, 39, 43-60. (14) Chan, L. Y.; Gunasekera, S.; Henriques, S. T.; Worth, N. F.; Le, S. J.; Clark, R. J.; Campbell, J. H.; Craik, D. J.; Daly, N. L. Blood 2011, 118, 6709-6717. (15) Levin, E. R.; Gardner, D. G.; Samson, W. K. The New England journal of medicine 1998, 339, 321-328. (16) de Graaf, E. L.; Altelaar, A. F.; van Breukelen, B.; Mohammed, S.; Heck, A. J. Journal of proteome research 2011, 10, 4334-4341. (17) Erve, J. C.; Gu, M.; Wang, Y.; DeMaio, W.; Talaat, R. E. Journal of the American Society for Mass Spectrometry 2009, 20, 2058-2069. (18) Gallien, S.; Duriez, E.; Crone, C.; Kellmann, M.; Moehring, T.; Domon, B. Molecular & cellular (19) Peterson, A. C.; Russell, J. D.; Bailey, D. J.; Westphall, M. S.; Coon, J. J. Molecular & cellular proteomics : MCP 2012, 11, 1475-1488. (20) Duan, X.; Engler, F. A.; Qu, J. Journal of mass spectrometry : JMS 2010, 45, 1477-1482. proteomics : MCP 2012, 11, 1709-1723. (21) McDonald, N. Q.; Hendrickson, W. A. Cell 1993, 73, 421-424.

ASSOCIATED CONTENT Supporting Information As noted in text: Supplemental Table 1 (Quantitative Performance of HRAM SIM for Analysis of ANP Extracted from Plasma), Supplemental Table 2 (Quantitative Performance of HRAM Survivor-SIM for Analysis of ANP Extracted from Plasma), and Supplemental Figure 1 (HRAM survivor-SIM apex spectra at increasing ANP concentration extracted from plasma) are available free of charge via the Internet at http://pubs.acs.org.

AUTHOR INFORMATION Corresponding Author *Address: Route 206 and Province Line Rd, Princeton, NJ 08543. Tel: (609) 252-5590. E-mail: [email protected]

Additional Addresses †ThermoFisher Scientific, San Jose, CA

Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.

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