Photodissociation at 193 nm of some singly protonated peptides and proteins with <i>m/z</i> 2000–9000 using a tandem time‐of‐flight mass spectrometer equipped with a second source for delayed extraction/post‐acceleration of product ions

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Time-evolution of product ion signals in ultraviolet photodissociation (UV-PD) of singly protonated peptides with an arginine at the N-terminus was investigated by using a tandem time-of-flight mass spectrometer equipped with a cell floated at high voltage. Observation of different time-evolution patterns for different product ion types-an apparently nonstatistical behavior-could be explained within the statistical framework by invoking consecutive formation of some product ions and broad internal energy distributions for precursor ions. a n ϩ 1 and b n ions were taken as the primary product ions from this type of peptide ions. Spectral characteristics in post-source decay, UV-PD, and collisionally activated dissociation at low and high kinetic energies could be explained via rough statistical calculation of rate constants. Specifically, the striking characteristics in high-energy CAD and UV-PD-dominance of a n and d n formed via a n ϩ 1-were not due to the peculiarity of the excitation processes themselves, but due to quenching of the b n channels caused by the presence of arginine. ( T andem mass spectrometry has been widely used for identification and sequence determination of polypeptides and proteins [1][2][3]. In spite of extensive studies made so far, fundamental understanding on the dissociation of activated peptide ions observed by tandem mass spectrometry is still lacking. This is in contrast with the case of the dissociation of small polyatomic ions, for which nearly quantitative theoretical description and even prediction are possible [4]. The main reasons for such a lack of fundamental understanding are experimental and computational difficulties to get structural, mechanistic, and kinetic data for large polyatomic systems consisting of more than 100 atoms. In this regard, it is to be mentioned that we recently developed a systematic method to calculate sequence-specific statistical (Rice-Ramsperger-KasselMarcus, RRKM) rate constants for dissociations of peptide and protein ions [5][6][7].The most popular method to activate a peptide ion and hence to induce its dissociation is the collisionally activated dissociation (CAD) [8 -12]. The kinetic energy of a peptide ion is an important factor affecting the CAD spectral pattern. Hence, CAD of a peptide ion is classified into two categories, low (around 100 eV) and high (higher than 1 keV) energy regimes. In the lowenergy CAD [11], which is typically done with triple quadrupole ion trap and ion cyclotron resonance mass spectrometers, a peptide ion gains sufficient energy for dissociation usually via multiple collisions, each collision supplying rather small amounts of internal energy through vibrational excitation. Most of the product ions are b and y types (see Scheme 1) formed via rearrangement reactions.Presence of arginine, proline and aspartic acid residues and the charge state of a peptide ion are known to affect the relative intensities of these product ions. The "mobile proton" model [13,14] has been devised to explain this. In the high-energy CA...

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confidence: 66%

Time-resolved photodissociation of singly protonated peptides with an arginine at the N-terminus: A statistical interpretation

Yoon

Chung

Kim

2008

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“…The resulting fragmentation patterns exhibit significant similarity with our 157 nm tandem-TOF photodissociation results. They have recently developed a MALDI tandem-TOF instrument and performed 193 nm photodissociation of several large peptides [27].…”

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confidence: 99%

Factors that impact the vacuum ultraviolet photofragmentation of peptide ions

Thompson

Cui

Reilly

2007

101

Several groups have investigated the photodissociation of peptide ions with ultraviolet light. Significant differences have been reported with 157 and 193 nm excitation. Recent studies have shown that the mass analyzer can also influence the observed photofragment distribution.Comparison of experiments using different peptides, wavelengths, and mass analyzers is undesirably complicated. In the present work, several peptides are analyzed with both 157 and 193 nm photodissociation in tandem-TOF and linear ion trap mass spectrometers. The results indicate that the fragment ion distribution can be influenced by both the photodissociation wavelength and the mass analyzer. The two wavelengths generate similar spectra in an ion trap but quite different results in a tandem

“…Photodissociation at 193 nm has also been exploited for fragmentation of singly protonated peptides [15][16][17][18]. Similar to 157 nm dissociation, formation of a-and d-type product ions was observed when arginine residues were in close proximity to the N-terminus and y-, x-, v-and w-type fragments were detected when Arg residues were located near the C-terminus [17,19]. Detailed investigations of 193 nm photodissociation revealed that the fragmentation behavior is significantly affected by the presence and location of arginine residues [16], and that product ion types and abundances vary depending on precursor ion charge location [20].…”

Section: Introductionmentioning

confidence: 99%

Electron Induced Dissociation of Singly Deprotonated Peptides

Kalli

Grigorean

Håkansson

2011

Dissociation of singly charged species is more challenging compared with that of multiply charged precursor ions because singly charged ions are generally more stable. In collision activated dissociation (CAD), singly charged ions also gain less kinetic energy in a fixed electric field compared with multiply charged species. Furthermore, ion-electron and ion-ion reactions that frequently provide complementary and more extensive fragmentation compared with CAD typically require multiply charged precursor ions. Here, we investigate electron induced dissociation (EID) of singly deprotonated peptides and compare the EID fragmentation patterns with those observed in negative ion mode CAD. Fragmentation induced upon electron irradiation and collisional activation is not specific and results in the formation of a wide range of product ions, including b-, y-, a-, x-, c-, and z-type ions. Characteristic amino acid side chain losses are detected in both techniques. However, differences are also observed between EID and CAD spectra of the same species, including formation of odd-electron species not seen in CAD, in EID. Furthermore, EID frequently results in more extensive fragmentation compared with CAD. For modified peptides, EID resulted in retention of sulfonation and phosphorylation, allowing localization of the modification site. The observed differences are likely due to both vibrational and electronic excitation in EID, whereas only the former process occurs in CAD.