Abstract:The collision-induced dissociation (CID) fragmentation reactions of a variety of deprotonated peptides containing proline have been studied in detail using MS(2) and MS(3) experiments, deuterium labelling and accurate mass measurements when necessary. The [M--H--CO(2)](-) (a(2)) ion derived from H-Pro-Xxx-OH dipeptides shows an unusual fragmentation involving loss of C(2)H(4); this fragmentation reaction is not observed for larger peptides. The primary fragmentation reactions of deprotonated tripeptides with a… Show more
“…This propensity for selective fragmentation has also been reported for singlyprotonated peptides [13][14][15][16][17][18] and multiply-charged protein ions [19]. This phenomenon is sometimes known as the proline effect and was first attributed to the relatively high proton affinity of Pro [20].…”
Abstract. UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of prolinecontaining peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S 2 and S 3 , lie close to 213 nm. Non-adiabatic MD simulation starting from S 2 and S 3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.
“…This propensity for selective fragmentation has also been reported for singlyprotonated peptides [13][14][15][16][17][18] and multiply-charged protein ions [19]. This phenomenon is sometimes known as the proline effect and was first attributed to the relatively high proton affinity of Pro [20].…”
Abstract. UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of prolinecontaining peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S 2 and S 3 , lie close to 213 nm. Non-adiabatic MD simulation starting from S 2 and S 3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.
“…In this particular case, no clear evidence for electrostatic binding, such as the appearance of [FBDSA-H] â or the attachment of FBDSA to a product ion (see below) is apparent. The most abundant products are consistent with modified y-type and b-type ions, using the nomenclature that is adapted [23] from the protonated peptide literature [24], which would correspond to Îą-ions and β-ions, respectively, in the nomenclature employed by Bowie [25]. When compared to the unmodified anion (i.e., the [M-H] â ion), the CID of the modified peptide in this case generates more sequence information (compare Figures 1(a) and 1(b)).…”
Protonated tryptic peptides, somatostatin-14, and oxytocin have been subjected to reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas phase. The major product is a negatively-charged complex comprised of the peptide and the reagent. Upon dehydration of the complex, all peptides show evidence for Schiff base formation involving a primary amine of the peptide. Some peptides also show evidence for the formation of a relatively strong electrostatic interaction without Schiff base formation (i.e., a mixture of isomeric precursor ions is generated upon dehydration of the complex). Ion trap collision-induced dissociation of the dehydration products from all peptides examined gave distinct product ion spectra relative to the deprotonated and protonated forms of the peptides. The distinct behavior of the modified ions is attributed to the highly stable charge carrying sulfonate group, which tends to inhibit intramolecular proton transfer in negatively charged species. Modified anions of the peptides with an intramolecular disulfide linkage show evidence for cleavage of both the disulfide linkage and an amide bond in the loop defined by the disulfide bond. Modification of protonated peptides via charge inversion with FBDSA is a useful means for generating novel and distinct ion-types that can provide complementary structural information upon subsequent activation to that obtained from dissociation of protonated or deprotonated forms of the peptide.
“…The same pathway can lead to the y 1 fragment if the negative charge remains on the C-terminal fragment. Formation of b 2 ions via the a 3 -fragment also occurs via an amidate intermediate structure [32], see Scheme 3, although this pathway was suggested to be active especially for residues without an amidic hydrogen, such as Pro [29]. The b 2 fragment can then be formed via a similar nucleophilic attack.Scheme 2Mechanism for formation of b 2 oxazolone fragments from deprotonated peptides as proposed by Harrison and coworkers [29]Scheme 3Alternative mechanism to form a b 2 oxazolone structure, involving the a 3 â fragment as an intermediate [32], as proposed particularly for residues without an amidic hydrogen by Harrison et al [29]…”
Infrared spectra of anionic b-type fragments generated by collision induced dissociation (CID) from deprotonated peptides are reported. Spectra of the b2 fragments of deprotonated AlaAlaAla and AlaTyrAla have been recorded over the 800â1800Â cmâ1 spectral range by multiple-photon dissociation (MPD) spectroscopy using an FTICR mass spectrometer in combination with the free electron laser FELIX. Structural characterization of the b-type fragments is accomplished by comparison with density functional theory calculated spectra at the B3LYP/6-31++G(d,p) level for different isomeric structures. Although diketopiperazine structures represent the energetically lowest isomers, the IR spectra suggest an oxazolone structure for the b2 fragments of both peptides. Deprotonation is shown to occur on the oxazolone Îą-carbon, which leads to a conjugated structure in which the negative charge is practically delocalized over the entire oxazolone ring, providing enhanced gas-phase stability.Electronic supplementary materialThe online version of this article (doi:10.1007/s13361-011-0297-3) contains supplementary material, which is available to authorized users.
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