Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns

Huang, Yingying; Triscari, Joseph; Tseng, George C.; Paša‐Tolić, Ljiljana; Lipton, Mary; Smith, Richard D.; Wysocki, Vicki H.

doi:10.1021/ac0480949

Cited by 217 publications

(325 citation statements)

References 30 publications

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“…Note also that for the singly charged peptides in which the proton is expected to be localized on the C-terminal basic residue, E 1/2 values follow the same order as their gas-phase proton affinities, a trend consistent with the "mobile proton hypothesis" [2]. For H, K, and R the proton affinities are 988, 996, and 1051 kJ mol Ϫ1 [12], respectively, while the corresponding E 1/2 values are 36.5, 39.4, and 48.8 ( Table 1).…”

Section: Comparison Of Neutral Losses From N-terminal Glutamine To Frsupporting

confidence: 62%

“…However, relative abundances of these ions and ions derived from them are not generally used for this process, despite the fact that they can carry additional sequence-specific information. The development of a sound basis for interpreting abundances can therefore be expected to aid peptide identification algorithms and has motivated the work of several laboratories [1][2][3][4][5][6][7]. It is also the motivation of the present work, which examines a highly specific fragmentation process, the "neutral loss" of ammonia and water from a glutamine residue at the amino terminus of a peptide.…”

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confidence: 99%

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Dehydration versus deamination of N-terminal glutamine in collision-induced dissociation of protonated peptides

Neta

Kilpatrick

et al. 2007

J. Am. Soc. Mass Spectrom.

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Some of the most prominent "neutral losses" in peptide ion fragmentation are the loss of ammonia and water from N-terminal glutamine. These processes are studied by electrospray ionization mass spectrometry in singly-and doubly-protonated peptide ions undergoing collision-induced dissociation in a triple quadrupole and in an ion trap instrument. For this study, four sets of peptides were synthesized: (1) QLLLPLLLK and similar peptides with K replaced by R, H, or L, and Q replaced by a number of amino acids, (2) QL n K (n ϭ 0, 1, 3, 5, 7, 9, 11), (3) QL n R (n ϭ 0, 1, 3, 5, 7, 9), and (4) QL n (n ϭ 1, 2, 3, 4, 8). The results for QLLLPLLLK and QLLLPLLLR show that the singly protonated ions undergo loss of ammonia and to a smaller extent loss of water, whereas the doubly protonated ions undergo predominant loss of water. The fast fragmentation next to P (forming the y 5 ion) occurs to a larger extent than the neutral losses from the singly protonated ions but much less than the water loss from the doubly protonated ions. The results from these and other peptides show that, in general, when N-terminal glutamine peptides have no "mobile protons", that is, the number of charges on the peptide is no greater than the number of basic amino acids (K, R, H), deamination is the predominant neutral loss fragmentation, but when mobile protons are present the predominant process is the loss of water. Both of these processes are faster than backbone fragmentation at the proline. These results are rationalized on the basis of resonance stabilization of the two types of five-membered ring products that would be formed in the neutral loss processes; the singly protonated ion yields the more stable neutral pyrrolidinone ring whereas the doubly protonated ion yields the protonated aminopyrroline ring (see Schemes). The generality of these trends is confirmed by analyzing an MS/MS spectra library of peptides derived from tryptic digests of yeast. In the absence of mobile protons, glutamine deamination is the most rapid neutral loss process. For peptides with mobile protons, dehydration from glutamine is far more rapid than from any other amino acid. Most strikingly, end terminal glutamine is by far the most labile source of neutral loss in excess-proton peptides, but not highly exceptional when mobile protons are not available. In addition, rates of deamination are faster in lysine versus arginine C-terminus peptides and 20 times faster in positively charged than negatively charged peptides, demonstrating that these formal neutral loss reactions are not "neutral reactions" but depend on charge state and stability. (J Am Soc Mass Spectrom 2007, 18, 27-36)

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Section: Comparison Of Neutral Losses From N-terminal Glutamine To Frsupporting

confidence: 62%

mentioning

confidence: 99%

Dehydration versus deamination of N-terminal glutamine in collision-induced dissociation of protonated peptides

Neta

Kilpatrick

et al. 2007

J. Am. Soc. Mass Spectrom.

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“…In traditional sequence search methods, because the expected fragment-ion peak intensities are not known and not easily predicted, they are often simply ignored or given an ad-hoc value based on the ion type. This fails to take into account that the peak intensities are strong functions of the peptide sequence and the charge state, as has been reported in numerous publications [38][39][40]. Moreover, spectral searching needs no assumption on what fragment ions one should expect to see in the MS/MS spectra; it simply gathers similarity information from all peaks, assigned or not, that are consistently present in many experimentally observed spectra.…”

Section: Advantages Of Spectral Searchingmentioning

confidence: 99%

Development and validation of a spectral library searching method for peptide identification from MS/MS

et al. 2007

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A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods, which often are time-consuming and error-prone. A more precise and efficient method, in which previously observed and identified peptide MS/MS spectra are catalogued and condensed into searchable spectral libraries to allow new identifications by spectral matching, is seen as a promising alternative. To that end, an open-source, functionally complete, high-throughput and readily extensible MS/MS spectral searching tool, SpectraST, was developed. A high-quality spectral library was constructed by combining the high-confidence identifications of millions of spectra taken from various data repositories and searched using four sequence search engines. The resulting library consists of over 30 000 spectra for Saccharomyces cerevisiae. Using this library, SpectraST vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits. A unique advantage of SpectraST is its full integration into the popular Trans Proteomic Pipeline suite of software, which facilitates user adoption and provides important functionalities such as peptide and protein probability assignment, quantification, and data visualization. This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching.

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“…While many fundamental studies and statistical analyses have examined the influence of amino acid content on the gas-phase dissociation of unmodified peptides [25][26][27][28][29], no similar work to date has been performed for crosslinked peptides. It has been shown that certain amino acids, including aspartic acid and proline, enhance or promote specific backbone cleavage of peptides [30 -38].…”

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confidence: 99%

Impact of proline and aspartic acid residues on the dissociation of intermolecularly crosslinked peptides

Gardner

Brodbelt

2008

J. Am. Soc. Mass Spectrom.

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The dissociation of intermolecularly crosslinked peptides was evaluated for a series of peptides with proline or aspartic acid residues positioned adjacent to the crosslinking sites (lysine residues). The peptides were crosslinked with either disuccinimidyl suberate (DSS) or disuccinimidyl L-tartrate (DST), and the influence of proline and aspartic acid residues on the fragmentation patterns were investigated for precursor ions with and without a mobile proton. Collisionally activated dissociation (CAD) spectra of aspartic acid-containing crosslinked peptide ions, doublycharged with both protons sequestered, were dominated by cleavage C-terminal to the Asp residue, similar to that of unmodified peptides. The proline-containing crosslinked peptides exhibited a high degree of internal ion formation, with the resulting product ions having an N-terminal proline residue. Upon dissociation of the doubly-charged crosslinked peptides, twenty to fifty percent of the fragment ion abundance was accounted for by multiple cleavage products. Crosslinked peptides possessing a mobile proton yielded almost a full series of b-and y-type fragment ions, with only proline-directed fragments still observed at high abundances. Interestingly, the crosslinked peptides exhibited a tendency to dissociate at the amide bond C-terminal to the crosslinked lysine residue, relative to the N-terminal side. One could envision updating computer algorithms to include these crosslinker specific product ions-particularly for precursor ions with localized protons-that provide complementary and confirmatory information, to offer more confident identification of both the crosslinked peptides and the location of the crosslink, as well as affording predictive guidelines for interpretation of the product-ion spectra of crosslinked peptides. (J

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Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns

Cited by 217 publications

References 30 publications

Dehydration versus deamination of N-terminal glutamine in collision-induced dissociation of protonated peptides

Dehydration versus deamination of N-terminal glutamine in collision-induced dissociation of protonated peptides

Development and validation of a spectral library searching method for peptide identification from MS/MS

Impact of proline and aspartic acid residues on the dissociation of intermolecularly crosslinked peptides

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