Enrichment of Cysteine-Containing Peptides from Tryptic Digests Using a Quaternary Amine Tag

Ren, Diya; Julka, Samir; Inerowicz, Halina D.; Regnier, Fred E.

doi:10.1021/ac0354645

Cited by 65 publications

(80 citation statements)

References 24 publications

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“…It also contains a sulfonium ion moiety, whose permanent charge potentially enhances the ionization efficiency [43], and which serves as an efficient leaving group to facilitate the thermodynamically favored exclusive neutral loss(es) of dimethylsulfide upon CID-MS/MS, independently of the amino acid composition and charge state of the precursor peptide ion (i.e., proton mobility), thereby allowing modified peptides to be readily identified from within a mixture of unmodified peptides, i.e., 'finding the needle in the haystack'. Furthermore, the number of neutral losses observed in the MS/MS spectrum is indicative of the number of modified residues within the peptide.…”

Section: Design Of the Dmbnhs Protein Modification Reagentmentioning

confidence: 99%

“…The results are discussed in detail below. Note that the plots shown herein were generated assuming that the ionization efficiency of a given peptide was not affected by the DMBNHS modification, even though potential enhancement of the ionization efficiencies caused by the incorporation of the sulfonium ion may occur [43]. Also, it was assumed that the magnitude of any enhancement in ionization efficiencies would be similar between peptides, and would therefore not have an impact on determination of the relative solvent accessibilities.…”

Section: Correlation Of the Modified Peptide Ion Abundances With The mentioning

confidence: 99%

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‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

Zhou

Wang

et al. 2010

J. Am. Soc. Mass Spectrom.

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Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand binding. However, a common problem associated with the use of selective chemical labeling methods for mapping protein solvent accessible residues is that when a complicated peptide mixture resulting from a large protein or protein complex is analyzed, the modified peptides may be difficult to identify and characterize amongst the largely unmodified peptide population (i.e., the 'needle in a haystack' problem). To address this challenge, we describe here the development of a strategy involving the synthesis and application of a novel 'fixed charge' sulfonium ion containing lysine-specific protein modification reagent, S,S'-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS), coupled with capillary HPLC-ESI-MS, automated CID-MS/MS, and data-dependant neutral loss mode MS 3 in an ion trap mass spectrometer, to map the surface accessible lysine residues in a small model protein, cellular retinoic acid binding protein II (CRABP II). After reaction with different reagent:protein ratios and digestion with Glu-C, modified peptides are selectively identified and the number of modifications within each peptide are determined by CID-MS/MS, via the exclusive neutral loss(es) of dimethylsulfide, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility) of the peptide. The observation of these characteristic neutral losses are then used to automatically 'trigger' the acquisition of an MS 3 spectrum to allow the peptide sequence and the site(s) of modification to be characterized. Using this approach, the experimentally determined relative solvent accessibilities of the lysine residues were found to show good agreement with the known solution structure of CRABP II. (J Am Soc Mass Spectrom 2010, 21, 1339 -1351) © 2010 American Society for Mass Spectrometry M ass spectrometry (MS) combined with protein labeling has found increasing utility as an alternative tool to conventional high-resolution methods such as X-ray crystallography or NMR for the examination of higher order protein structure (e.g., tertiary and quaternary), conformation, ligand binding, and dynamics [1]. Although typically providing lower resolution than these more established approaches, MS-based analysis strategies have particular advantages in sensitivity and speed, and the capability of analyzing proteins or protein complexes that are not amenable to crystallization, or that fall outside the mass range routinely accessible by NMR.A variety of MS/protein labeling methods have been developed, and are based on either the use of (1) hydrogen-deuterium exchange (HDX) [2,3] or (2) stable chemical modification [4 -6], before proteolytic digestion and analysis by HPLC-MS and/or tandem mass spectrometry (MS/MS). HDX may potentially be used to probe the entire protein backbone, thereby providing the highest resolution of the MS-based approaches. However, limitations of HDX that can hamper determination...

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Section: Design Of the Dmbnhs Protein Modification Reagentmentioning

confidence: 99%

Section: Correlation Of the Modified Peptide Ion Abundances With The mentioning

confidence: 99%

‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

Zhou

Wang

et al. 2010

J. Am. Soc. Mass Spectrom.

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“…Regnier et al [30] applied quaternary amine tag, (3-acrylamidopropyl) trimethylammonium chloride (APTA), to derivatizing cysteine-containing peptides. Because the positive charge of derivatized peptides increased, it could be selectively enriched by the strong cation exchange chromatography.…”

Section: Derivatization Of Thiol Groupmentioning

confidence: 99%

Recent Advancement of Chemical Derivatization and Its Applications to High Sensitive Analysis of Peptide in Mass Spectrometry

Qiao

Rui

Zhang

et al. 2012

Chinese Journal of Analytical Chemistry

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“…Several charge tags have been investigated on the basis of their chemical availability or synthetic convenience, e.g., 2,4,6-trimethylpyridinium [4], 2,2'-bipyridyl [5], tris(2,4,6-trimethoxyphenyl)phosphonium (TMPP) [6][7][8], and trimethylammoniumalkyl [9,10]. Enhanced charging can also be achieved by introducing into the peptide the basic guanidine group by various guanidination strategies [11][12][13][14][15][16][17].…”

mentioning

confidence: 99%

Tunable Charge Tags for Electron-Based Methods of Peptide Sequencing: Design and Applications

Zimnicka

Moss

Chung

et al. 2011

J. Am. Soc. Mass Spectrom.

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Charge tags using basic auxiliary functional groups 6-aminoquinolinylcarboxamido, 4-aminopyrimidyl-1-methylcarboxamido, 2-aminobenzoimidazolyl-1-methylcarboxamido, and the fixedcharge 4-(dimethylamino)pyridyl-1-carboxamido moiety are evaluated as to their properties in electron transfer dissociation mass spectra of arginine C-terminated peptides. The neutral tags have proton affinities that are competitive with those of amino acid residues in peptides. Charge reduction by electron transfer from fluoranthene anion-radicals results in peptide backbone dissociations that improve sequence coverage by providing extensive series of N-terminal ctype fragments without impeding the formation of C-terminal z fragments. Comparison of ETD mass spectra of free and tagged peptides allows one to resolve ambiguities in fragment ion assignment through mass shifts of c ions. Simple chemical procedures are reported for Nterminal tagging of Arg-containing tryptic peptides.

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Enrichment of Cysteine-Containing Peptides from Tryptic Digests Using a Quaternary Amine Tag

Cited by 65 publications

References 24 publications

‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

Recent Advancement of Chemical Derivatization and Its Applications to High Sensitive Analysis of Peptide in Mass Spectrometry

Tunable Charge Tags for Electron-Based Methods of Peptide Sequencing: Design and Applications

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