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Surrogate H/D Detection Strategy for Protein Conformational Analysis Using .... The potential of extracting H/D data from amide linkages using product...
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Anal. Chem. 2009, 81, 7900–7907

Articles Surrogate H/D Detection Strategy for Protein Conformational Analysis Using MS/MS Data Andrew J. Percy, Gordon W. Slysz, and David C. Schriemer* Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada Amide hydrogen/deuterium exchange (H/DX) measurements by mass spectrometry provide a powerful tool for probing the structure and dynamics of proteins. In order to extend such measurements to complex multiprotein systems, new methods for delivering higher sensitivity and sequence coverage are required. In this study, we investigated the utility of tandem mass spectrometry (MS/MS) for providing an alternative to the conventional MS mode of operation applied to bottom-up H/DX experiments. Specifically, we aimed to determine whether differential deuteration measurements of collisionally induced dissociation (CID)-generated product ions can serve as effective surrogates for their corresponding intact peptide, thus providing an additional dimension for analysis. Replicate deuterium measurements of calmodulin (in its apo and holo forms) were obtained from peptic digests in both the MS and MS/MS domains and studied as a function of % deuteration, fragment ion selection, and contaminant level. We show that successful acquisition of MS/MS data for deuterated peptides requires controlled expansion of the isotopic envelope by limiting the range of deuterium label applied in the exchange-in reaction (e50%) and that automation of ion selection via data-dependent acquisition is ultimately dependent upon peak detection algorithms. Upon full transmission of the isotopic envelope, fragment data demonstrate that all ions, with the exception of neutral loss fragment ions, return deuteration ratios reflecting the apo/holo transition that are in general agreement with values obtained from the corresponding precursor ions. The agreement is limited primarily by the ion statistics for each fragment, as the base peak in the MS/MS spectra provided the best correlation regardless of its m/z. We highlight that the freedom to select the base peak as a surrogate for the precursor ion derives from extensive H/D scrambling inducible under conventional CID conditions. When spectral interference prohibits conventional H/DX-MS measurements, we further show that the surrogate approach recovers accurate and precise per-peptide deuteration levels. Thus, a generalized strategy is presented in which CID-based automated H/DX-MS/MS acquisition can be used to extend measurements to complex protein 7900

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systems, exceeding the peptide capacity of conventional H/DX-MS alone. The structural analysis of proteins and their complexes is essential for understanding function and translating this understanding into the development of molecular therapies. However, conventional techniques for structural analysis, such as X-ray crystallography, provide only snapshots of structure. As function ultimately derives from structural dynamics,1 methods for monitoring the flux in protein conformations under biologically relevant conditions are needed. An array of MS-based methodologies have been developed to probe both the structure and dynamics of individual proteins as well as multicomponent complexes. These include cross-linking strategies to define nearest neighbors2-7 and a growing number of monovalent chemical labeling approaches with temporal resolution ranging from µs to minutes.8-12 Mass spectrometry is usually applied to proteolytic digests to localize the labels at peptide-level resolution or, in select cases, at amino acid resolution using tandem MS strategies. Of the various labeling strategies available, hydrogen/ deuterium exchange (H/DX) techniques remain most popular, partly due to the simplicity of the experiment and the availability of scaleable computational strategies for data analysis.13-18 H/DX allows a direct measure of both local and global protein stability, * To whom correspondence should be addressed. Phone: 403-210-3811. Fax: 403-270-0834. E-mail: [email protected]. (1) Henzler-Wildman, K.; Kern, D. Nature 2007, 450, 964–972. (2) Iglesias, A. H.; Santos, L. F. A.; Gozzo, F. C. J. Am. Soc. Mass. Spectrom. 2009, 20, 557–566. (3) Tanaka, Y.; Bond, M. R.; Kohler, J. J. Mol. Biosyst. 2008, 4, 473–480. (4) Wilkins, B. J.; Daggett, K. A.; Cropp, T. A. Mol. Biosyst. 2008, 4, 934–936. (5) Novak, P.; Giannakopulos, A. E. J. Mass Spectrom. 2007, 13, 105–113. (6) Nadeau, O. W.; Artigues, A.; Jeyasingham, M. D.; Sage, J.; Villar, M. T.; Wyckoff, G. J.; Carlson, G. M. Mol. Cell Proteomics 2008, 7, 739–749. (7) Gingras, A. C.; Gstaiger, M.; Raught, B.; Aebersold, R. Nat. Rev. Mol. Cell Biol. 2007, 8, 645–654. (8) Mendoza, V. L.; Vachet, R. W. Anal. Chem. 2008, 80, 2895–2904. (9) Konermann, L.; Tong, X.; Pan, Y. J. Mass Spectrom. 2008, 43, 1021–1036. (10) Xu, G. H.; Chance, M. R. Chem. Rev. 2007, 107, 3514–3543. (11) Hambly, D. M.; Gross, M. L. J. Am. Soc. Mass. Spectrom. 2005, 16, 2057– 2063. (12) Simmons, D. A.; Konermann, L. Biochemistry 2002, 41, 1906–1914. (13) Slysz, G. W.; Baker, C. J.; Bozsa, B. M.; Dang, A.; Percy, A. J.; Bennett, M.; Schriemer, D. C. BMC Bioinf, 2009, 10, 162–175. (14) Pascal, B. D.; Chalmers, M. J.; Busby, S. A.; Griffin, P. R. J. Am. Soc. Mass. Spectrom. 2009, 20, 601–610. (15) Chalmers, M. J.; Busby, S. A.; Pascal, B. D.; He, Y.; Hendrickson, C. L.; Marshall, A. G.; Griffin, P. R. Anal. Chem. 2006, 78, 1005–1014. 10.1021/ac901148u CCC: $40.75  2009 American Chemical Society Published on Web 08/14/2009

and it can be used to characterize both kinetic and equilibrium intermediatestatesunderawiderangeofexperimentalconditions.19-21 The experiment involves exchanging labile hydrogen with deuterium using D2O-containing solutions. Amide hydrogens within the protein function as reporters, as they offer measurable exchange rates and near-complete representation of the protein at residue-level resolution. While NMR spectroscopy retains a role for the measurement of deuterium exchange rates, particularly for individual residues in smaller protein systems, mass spectrometry provides new opportunities for the analysis of much larger protein systems. This includes the analysis of protein polymers,22,23 viral particles,24 protein-protein complexes,25 protein-ligand interactions,15,26-29 and the impact of co/ post-translational modifications on conformational states and function.30,31 Experimentally, the most common implementation of H/DXMS involves the measurement of deuteration data from LC/MS analyses of pepsin digests under slowed exchange conditions arising from reduced pH and temperature.17,32,33 Under these “quenched” conditions, back-exchange still exists, thus creating an operational requirement for rapid LC analyses in order to preserve maximum labeling information.34 In this environment, the peak capacity of the LC/MS system is limited and likely insufficient for interrogating protein states of any great size and complexity. Higher resolution LC and MS systems,34,35 coupled with reduced labeling strategies,36 extend the protein molecular weight range considerably, but the analysis of large proteins with low-specificity enzymes inevitably generates substantial isobaric (16) Hotchko, M.; Anand, G. S.; Komives, E. A.; Eyck, L. F. T. Protein Sci. 2006, 15, 583–601. (17) Englander, J. J.; Mar, C. D.; Li, W.; Englander, S. W.; Kim, J. S.; Stranz, D. D.; Hamuro, Y.; Woods, V. L. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7057–7062. (18) Palmblad, M.; Buijs, J.; Hå´kansson, P. J. Am. Soc. Mass. Spectrom. 2001, 12, 1153–1162. (19) Krishna, M. M.; Hoang, L.; Lin, Y.; Englander, S. W. Methods 2004, 34, 51–64. (20) Bai, Y.; Sosnick, T. R.; Mayne, L.; Englander, S. W. Science 1995, 269, 192–197. (21) Bai, Y.; Milne, J. S.; Mayne, L.; Englander, S. W. Proteins: Struct., Funct., Genet. 1993, 17, 75–86. (22) Xiao, H.; Verdier-Pinard, P.; Fernandez-Fuentes, N.; Burd, B.; Angeletti, R.; Fiser, A.; Horwitz, S. B.; Orr, G. A Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 10166–10173. (23) Chik, J. K.; Schriemer, D. C. J. Mol. Biol. 2003, 334, 373–385. (24) Lanman, J.; Lam, T. T.; Emmett, M. R.; Kirk, M.; Sakalian, M.; Barnes, S.; Marshall, A. G.; Prevelige, P. Biophys. J. 2002, 82, 324A–325A. (25) Komives, E. A. Int. J. Mass Spectrom. 2005, 240, 285–290. (26) Huzil, J. T.; Chik, J. K.; Slysz, G. W.; Freedman, H.; Tuszynski, J.; Taylor, R. E.; Sackett, D. L.; Schriemer, D. C. J. Mol. Biol. 2008, 378, 1016–1030. (27) Tsutsui, Y.; Wintrode, P. L. Curr. Med. Chem. 2007, 14, 2344–2358. (28) Yan, X.; Broderick, D.; Leid, M. E.; Schimerlik, M. I.; Deinzer, M. L. Biochemistry 2004, 43, 909–917. (29) Xiao, H.; Kaltashov, I. A.; Eyles, S. J. J. Am. Soc. Mass. Spectrom. 2003, 14, 506–515. (30) Houde, D.; Arndt, J.; Domeier, W.; Berkowitz, S.; Engen, J. R. Anal. Chem. 2009, 81, 2644–2651. (31) Betts, G. N.; Geer, P. v. d.; Komives, E. A J. Biol. Chem. 2008, 283, 15656– 15664. (32) Hoofnagle, A. N.; Resing, K. A.; Ahn, N. G. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 1–25. (33) Zhang, Z. Q.; Smith, D. L. Protein Sci. 1993, 2, 522–531. (34) Zhang, H. M.; Bou-Assaf, G. M.; Emmett, M. R.; Marshall, A. G. J. Am. Soc. Mass. Spectrom. 2009, 20, 520–524. (35) Wales, T. E.; Fadgen, K. E.; Gerhardt, G. C.; Engen, J. R. Anal. Chem. 2008, 80, 6815–6820. (36) Slysz, G. W.; Percy, A. J.; Schriemer, D. C. Anal. Chem. 2008, 80, 7004– 7011.

interferences. Ion suppression effects also worsen with larger protein systems as chromatographic runtimes cannot be extended, which together with high ion loads at any given time point reduces dynamic range. As the analytical goal is 100% sequence coverage, with maximum sequence redundancy, this overlap reduces the quality of the analysis. In a recent study of R/β tubulin by H/DXTOF-MS (a protein with MW 110,000), approximately 50% of detectable peptic peptides were rejected because of m/z redundancy and reduced dynamic range under H/DX-MS conditions.26 Tandem MS methods have the potential to increase the sensitivity and comprehensiveness of H/DX analyses. Numerous studies assessing the utility of MS/MS for H/DX measurements have focused on the question of spatial resolution, in which MS/ MS data are evaluated for returning single-amide resolution of labeling. This would provide an NMR-like quality to the MS data sets. The potential of extracting H/D data from amide linkages using product ions was first suggested by Chait37 and Anderegg38 and has been examined further since. The general consensus of many studies, reviewed in recent work by Hamuro39 and Konermann,40 is that intrapeptide deuterium randomization (or scrambling) is common under conventional CID conditions applied to peptide digests. This may imply that CID-based MS/MS would have little value in supporting H/DX-MS measurements and that electron-based fragmentation techniques (e.g., electron capture or electron transfer dissociation), which do not appear to induce scrambling, should instead be implemented.41-43 However, there remains an important role for peptide-level measurements in many applications, thus the potential for improving peptide-level deuteration measurements via CID-based MS/MS still exists. This study extends our investigations of enhanced methods for deuteration measurement.36 It explores conditions under which CID, after mass selection, may be used for quantitating differential deuteration, in which fragment ions function as surrogates for the precursor ion. As most applications of H/DX-MS involve a comparison between two or more protein states, accurate and precise differential measurements are essential for supporting a functional understanding of a perturbed system. We therefore investigated deuteration ratios in the MS and MS/MS domains using calmodulin (CaM), a bilobed protein with four Ca2+ binding sites,44 as a model system. This protein has been extensively investigated in earlier studies by NMR spectroscopy45,46 as well as H/DX-MS methods.36,47,48 Since differences in deuterium (37) Katta, V.; Chait, B. T. J. Am. Chem. Soc. 1993, 115, 6317–6321. (38) Anderegg, R. J.; Wagner, D. S.; Stevenson, C. L.; Borchardt, R. T. J. Am. Soc. Mass Spectrom. 1994, 5, 425–433. (39) Hamuro, Y.; Tomasso, J. C.; Coales, S. J. Anal. Chem. 2008, 80, 6785– 6790. (40) Ferguson, P. L.; Konermann, L. Anal. Chem. 2008, 80, 4078–4086. (41) Rand, K. D.; Zehl, M.; Jensen, O. N.; Jørgensen, T. J. D. Anal. Chem. 2009, 81, 5577–5584. (42) Rand, K. D.; Adams, C. M.; Zubarev, R. A.; Jørgensen, T. J. D. J. Am. Chem. Soc. 2008, 130, 1341–1349. (43) Zehl, M.; Rand, K. D.; Jensen, O. N.; Jørgensen, T. J. D. J. Am. Chem. Soc. 2008, 130, 17453–17459. (44) Chattopadhyaya, R.; Meador, W. E.; Means, A. R.; Quiocho, F. A. J. Mol. Biol. 1992, 228, 1177–1192. (45) Zhang, M.; Tanaka, T.; Ikura, M. Nat. Struct. Biol. 1995, 2, 758–767. (46) Kuboniwa, H.; Tjandra, N.; Grzesiek, S.; Ren, H.; Klee, C. B.; Bax, A. Nat. Struct. Biol. 1995, 2, 768–776. (47) Zhu, M. M.; Rempel, D. L.; Zhao, J.; Giblin, D. E.; Gross, M. L. Biochemistry 2003, 42, 15388–15397. (48) Nemirovskiy, O.; Giblin, D. E.; Gross, M. L. J. Am. Soc. Mass. Spectrom. 1999, 10, 711–718.

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uptake between the apo and holo protein states lead to extensive but variable perturbation of deuterium exchange rates throughout the structure, CaM served as an excellent model system for assessing the sensitivity of MS/MS methods for perturbation analyses. Data analysis was facilitated by Hydra, a multifunctional software package for H/DX-MS that we revised to automate the extraction of deuteration levels and ratios from product ions.13 In the current study, we show that primary sequence ions (b or y) are effective surrogates for the precursor in reporting differential deuteration levels. The implications of these findings are discussed. EXPERIMENTAL SECTION Chemicals and Reagents. Trifluoroacetic acid (TFA), ethylenediaminetetraacetic acid (EDTA), sodium dihydrogen phosphate (NaH2PO4), potassium chloride (KCl), calcium chloride dihydrate (CaCl2 · 2H2O), sodium hydroxide (NaOH), D2O, horse heart myoglobin (MW 16,940), porcine renin substrate (all >95% pure), and hydrochloric acid (HCl, 37%) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Formic acid (FA, 98%) was acquired from Fluka (Buchs, Switzerland), while glycine (Gly, 99.7%) was obtained from GE Healthcare (Uppsala, Sweden). Immobilized pepsin (supplied as a slurry in 50% glycerol and 0.05 M sodium azide) was obtained from Pierce (Rockford, IL, USA), and C18 beads (Magic 200 Å, 5 µm) were purchased from Michrom Bioresources (Auburn, CA, USA). Ca2+-free CaM (MW 16,707) was prepared and purified according to a previously established procedure49 and provided by Dr. H. Vogel (Department of Biological Sciences, University of Calgary, Calgary, AB, Canada). Mobile phases were prepared using HPLC-grade water and acetonitrile from Fisher Scientific (Fair Lawn, NJ, USA). Solutions. Aqueous stock solutions of myoglobin (290 µM) and Ca2+-free CaM (360 µM) in 5 mM EDTA were prepared, aliquoted, and stored at -80 °C until use. The buffer solutions for the apo-CaM labeling experiments consisted of KCl (100 mM), NaH2PO4 (10 mM), and EDTA (5 mM) at pH 7.0. The holo-CaM buffer was similar except for the substitution of CaCl2 (2.1 mM) for EDTA. Chromatographic mobile phases consisted of 0.02% FA, 0.03% TFA, and 3% ACN (for mobile phase A) and 0.02% FA, 0.03% TFA, and 97% ACN (for mobile phase B). These solutions were vacuum degassed, with sonication, prior to use. Deuterium Labeling Conditions. Prior to conducting the deuterium exchange-in reaction, CaM stock solutions were diluted with an equal volume of 10X EDTA buffer (for apo-CaM) or 10X Ca2+ buffer (for holo-CaM) and to initiate labeling, these solutions were 5-fold diluted with 0, 5, 10, 20, 30, 40, and 50% (v/v) D2O to a protein concentration of 4.5 µM CaM. Deuterium exchange-in was conducted for 2 min at 20 °C. The termination of labeling and the initiation of peptic digestion were achieved by the addition of an aliquot of the labeled sample (10 µL) to a chilled slurry of immobilized pepsin in 0.1 M Gly-HCl (pH 2.3). Digestion proceeded for 2.5 min at 0 °C with gentle mixing. Digestion was terminated by centrifugation, and an aliquot of the chilled supernatant (45 pmol) was immediately injected onto the HPLC-MS system for analysis. All analyses were performed in quintuplicate (from labeling to (49) Matsuura, I.; Ishihara, K.; Nakai, Y.; Yazawa, M.; Toda, H.; Yagi, K. J. Biochem. 1991, 109, 190–197.

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detection), while the order of runs within each trial was randomized to minimize the introduction of systematic error. In experiments testing for spectral overlap, myoglobin was added to CaM in equimolar amounts. HPLC-MS System. The LC/MS system is similar to that described previously.36 Briefly, prototype splitless low flow binary and loading pumps were used for peptide separation by reversed phase chromatography, and the eluant was monitored with a QSTAR Pulsar i QqTOF mass spectrometer fitted with a Turbo Ion Spray source (AB/Sciex, Foster City, CA). Electrospray ionization was performed in positive ion mode at 4.5 kV with nebulization. For CID-based MS/MS analysis of H/D exchange, the mass spectrometer was operated in information dependent acquisition (IDA) mode with an inclusion list representing 96% of the CaM sequence (38 peptides). In these experiments a cycle involved 0.5 s for TOF-MS acquisition followed by two production acquisitions (1.5 s/acquisition) using rolling collision energy. For maximal ion statistics, product ion spectra were recorded with low Q1 resolution during ion selection and ion bunching of CIDgenerated fragments (“enhance” mode) prior to TOF detection. All data sets were externally calibrated. Peptide Identification. Peptide identification was based on accurate mass measurements (50%) are not a requirement for sensitive measurements of deuteration levels.36 In addition to diluting protein samples and diminishing signal intensity, the isotopic distribution at high labeling does not promote straightforward precursor ion selection (Figure 1). As the extent of labeling is influenced by structural context and the degree of back-exchange in the system, the position of the isotopic distribution is not easily predicted. This renders the programmed acquisition of product ion spectra difficult. Further, as the monoisotopic ion for a heavily labeled peptide may be of very low abundance, data-dependent acquisition

triggers on M+x isotopic peaks, where x is dictated by the degree of label retained (data not shown). MS/MS spectral acquisition is thus irreproducible under conditions of high labeling. We therefore tested a limited expansion of the isotopic envelope, using reduced levels of D2O, for robust ion selection in automated MS/MS acquisition experiments. A range of D2O (0-50%) was applied to apo- and holo-CaM in forward exchange measurements and processed by a bottom-up strategy, as described above (Experimental Section). Given the degree of back-exchange in these experiments, this corresponds to a maximum deuterium incorporation range of 0-33%, when considering the full range of structure-induced alteration of deuterium incorporation. The efficiency of ion selection based on the monoisotopic peptide mass was assessed over multiple trials, as a function of %D2O applied to apo-CaM (Figure 2A). For MS/MS to be deemed successful, selection of the monoisotopic peak was required with the generation of at least one detectable fragment ion in the product ion spectrum. Although the inclusion list represented 38 peptides, only 29 peptides (76%) were selected in at least one of the five trials, corresponding to 92% coverage of the CaM sequence for 20% D2O applied. When considering replicate analysis, only 15 peptides (39%) were consistently mass-selected in all five trials of 20% D2O labeling, which corresponds to a sequence coverage of 57%. InterestAnalytical Chemistry, Vol. 81, No. 19, October 1, 2009

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Figure 3. Evaluation of the ion transmission window for capturing the full isotopic profile for the deuterated peptide state. (A) Normalized distributions for the unlabeled peptide IREAF, showing the precursor ion from MS data (solid trace) and the residual precursor ion from MS/MS data (dotted trace), generated from an information-dependent acquisition. (B) As in (A) but for 40% D2O applied. Table 1. Comparison of MS and MS/MS Modes for Quantitation of Deuteration and Deuteration Ratiosd unlabeled peptidea peptide sequence

residues

MS

MS/MS

KEAFSL FKEAFSL KEAFSLF IREAF AELRHVMTNL RHVMTNL VQMMTAK

13-18 12-18 13-19 85-89 103-112 106-112 142-148

693.76 (0.01) 840.90 (0.01) 840.90 (0.01) 634.61 (0.01) 1183.39 (0.01) 869.98 (0.01) 807.93 (0.01)

693.79 (0.02) 840.94 (0.05) 840.94 (0.05) 634.63 (0.01) 1183.39 (0.01) 869.97 (0.01) 807.92 (0.01)

Dapob MS 0.47 0.58 0.58 0.43 1.03 0.73 0.88

(0.03) (0.04) (0.04) (0.03) (0.03) (0.02) (0.02)

Dholo/Dapoc MS/MS 0.51 0.63 0.63 0.45 1.06 0.82 0.92

(0.03) (0.06) (0.05) (0.03) (0.03) (0.03) (0.03)

MS 0.18 0.18 0.18 0.42 0.32 0.39 0.37

(0.04) (0.04) (0.04) (0.05) (0.01) (0.02) (0.01)

MS/MS 0.16 0.18 0.18 0.42 0.31 0.41 0.42

(0.04) (0.09) (0.09) (0.04) (0.02) (0.02) (0.02)

a The measured peptide average masses (using the same number of isotopic peaks as in the deuteration level calculations) for unlabeled CaM peptides from precursor ions (MS) and residual precursor ions (MS/MS). b Deuterium levels measured from precursor ions (MS) and residual precursor ions (MS/MS) under 20% D2O labeling conditions. c Deuteration ratios, expressed as Dholo/Dapo, at 20% labeling are indicated for precursor (MS) and residual precursor (MS/MS) CaM ions. d Standard deviations from replicate measurements (n ) 3-5) are indicated in parentheses.

ingly, this reduction in the success of MS/MS triggering with accumulating runs appears independent of the %D2O applied (Figure 2A). To explore this further, the success in ion selection over five runs was monitored as a function of %D2O applied, for both apo- and holo-CaM (Figure 2B,C). This revealed that ion selection and sequence coverage are negligibly affected over this range of labeling reagent, with perhaps a weak negative effect for apo-CaM. Collectively, this indicates that a modest expansion of the isotopic distribution does not severely impact ion selection efficiency for this model system, at least up to 33% deuterium incorporation. The low sequence coverage using inclusion lists is surprising, indicating the difficulty of peak detection algorithms to accurately select ions on-the-fly.51,52 This is worsened by the compressed chromatographic runtime in the H/DX experiments and the use of a low-specificity protease for digestion, both of which lead to large numbers of peptides with similar retention times. These limitations are commonly experienced in bottom-up proteomics experiments as well.53 Notwithstanding, an inclusion list does provide a 2-fold improvement in ion selection efficiency (not shown). For the purposes of this study, Figure 2 illustrates that reasonable replicative sequence coverage is attainable for this model system. Revised methods involving gas-phase fraction(51) Renard, B. Y.; Kirchner, M.; Steen, H.; Steen, J. A.; Hamprecht, F. BMC Bioinf. 2008, 9, 355–372. (52) Kohli, B. M.; Eng, J. K.; Nitsch, R. M.; Konietzko, U. Rapid Commun. Mass Spectrom. 2005, 19, 589–596. (53) Jaffe, J. D.; Keshishian, H.; Chang, B.; Addona, T. A.; Gillette, M. A.; Carr, S. A. Mol. Cell Proteomics 2008, 7, 1952–1962.

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ation54 or time-scheduled product ion acquisition would likely improve sequence coverage but are not required to further explore the utility of MS/MS data for deuterium incorporation measurements. By avoiding excessive expansion of the isotopic distribution, the ion selection window for MS/MS may also be constrained to a reasonable size, transmitting a range of only slightly greater width than the native isotopic distribution (Figure 1) and avoiding large windows that would only increase chemical noise in the MS/ MS spectra. The transmission window was set to ∼5Th from the monoisotopic ion, using peptide standards to monitor window size (not shown). To confirm whether this selection window is sufficient to transmit the full isotopic distribution into the collision cell for peptide fragmentation, the precursor ion distribution in the MS domain and the residual precursor distribution in the MS/ MS domain were compared. Figure 3, for example, displays the peak profiles for peptide IREAF in the MS and MS/MS domains, at D2O concentrations of 0 and 40%. This figure suggests that the integrity of the ion envelope passed onto Q2 is preserved across a reasonable range of %D2O applied. This is supported by a more complete analysis of a set of seven peptides that returned residual precursor ions under optimized fragmentation conditions, in the absence and presence of 20% D2O labeling (Table 1). Comparing the masses of the unlabeled peptides reveals that there are no obvious differences between the MS and MS/ MS domains based on an analysis of variance (ANOVA) (P ) 0.05), indicating that the full isotopic envelope is transmitted. This (54) Blonder, J.; Rodriguez-Galan, M. C.; Lucas, D. A.; Yound, H. A.; Issaq, H. J.; Veenstra, T. D.; Conrads, T. P. Biochim. Biophys. Acta 2004, 1698, 87–95.

Figure 4. Observed deuteration levels for a series of precursor ions (filled symbols) and their corresponding fragments (open symbols) from representative peptides of the apo-CaM data set at 20% D2O. Product ions listed include sequence and neutral loss ions. Reported values are an average of 5 replicates for the precursor ions and 3-5 replicates for the products. Error distributions are excluded for clarity of presentation.

is also true for 20% D2O labeling (Table 1). As perturbed deuteration levels are implemented in the analysis of structural or conformational changes, we also measured the deuteration ratio (expressed as Dholo/Dapo) for the same set of peptides, in both MS and MS/MS domains (Table 1). Under conditions optimized for high quality peptide fragmentation maps, the residual precursor ion offers an accurate measure of perturbation and confirms that fragmentation does not lead to measurable enrichment or depletion of deuterium upon ion activation in CID. That is, there is no apparent selective dissociation of peptide based on the isotopic content. Furthermore, the ratios obtained from the precursor ions confirm that Ca2+-induced perturbation measurements of this study are in good agreement with previous structural work.36,45-48 We then tested fragment ions for deuteration levels. Using 20% D2O, mean absolute deuterium incorporations of 12.3 ± 2.9% for apo-CaM and 4.1 ± 2.2% for holo-CaM were generated, based on the average deuterium incorporation measured at the peptide level in the MS domain. While higher levels of D2O could be applied based on Figure 2, 20% was selected to challenge the sensitivity of fragment-level quantitation, and 12 peptides with a wide m/z range of fragments were monitored. Hydra software was modified to automate data extraction from multiple LC-MS/MS runs to facilitate data analysis.13 The average fragment deuteration levels relative to the unfragmented precursor ion are displayed in Figure 4 for apoCaM. Product ions include b- and y-type primary sequence ions, and neutral loss ions arising from the elimination of water or ammonia, and represent a minimum of three successful trials. A broad range of deuteration levels was measured for the precursor and product ions. Since no external source of deuterium is present in the gas-phase post mass-selection, deuterium levels in the fragment ions are less than their precursors, as expected. Further inspection of the deuteration levels acquired for the product ions show a correlation between the size of the fragment and the measured deuteration level. Plotting the measured deuteration level as a function of the theoretical deuteration level

(where complete deuterium scrambling is assumed)39,55 results in a linear trend as representative plots in Figure 5 highlight.40,56 Scrambling is further illustrated by the b2+ ions from peptides GEKLTDEE and RHVMTNL in this figure. These fragments acquired measurable deuteration levels of 0.10 ± 0.01 and 0.31 ± 0.02, respectively. The corresponding regions of the peptide sequences retain no deuterium in the absence of scrambling, due to their high intrinsic chemical exchange rates in solution, under H/D quench conditions.21 The degree of gas-phase scrambling that is evident is consistent with previous findings on CID-based QqTOF instruments.40,55-58 Whether scrambling occurs prior to or during ion activation by CID cannot be determined from these data, but, under the conditions used in this study, all 12 peptides demonstrate complete scrambling regardless of the sequence ion (b- or y-type). To ensure the absence of spectral overlap in fragment ion isotopic envelopes, which could generate erroneous deuteration levels, isotopic distributions of unlabeled product ions were also inspected. This exercise revealed an unexpected distribution for the b9-ion of peptide AELRHVMTNL (see Figure 5 inset for b92+) as well for as the b6-ion from RHVMTNL. Additional MSn experiments confirmed the sequence identity of these ions (see Supplementary Figure 1 for AELRHVMTN), where the uncharacteristic envelopes resulted from rearrangements involving the C-terminus. Concurrent asparagine deamidation and C-terminal amidation, yielding a +1 and -1 mass difference, respectively, is consistent with the data. This is likely a gas-phase process mediated by cyclization with the C-terminus, as solution-phase deamidation via hydrolysis does not offer an explanation for the C-terminal amidation.59 This observation argues for isotopic distribution analysis of controls, in both MS and MS/MS domain data, as a means of detecting when non-native isotopic distributions arise. With evidence that deuterium scrambling in CID experiments is complete, several strategies were evaluated for quantitating perturbations in deuteration levels using MS/MS data, shown as deuteration ratios in Figure 6A. These deuteration ratios reflect the impact of calcium binding on CaM,36 where a ratio approaching zero shows a strong reduction in protein dynamics resulting from the ion binding events. A per-peptide comparison between the product ions and their corresponding precursor reveals that conformational perturbations can be accurately measured via H/DX-MS/MS, using one or a multiple of sequence ions. The base peaks of the product ion spectra, which correspond to sequence ions spanning a m/z range of 187 to 656, provide the most accurate and precise deuteration ratios of the intact peptide overall. The slightly larger errors observed on the deuteration ratios for peptides 85-89, 113-120, and 120-124 are attributed to very low deuteration levels in the holo-CaM b2+ ions, selected as the base peak for these peptides. Figure 6B shows a typical spread in deuteration ratios for one of the peptides (AELRH(55) Rand, K. D.; Jørgensen, T. J. D. Anal. Chem. 2007, 79, 8686–8693. (56) Ferguson, P. L.; Pan, J.; Wilson, D. J.; Dempsey, B.; Lajoie, G.; Shilton, B.; Konermann, L. Anal. Chem. 2007, 79, 153–160. (57) Jørgensen, T. J. D.; Gå´rdsvoll, H.; Ploug, M.; Roepstorff, P. J. Am. Chem. Soc. 2005, 127, 2785–2793. (58) Demmers, J. A. A.; Rijkers, D. T. S.; Haverkamp, J.; Killian, J. A.; Heck, A. J. R. J. Am. Chem. Soc. 2002, 124, 11191–11198. (59) Catak, S.; Monard, G.; Aviyente, V.; Ruiz-Lopez, M. F. J. Phys. Chem. A 2009, 113, 1111–1120.

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Figure 5. Measured deuteration levels for three representative apo-CaM peptides arising from replicate analyses, expressed relative to the theoretical deuterium incorporation expected for complete intramolecular H/D scrambling (precursor ions, squares; product ions, triangles). Inset corresponds to the isotopic envelope of an unlabeled b92+-ion from peptide AELRHVMTNL.

Figure 6. Measurement of deuteration ratios for a series of peptides from CaM digests, (A) comparing a conventional approach (“precursor ion”) to a series of approaches utilizing MS/MS data. Error bars represent standard deviations from 3-5 replicates. Values lower than one indicate Ca2+-induced perturbations in CaM. (B) Spread in deuteration ratio measurements for fragments of AELRHVMTNL (residues 103-112), for both sequence ions and neutral loss ions. 7906

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VMTNL, residues 103-112). While the average ratio (0.31 ± 0.15) agrees with that of the precursor ion (0.32 ± 0.01) and the base peak (0.34 ± 0.01), individual values range from 0.17 to 0.42 for primary sequence ions. This wide range appears to arise from poor peak definition in the isotopic envelopes of certain fragment ions, particularly those of lower intensity, which would increase the noise in the deuteration ratio measurement. Thus, it is sensible that the most accurate representation of the deuteration ratio arises from the base peak, as this fragment would be most likely to present a well-sampled ion envelope. When this is absent, averaging over a multiple of sequence ions provides an alternative of slightly reduced quality. As shown in Figure 6A, neutral-loss ions do not preserve the accuracy of deuteration ratio measurements. This is highlighted in Figure 6B, where the deuteration ratio for [b8-H2O]+ drops to 0.05 from a value of 0.36 for the b8+ ion. This suggests that neutral losses are sensitive to isotope effects, which will be explored in future studies. Overall, a single fragment ion with measurable deuterium levels is an effective surrogate for the precursor ion, provided it is a primary sequence ion and good isotopic peak definition is maintained. The extent to which these findings depend upon complete scrambling warrants additional discussion. While most studies of smaller peptides, such as generated by peptic digestion, indicate that scrambling is complete or nearly so, complexities such as isotope fractionation have been proposed to rationalize inconsistencies seen in the analysis of some peptides and proteins.40,56 We do not see any evidence for isotope fractionation in our MS/ MS data, except perhaps during the generation of neutral loss fragments, but under certain conditions primary sequence ions

Table 2. Impact of Spectral Overlap on Deuteration Measurements, Using Conventional and Surrogate Strategiesa controla domain MS MS/MS

ion +

AELQD ([M+H] ) AE (b2+)

mixtureb

Dapo

Dholo

Dapo

Dholo

0.61 (0.06) 0.09 (0.01)

0.18 (0.02) 0.02 (0.01)

1.41 (0.05) 0.09 (0.02)

1.22 (0.06) 0.02 (0.02)

a Expected deuteration values for AELQD in the absence of spectral interference from myoglobin, for both apo- and holo-CaM, using both the conventional (MS) and surrogate (MS/MS) methods. b Impact of added myoglobin on deuterium quantitation for apo- and holo-CaM, using both the conventional (MS) and surrogate (MS/MS) methods a Standard deviations from replicate measurements (n ) 3-5) are shown in parentheses.

turbations of structure and dynamics. In this example, selecting the M and M+1 ions in the MS domain would provide an alternative option for quantitation.36 However, the surrogate approach is effective in situations where the overlap is more extensive and where the selective use of isotopic peaks would not be possible.

Figure 7. Spectral interference of a myoglobin peptic peptide (monoisotopic m/z 577.26) with the isotopic distribution of the CaMderived AELQD peptide at a D2O labeling percentage of 20%.

may not preserve the same % deuteration level as the precursor ion (for example, perhaps in larger peptides retaining secondary structure). For complete freedom in fragment ion selection, full scrambling would benefit from independent verification using control experiments. For example, retaining a measurable precursor ion in the MS/MS spectrum would provide an opportunity to verify if scrambling is evident in the fragment of choice. In situations where some measure of deuterium localization is preserved or suspected, the method should be adapted to monitor multiple fragment ions as needed. Alternatively, ion source conditions could be modified to induce scrambling, as shown recently by the Jorgensen group.43,60 The CaM data have not highlighted the challenges associated with spectral overlap, as could easily occur in more complex systems. To test this, the surrogate method for perturbation measurement was explored with CaM in the presence of myoglobin. As a simple example, experiments with this protein blend showed spectral overlap in the MS domain between a singly charged myoglobin peptide (GLSDGE) and a singly charged CaM peptide (AELQD), illustrated in Figure 7. The MS-derived deuteration levels for apo-/holo-CaM are listed in Table 2, with and without this interference. The interfering peptide in the mixture clearly skews the deuteration measurements of AELQD, which may go unnoticed in automated analyses. Monitoring the b2+ ion of AELQD as the surrogate for the intact peptide shows that the deuteration levels are insensitive to the presence of the interference, preserving an ability to accurately monitor per(60) Rand, K. D.; Zehl, M.; Jensen, O. N.; Jorgensen, T. J. Anal. Chem. 2009, 81, 5577–5584.

CONCLUSIONS AND SIGNIFICANCE The present study demonstrated that deuteration levels can be successfully extracted from CID-derived product ions for differential deuteration measurements in bottom-up H/DX experiments. Specifically, using CaM as the model protein, Ca2+-induced perturbations were accurately and precisely measured on a perpeptide basis using product ion base peaks as surrogates. Although these results were based on 20% D2O in the labeling reaction, a wider range of D2O (up to 50%) can easily be tolerated with this approach. When spectral interference in the MS domain is severe, as illustrated by a simple protein blend, accurate and precise peptide deuteration ratios can nonetheless be recovered using the product ion base peak. This approach benefits from deuterium scrambling for the freedom in selecting the surrogate on the basis of intensity, which may be readily induced by regulating ion activation conditions as needed43 and tested with control digests where necessary. Overall, this surrogate approach is anticipated to extend sensitivity and sequence coverage, paving the way for the interrogation of highly complex protein mixtures, as MS/MS techniques extend both the dimensionality of analysis and the dynamic range. ACKNOWLEDGMENT This research was funded by the Natural Sciences and Engineering Research Council of Canada, the Canadian Institutes of Health Research, Canada Foundation for Innovation, and the Canada Research Chair program. We are grateful to Morgan Khan (Southern Alberta Mass Spectrometry Center, Calgary) for acquiring the MS3 data. SUPPORTING INFORMATION AVAILABLE Additional figure as noted in the text (Supplementary Figure 1). This material is available free of charge via the Internet at http://pubs.acs.org. Received for review May 26, 2009. Accepted August 4, 2009. AC901148U

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