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Appropriate solubilization of membrane proteins can be achieved by incorporating detergents such as sodium dodecyl sulfate (SDS). Unfortunately, SDS interferes with liquid chromatography (LC) and mass spectrometry (MS). This thesis presents “MS-friendly’ alternatives to solubilize membrane proteins and provides an evaluation of current protocols for SDS removal. Considering the limitation of SDS in a proteome analysis workflow, fluorinated surfactants have previously been proposed. Our results showed that APFO similar proteome solubilization to that of SDS. Unfortunately, APFO was only marginally more tolerable to LC and MS than SDS. Nonetheless, an important advantage of using APFO is that it can be easily removed from the sample by evaporation. The efficiency of precipitation protocols was explored. Our results demonstrate that high recovery is possible. Quantitative re-solubilization of membrane proteins following precipitation was made possible through addition of 80% formic acid. This solvent system may present a promising pathway for top-down MS analysis.

Carbapanems are a class of β-lactam antibiotics with broad-spectrum potency and high β-lactamase resistance. Ertapenem, a member of this class, sold under the trade name Invanz™, has been of interest in the world of antibiotic therapeutic drug monitoring owing to its highly standardized 1 g dose and its high degree of plasma protein binding. Owing to the relative newness of this drug, fewer than 30 methods for ertapenem quantification have been published. Among these about half utilize biological matrices at the sample type. Liquid-liquid extraction and protein precipitation prevail as the most frequently used sample preparation techniques, despite their low recoveries compared with solid-phase extraction. Additionally, high-performance liquid chromatography with ultraviolet detection (HPLC-UV) is the instrumentation choice for most ertapenem assays. While these approaches may not achieve the highest possible sensitivity for ertapenem quantification, they provide clinically relevant tools for monitoring ertapenem in real patients. Sample stability is an ongoing concern for laboratories that handle ertapenem analysis, with buffering being of paramount importance, as well as low temperature (

The conditioning effect in metabolomic studies is the phenomenon of initial variation of analytical results in the first 5-10 injections of a biological sample in chromatographic systems. The deviation manifests itself as a drift in retention time, peak area and in multivariate analysis. It is a major quality assurance problem in the metabolomic field and if not accounted for would result in high analytical variance. The aim of this study was to investigate the conditioning effect and to gain further knowledge about it. The study was carried out on UPLC of hydrophilic liquid chromatography (HILIC) type coupled to quadrupole time of flight (QTOF) MS. A systematic study was designed to investigate the effects of the age of the analytical column. An investigation into certain matrix components as a possible cause of the conditioning effect was made. Different sample preparation methods were investigated. One result showed that no conditioning could be seen and the system appeared stable from the first injection. Differences in sample composition between samples with conditioning effect and samples without conditioning effect were investigated. No correlation between conditioning effect and levels of certain matrix compounds could be found. More studies of correlation between sample composition and the amount of conditioning occurring is needed. Some samples appear to have no retention time drift but have a significant drift in peak area and in multivariate analysis. This is an indication that the conditioning effect should be analysed in more ways than one before determining if a system is stable.

The aim of this research was the development of mass spectrometry-based methodologies for the high-throughput quantitation of peptides in biological matrices. Glucagon and GLP-1, which are of interest as biomarkers and in the development of therapeutics, were chosen as model peptides. Immunoassays that are traditionally used to quantify these often perform poorly; therefore, necessitating the development of alternative methodologies. Application of mass spectrometry-based methodologies to these analytes has, however, been limited, primarily due to sensitivity challenges, but also due to analytical challenges associated with their endogenous nature and instability in biological matrices. Chapter 2 describes the development and qualification of the first liquid-chromatography coupled tandem mass spectrometry (LC-MS/MS) method for the quantitation of endogenous glucagon from human plasma. A novel 2D extraction procedure was developed to ensure robustness and sensitivity, whilst a novel surrogate matrix quantitation strategy took into account the endogenous nature of the analyte. A lower limit of quantitation (LLOQ) of 25 pg/mL was qualified, which was a considerable improvement over that previously reported in the literature (250 pg/mL) for a LC-MS/MS method. Clinical samples were cross-validated against a conventional radioimmunoassay (RIA), and similar pharmacokinetic (PK) profiles resulted, demonstrating that the methods were complementary. In Chapter 2 glucagon instability in biological matrix was noted. To characterise this further, in Chapter 3 in vitro glucagon metabolites were identified using high-resolution mass spectrometry (HRMS). Metabolites observed by others (glucagon19-29, glucagon3 29 and [pGlu]3glucagon3 29) in alternative matrices were identified, alongside novel metabolites (glucagon20-29 and glucagon21-29). Cross-interference of these metabolites in immunoassays may help to explain their poor performance, whilst knowledge of metabolism may also aid the development of future stabilisation strategies. The method developed in Chapter 2 was refined in Chapter 4 to improve sensitivity, robustness and throughput, and to add GLP-1 as a secondary analyte. The sensitivity achieved (glucagon: 15 pg/mL LLOQ, GLP-1: 25 pg/mL LLOQ) is the highest reported for both peptides for an extraction avoiding immunoenrichment. Specificity of endogenous glucagon quantitation was assured using a novel approach with a supercharging mobile phase additive to access a sensitive qualifier transition. A cross-validation against established immunoassays using physiological study samples demonstrated some similarities between the methods. Differences between the immunoassay results exemplified the need to develop alternative methodologies. The resulting LC-MS/MS method is considered a viable alternative to immunoassays, for the quantitation of endogenous glucagon, dosed glucagon and/or dosed GLP-1 in human plasma.