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Highly efficient and selective enrichment of peptide subsets combining fluorous chemistry with reversed-phase chromatography.

ABSTRACT: The selective capture of target peptides poses a great challenge to modern chemists and biologists, especially when enriching them from proteome samples possessing extremes in concentration dynamic range and sequence diversity. While approaches based on traditional techniques such as biotin-avidin pairing offer versatile tools to design strategies for selective enrichment, problems are still encountered due to sample loss or poor selectivity of enrichment. Here we show that the recently introduced fluorous chemistry approach has attractive properties as an alternative method for selective enrichment. Through appending a perfluorine group to the target peptide, it is possible to dramatically increase the peptide's hydrophobicity and thus enable facile separation of labeled from non-labeled peptides. Use of reversed-phase chromatography allowed for improved peptide recovery in comparison with results obtained using the formerly reported fluorous bonded phase methods. Furthermore, this approach also allowed for on-line separation and identification of both labeled and unlabeled peptides in a single experiment. The net result is an increase in the confidence of protein identification by tandem mass spectrometry (MS2) as all peptides and subsequent information are retained. Successful off-line and on-line enrichment of cysteine-containing peptides was obtained, and high quality MS2 spectra were obtained by tandem mass spectrometry due to the stability of the tag, allowing for facile identification via standard database searching. We believe that this strategy holds great promise for selective enrichment and identification of low abundance target proteins or peptides.

SUBMITTER: Ying W

PROVIDER: S-EPMC3584324 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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Highly efficient and selective enrichment of peptide subsets combining fluorous chemistry with reversed-phase chromatography.

Ying Wantao W Perlman David H DH Li Lei L Théberge Roger R Costello Catherine E CE McComb Mark E ME

Rapid communications in mass spectrometry : RCM 20091201 24

The selective capture of target peptides poses a great challenge to modern chemists and biologists, especially when enriching them from proteome samples possessing extremes in concentration dynamic range and sequence diversity. While approaches based on traditional techniques such as biotin-avidin pairing offer versatile tools to design strategies for selective enrichment, problems are still encountered due to sample loss or poor selectivity of enrichment. Here we show that the recently introduc ...[more]

PMID: 19924777

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Project description:Manganese(III) complexes of three fluorophilic salen derivatives were used to prepare ion-selective electrodes (ISEs) with ionophore-doped fluorous sensing membranes. Because of their extremely low polarity and polarizability, fluorous media are not only chemically very inert but also solvate potentially interfering ions poorly, resulting in a much improved discrimination of such ions. Indeed, the new ISEs exhibited selectivities for CO(3)(2-) that exceed those of previously reported ISEs based on nonfluorous membranes by several orders of magnitude. In particular, the interference from chloride and salicylate was reduced by 2 and 6 orders of magnitude, respectively. To achieve this, the selectivities of these ISEs were fine-tuned by addition of noncoordinating hydrophobic ions (i.e., ionic sites) into the sensing membranes. Stability constants of the anion-ionophore complexes were determined from the dependence of the potentiometric selectivities on the charge sign of the ionic sites and the molar ratio of ionic sites and the ionophore. For this purpose, a previously introduced fluorophilic tetraphenylborate and a novel fluorophilic cation with a bis(triphenylphosphoranylidene)ammonium group, (R(f6)(CH(2))(3))(3)PN(+)P(R(f6)(CH(2))(3))(3), were utilized (where R(f6) is C(6)F(13)). The optimum CO(3)(2-) selectivities were found for sensing membranes composed of anionic sites and ionophore in a 1:4 molar ratio, which results in the formation of 2:1 complexes with CO(3)(2-) with stability constants up to 4.1 × 10(15). As predicted by established theory, the site-to-ionophore ratios that provide optimum potentiometric selectivity depend on the stoichiometries of the complexes of both the primary and the interfering ions. However, the ionophores used in this study give examples of charges and stoichiometries previously neither explicitly predicted by theory nor shown by experiment. The exceptional selectivity of fluorous membranes doped with these carbonate ionophores suggests their use not only for potentiometric sensing but also for other types of sensors, such as the selective separation of carbonate from other anions and the sequestration of carbon dioxide.

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Highly efficient and selective enrichment of peptide subsets combining fluorous chemistry with reversed-phase chromatography.

Publications

Highly efficient and selective enrichment of peptide subsets combining fluorous chemistry with reversed-phase chromatography.

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