Thesis (Ph. D.)--Ohio State University, 2006. / Available online via OhioLINK's ETD Center; full text release delayed at author's request until 2009 Aug 16

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

 Proteomics is the systematic study of the proteome: the total protein expression of a cell or tissue under specified conditions. The multiplicity and complexity of proteins in cells requires sensitive, selective, and comprehensive methodologies for their distinction and characterization. Multidimensional liquid chromatography (MDLC) coupled with biological tandem mass spectrometry (MS/MS) is uniquely suited to fulfill those requirements and has become an indispensable tool in MS-based proteomics. Our laboratory has developed an online high-/low-pH reversed-phase/reversed-phase (RP–RP) LC system exhibiting fully automatable and reproducible performance. It is a promising alternative to the strong cation exchange/reversed-phase (SCX–RP) system commonly used in high-throughput comprehensive proteomics analyses. The first part of this Thesis (Chapter 2) describes the development of a variant of the high-/low-pH RP–RP platform—RP–SCX–RP—that integrates an additional SCX trap column between the two RP columns to enhance sample recovery. This new system allows the detection of larger numbers of hydrophilic peptides. Indeed, in the analyses of a lysate of Arabidopsis chloroplast proteins, it identified approximately 25% more non-redundant proteins than those identified using the previous version of the RP–RP system. The modified platform has been extended for the online removal of sodium dodecyl sulfate and other excess interference chemicals used in Isobaric Tags for Relative and Absolute Quantification (iTRAQ) reactions, thereby avoiding the need for time-consuming offline SCX clean-up prior to RP–RP separation in the quantitative proteomics analyses of crude biological samples at low-microgram levels. A novel online three-dimensional liquid chromatography (3DLC) system was derived from the RP–SCX–RP design, exhibiting remarkably enhanced orthogonality, resolution, and peak capacity. Peptides were separated in the first-dimension high-pH RP column based on their hydrophobicity, followed by sub-fractionation in the second-dimension SCX column, primarily based on charge; the third dimension was a typical low-pH RP separation, prior to MS analysis. The overall performance of the system was evaluated through analysis of a cell lysate of mouse embryonic fibroblasts. Relative to the two-dimensional high-/low-pH RP–RP system, the new 3D system yielded significant increases in the number of unique peptides and proteins identified, making it a good alternative to SCX–RP and high-/low-pH RP–RP as an efficient automated MDLC platform for high-throughput shotgun proteomics. An optimized and miniaturized variant of the three-dimensional LC platform was also developed. Its simplified setup and operation, by decreasing the number of six-port switching valves (from three to two) and the number of SCX fractionation steps, minimized both the potential sample loss and the total analysis time (by ca. 30%). Thus, a variety of novel, automatable, and robust RP–SCX–RP-based MDLC platforms have been developed for high-throughput qualitative and quantitative analysis. The performance of these systems complements conventional MDLC systems, with enhanced quality, quantity, reproducibility, and throughput of protein identification and quantification. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

This investigation has produced four major results: (1) Thermodynamic properties of chromium metal, aqueous ions, hydrolysis species, oxides and hydroxides were compiled. Data were critically evaluated, some data were recalculated, and thermodynamic properties were selected. (2) A method was developed for separating chromium from its natural water matrix using sequential anion and cation exchange chromatography. (3) A method for determining the ⁵³Cr/⁵²Cr ratio using solid-source thermal ionization mass spectrometry with the silica gel-boric acid ionization- - enhancement technique was developed. (4) Ground water samples from six locations were analyzed for their ⁵³Cr/⁵²Cr ratio using the above methods. Results from carefully measured electromotive force (emf) values for the reduction of Cr³⁺ to Cr²⁺ were recalculated for compatibility with the infinite dilution standard state, and a revised ∆G°(f) for Cr²⁺(aq) was calculated. Equilibrium constants for chromium(III) hydrolysis were taken from Rai, et al. (1987) and for chromium(VI) hydrolysis from Palmer, et al. (1987). The ion exchange method is based on retention of chromium(VI) on strongly basic anion exchange resin at pf1 4 and its reductive elution with 2N HNO₃ . Chromium(III) is retained on strongly acidic cation exchange resin at pH 1.3 and eluted with 5N HNO₃. Possible interferents include metals that form both oxyanions and cations. High-purity reagents and containers made of rigorously cleanable noncontaminating materials are required. Samples for mass spectrometry are pretreated with aqua regia and concentrated nitric acid, then mixed with silica and boric acid and transferred to the tantalum filament of a stainless steel and glass sample holder. The ⁵³Cr/⁵²Cr ratio was measured to avoid isobaric interferences with iron. To be significantly different from each other, isotopic signatures must differ by at least 0.5 per mil. Samples from six locations were examined for their ⁵³Cr/⁵²Cr ratio. For the samples with natural origin, the spread in δ⁵³Cr values of-2.0 to +3.0 per mil suggests that samples of chromium derived from differing source materials or from different geographic locations have distinct isotopic signatures. Conclusions regarding source-related variations in the isotopic signature of contaminant chromium are problematic, because specific information about the respective source materials is lacking.

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