linked peptides via identification of their distinct isotope patterns
during MS analysis.14-20 This can be realized by incorporation
of the isotope label within the protein or peptide14-17 or within
the cross-linker itself.18-20 Examples of the former approach
include the introduction of 18O to the C-terminal carboxyl group(s)
of the polypeptide chain(s) formed during proteolytic digestion.14,15
Intermolecular cross-linked peptides are readily distinguished by
a characteristic 8-Da mass shift compared to peptides formed by
proteolysis using naturally abundant water. However, nonmodified,
dead-end, and intramolecular cross-linked peptides are not able
to be distinguished, as they will all exhibit a common 4-Da mass
increment. In contrast, incorporation of the isotope label within
the cross-linking reagent potentially allows all cross-linked pep-
tides to be detected, via identification of their distinct isotope
patterns upon reaction with 1:1 mixtures of stable isotope-labeled
and nonlabeled cross-linking reagents.18,19 Recently, Seebacher
et al. have combined these two strategies in order to facilitate
the improved discrimination of intermolecular, intramolecular, and
dead-end cross-linked reaction products.20 However, limitations
to these approaches may be encountered when the m/z values of
differentially labeled cross-linked peptide products overlap with
unlabeled peptides also present in the mixture, thereby precluding
identification of the characteristic isotopic multiplets.
In recent years, therefore, several groups have initiated the
development and application of novel classes of gas-phase cleav-
able cross-linking reagents, whereby cross-linked reaction prod-
ucts are identified and characterized based on their characteristic
fragmentation behavior observed during tandem mass spec-
trometry.21-26 These gas-phase cleavage sites may be incorporated
into a side chain on the cross-linking reagent,21 resulting in
formation of a stable “reporter” ion (thereby maintaining the cross-
linked peptide linkages), or incorporated directly into the cross-
linker spacer chain,22-25 thereby resulting in cleavage of the cross-
link upon MS/MS. In each case, further structural interrogation
of the peptide product ions formed following the initial cleavage
reaction can be achieved by MSn analysis. However, consistent
with the current state of knowledge regarding the mechanisms
and other factors that influence the fragmentation reactions of
protonated peptide ions in the gas phase,27 the mechanisms
responsible for the fragmentation of protonated cross-linked
peptides are expected to be highly dependent on the charge state
and amino acid composition (i.e., proton mobility) of the mass
selected precursor ion, such that selective cleavage of the desired
bond within the cross-link may only be observed for a subset of
the peptides selected for MS/MS or observed as only one of many
dissociation channels. The inability to control the selectivity of
these fragmentation reactions thereby potentially limits the
sensitivity and widespread applicability of these approaches for
comprehensive cross-linked peptide identification and character-
ization.
Here, based on results from our recent studies aimed at the
development of fixed charge sulfonium ion chemical derivatization
strategies for “targeted” MS/MS-based identification, characteriza-
tion, and quantitative analysis of peptides containing specific
functional groups (e.g., the side chains of methionine or
cysteine),28-32 and as a first step toward the development of an
improved MS/MS-based approach for the comprehensive analysis
of protein-protein interactions using chemical cross-linking and
multistage tandem mass spectrometry, we describe the synthesis,
characterization, and initial demonstration of the selective gas-
phase fragmentation behavior of cross-linked peptide ions formed
by reaction with a novel amine reactive, sulfonium ion containing
cross-linking reagent, S-methyl 5,5′-thiodipentanoylhydroxysuc-
cinimide (1).
MATERIALS AND METHODS
Materials. All chemicals were analytical reagent (AR), or of a
comparable or higher grade, and used without further purification.
Dicyclohexylcarbodimide (DCC) was purchased from Fluka.
5-Bromovaleric acid, thiourea, neurotensin, angiotensin II, and
[Glu1]-fibrinopeptide B were from Sigma-Aldrich (St. Louis, MO).
Substance P was obtained from Bachem (Torrance, CA). N-
Hydroxysuccinimide (NHS) was purchased from Pierce (Rock-
ford, IL). The synthetic peptide VTMAHFWNFGK (pepVWK) and
GAILDGAILR (pepGDR) were obtained from Auspep (Parkville,
Australia). The phosphoserine containing peptide LSVPTpS-
DEEDEVPAPKPR (pepLpSR) was synthesized by Sigma-Genosys
(The Woodlands, TX) and used without further purification.
Deionized water was obtained from a Barnstead nanopure
diamond purification system (Dubuque, IA). Dimethylformamide
(DMF) was dried over 3-Å molecular sieves (Spectrum Chemicals)
and filtered prior to use. All reactions were performed in oven-
dried glassware.
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de Koster, C. G.; de Jong, L. Anal. Chem. 2002, 74, 4417–4422
(16) Chen, X.; Chen, Y. H.; Anderson, V. E. Anal. Biochem. 1999, 273, 192–
203
(17) Taverner, T.; Hall, N. E.; OHair, R. A. J.; Simpson, R. J. Biol. Chem. 2002,
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(18) Mu¨ller, D. R.; Schindler, P.; Towbin, H.; Wirth, U.; Voshol, H.; Hoving, S.;
Steinmetz, M. O. Anal. Chem. 2001, 73, 1927–1934
(19) Pearson, K. M.; Pannell, L. K.; Fales, H. M. Rapid Commun. Mass Spectrom.
2002, 16, 149–159
(20) Seebacher, J.; Mallick, P.; Zhang, N.; Eddes, J. S.; Aebersold, R.; Gelb, M. H.
J. Proteome Res. 2006, 5, 2270–2282
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de Jong, L. J. Am. Soc. Mass Spectrom. 2001, 12, 222–227
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.
Synthesis of Cross-Linking Reagent. Synthesis of the ionic
cross-linking reagent 1 (S-methyl 5,5′-thiodipentanoylhydroxysuc-
cinimide iodide 1′ or S-methyl 5,5′-thiodipentanoylhydroxysuc-
cinimide methylsulfate 1′′) was achieved by initial preparation of
.
.
.
(27) Kapp, E. A.; Schu¨tz, F.; Reid, G. E.; Eddes, J. S.; Moritz, R. L.; O’Hair, R. A. J.;
.
Speed, T. P.; Simpson, R. J. Anal. Chem. 2003, 75, 6251–6264
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Spectrom. 2005, 16, 1131–1150
(29) Amunugama, M.; Roberts, K. D.; Reid, G. E. J. Am. Soc. Mass Spectrom.
2006, 17, 1631–1642
(30) Sierakowski, J.; Amunugama, M.; Roberts, K. D.; Reid, G. E. Rapid Commun.
Mass Spectrom. 2007, 21, 1230–1238
(31) Froelich, J. M.; Kaplinghat, S.; Reid, G. E. Eur. J. Mass Spectrom. 2008,
14, 219–229
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9280 Analytical Chemistry, Vol. 80, No. 23, December 1, 2008