A collision cross-section database of singly-charged peptide ions

Tao, Ling; McLean, Janel R.; McLean, John A.; Russell, David H.

doi:10.1016/j.jasms.2007.04.003

Cited by 79 publications

(94 citation statements)

References 32 publications

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“…In repeated application of the algorithm to the same dataset, the resulting clustering very similar as measured by the adjusted Rand index [34]. is ϳ 5% larger than that expected for ions that fall on the globular mobility-mass trendlines [15], which suggests that the ion structures are somewhat elongated (partial helix). MD simulations as described above yield a total of 3600 candidate structures for the [M ϩ H] ϩ ions and 631 fall within Ϯ2% of ⍀ meas .…”

Section: Dynamic Clustering Algorithmmentioning

confidence: 87%

“…In previous work, we showed that a large proportion of singly charged peptide ions (formed by MALDI) appear on a single trendline in 2D mobility-m/z plots, i.e., plots of arrival-time distribution (ATD) or ion-neutral collision cross-section (⍀) versus m/z [15]; however, a few ion signals deviate (Ͼ3% to ϳ20%) from the expected trendline and nonpeptidic ion signals appear on separate, compound class specific trendlines [14,15]. Ruotolo et al showed that gas-phase [M ϩ H] ϩ ions of LLGNVLVVVLAR (derived from bovine hemoglobin) prefer extended (helical) structure(s) resulting in a larger collision cross-section than random coil structures having the same or similar m/z values [12,13], while some post-translationally modified (PTM) peptide ions (phosphopeptides) tend to pack more tightly than the unmodified protonated peptide ions owing to intra-molecular charge-solvation and/or formation of salt-bridged type structures [16,17].…”

mentioning

confidence: 99%

“…We selected this peptide because the ⍀ meas for [M ϩ H] ϩ ions formed by MALDI is about 5% larger than that expected for globular conformation [15] and smaller than that expected for helical structure. The observation raises the question of whether the ion population is composed of a number of very similar conformations and can we use statistical analysis tools to gain information about structural diversity.…”

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confidence: 99%

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The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

Tao

Dahl

Pérez

et al. 2009

J. Am. Soc. Mass Spectrom.

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Molecular dynamics (MD) is an essential tool for correlating collision cross-section data determined by ion mobility spectrometry (IMS) with candidate (calculated) structures. Conventional methods used for ion structure determination rely on comparing the measured cross-sections with the calculated collision cross-section for the lowest energy structure(s) taken from a large pool of candidate structures generated through multiple tiers of simulated annealing. We are developing methods to evaluate candidate structures from an ensemble of many conformations rather than the lowest energy structure. Here, we describe computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH 2 -Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI, and compare the structures of MIFAGIK derivatives to test the 'sensitivity' of the cluster analysis method. Cluster analysis suggests that [MIFAGIK ϩ H] ϩ ions formed by MALDI have a predominantly turn structure even though the low-energy ions prefer partial helical conformers. T he emphasis of mass spectrometry based biological chemistry is shifting from compound identification to structural studies of large biomolecules and biomolecule complexes [1][2][3][4][5][6][7], including membrane proteins [8]. The next phase of 'omics' related research must be aimed at obtaining and predicting additional dimensions of information, such as secondary, tertiary, and quaternary structures and linkage-specific information for glycans. Although sophisticated structural characterization tools, such as NMR and XRD, provide the most information, high throughput analysis of complex biological mixtures obtained by using these techniques is an underdeveloped technology. On the other hand, IMS is much more than a separation device, the structural information derived from 2D conformation space afforded by IM-MS is potentially well-suited to both high throughput applications and complex biological samples.A number of laboratories have focused their research on developing IM-MS for biophysical studies of peptides and proteins [9 -14]. In previous work, we showed that a large proportion of singly charged peptide ions (formed by MALDI) appear on a single trendline in 2D mobility-m/z plots, i.e., plots of arrival-time distribution (ATD) or ion-neutral collision cross-section (⍀) versus m/z [15]; however, a few ion signals deviate (Ͼ3% to ϳ20%) from the expected trendline and nonpeptidic ion signals appear on separate, compound class specific trendlines [14,15]. Ruotolo et al. showed that gas-phase [M ϩ H] ϩ ions of LLGNVLVVVLAR (derived from bovine hemoglobin) prefer extended (helical) structure(s) resulting in a larger collision cross-section than random coil structures having the same or similar m/z values [12,13], while some post-translationally modified (PTM) peptide ions (phosphopeptides) tend to pack more tightly than the unmodified protonated peptide ions owing to intra-molecular charge-solvation and/or formation of salt-...

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Section: Dynamic Clustering Algorithmmentioning

confidence: 87%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

Tao

Dahl

Pérez

et al. 2009

J. Am. Soc. Mass Spectrom.

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Section: Frips (B) Shows Greater Selectivity In Dissociation Than Cidmentioning

confidence: 98%

“…It is likely that such proximity results from the formation of multiple electrostatic interactions between the peptide backbone and the site of protonation at arginine to yield a globular peptide structure, a common effect observed in gas-phase protonated peptide structures. [6][7] The present study derives advantage from this observation, informing a choice of model peptides to optimize reaction around the seventh residue.In contrast to the FRIPS products of the alanine model peptide, the FRIPS spectrum of AARAAMAHA in Figure S1b shows little CO 2 loss or backbone a ion formation at alanine residues and is instead dominated by dissociation at methionine and histidine. The formation of the a 8 ion through hydrogen atom abstraction at C β followed by β-cleavage of the backbone C α −C bond suggests a low activation energy for these processes at the histidine residue.…”

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Hydrogen Bonding Constrains Free Radical Reaction Dynamics at Serine and Threonine Residues in Peptides

et al. 2014

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Synthesis of TEMPO-based FRIPS reagent. Scheme S1. Synthesis method for FRIPS reagentThe synthesis strategy for the second generation TEMPO-based FRIPS reagent (10) is summarized in Scheme S1. The previous development by Lee et al. 1 was modified by replacing 2-(bromomethyl)benzoic acid methyl ester with methyl 2-bromoacetate for the current study, as outlined briefly previously. 2 Further details are given here. Methyl 2-(2,2,6,6-tetramethylpiperidin-1-yloxy)acetate (ii)A 25 mL, 3-neck flask equipped with a teflon-coated, oval shaped magnetic bar was flamebaked under vacuum, charged with dry N 2 gas, and cooled down to room temperature. To the flask was added methyl 2-bromoacetate (i) (0.474 mL, 5 mmol, 1 equiv), TEMPO (957 mg,6 mmol, 1.2 equiv), Cu(OTf) 2 (185 mg, 0.5 mmol, 0.1 equiv), copper powder (318mg, 5 mmol, 1 equiv), 4,4′-dinonyl-2,2′-bipyridyl (Nbpy, 843 mg, 0.4 equiv), and benzene (10 mL, 0.5 M). The reaction mixture was degassed by bubbling dry N 2 gas and stirred at 70 °C for 15 h under a stream of dry N 2 gas while monitoring conversion by thin layer chromatography (hexane : ethyl 3 acetate = 10 : 1, KMnO 4 ). The crude mixture was cooled down to room temperature, briefly cleaned by filtration through a short pad of silica gel, and the silica gel pad was thoroughly washed by ethyl acetate (EtOAc) to recover the product. The filtrate was washed by saturated NH 4 Cl, and 1 M NH 4 OH to remove the residual copper ions. The organic layer was further washed by saturated brine, dried over anhydrous MgSO 4 , concentrated by a rotavap, and purified by silica gel column chromatography (hexane : EtOAc = 20 : 1). The desired product, methyl 2-(2,2,6,6-tetramethylpiperidin-1-yloxy)acetate (ii) (1.023g, 4.46 mmol) was obtained as a yellow 2-(2,2,6,6-tetramethylpiperidin-1-yloxy)acetic acid (iii)To a 25 mL, one-neck flask was added methyl 2-(2,2,6,6-tetramethylpiperidin-1-yloxy)acetate (ii) (246 mg, 1.07 mmol, 1 equiv), tetrahydrofuran (THF) (5 mL), and 2 M Potassium Hydroxide (KOH, 5 mL). The mixture was stirred at room temperature for 24 h. The reaction was monitored by thin layer chromatography and ESI-MS until the starting material was completely consumed.Upon completion of the reaction, THF was removed by rotavap, and the residual aqueous layer was neutralized by ~5 mL of 2 M HCl to yield a pH of ~6. The mixture was extracted by CH 2 Cl 2 (×5), and the combined organic layer was dried over anhydrous MgSO 4 , concentrated by rotavap, and purified by silica gel column chromatography (hexane : EtOAc = 2 : 1) to yield 2-(2,2,6,6-tetramethylpiperidin-1-yloxy)acetic acid (iii) (137 mg, 0.635 mmol) as a white powder. Yield: 10, 75.53, 59.86, 39.59, 32.82, 20.31, 16.99. 2,5-dioxopyrrolidin-1-yl 2-(2,2,6,6-tetramethylpiperidin-1-yloxy)acetate (iv)In a flame-baked 50 mL one neck flask, N-hydroxysuccinimide (2.75 g) was added to 14 mL of trifluoroacetic anhydride at room temperature under a stream of dry N 2 gas and stirred for 4 h.The solvent was removed by rotavap and further eliminated by high vacuum overnight....

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