Liquid chromatographic analysis and mass spectrometric identification of farnesylated peptides

Farnesylation involves the post-translational attachment of a 15 carbon unit to the C-terminus of proteins, thus allowing them to incorporate into membranes. The farnesylation reaction requires farnesyldiphosphate as the farnesyl group donor and is catalyzed by the farnesyltransferase. Some of the most familiar farnesylated proteins belong to the Ras protein superfamily, well-known oncoproteins. As Ras proteins require the membrane localization for the transduction of extracellular signals, farnesyltransferase inhibitors are discussed as chemotherapeutic agents. Despite the importance of this post-translational modification, farnesylated peptides have been investigated rarely by means of high-pressure liquid chromatography in combination with mass spectrometry. In this study, we examined the liquid chromatographic separation of farnesylated peptides with the help of the multidimensional protein identification technology. The peptides were further ionized by electrospray ionization and subsequently analyzed by tandem mass spectrometry. We demonstrated that farnesylated peptides are more strongly retained by reversed phase than nonfarnesylated peptides. This allowed for the identification of farnesylated peptides, if spiked into complex peptide samples. In some cases the farnesyl group was apparently split off from the peptide during the ionization process, and tandem mass spectra often revealed a neutral loss of the farnesyl moiety.     

Performance evaluation of an in-injection port thermal desorption/gas chromatographic/negative ion chemical ionization mass spectrometric method for trace explosive vapor analysis

A gas chromatographic method utilizing thermal desorption of Tenax TA and sol-gel sorbent traps has been developed and validated for the analysis of trace explosive vapor with negative ion chemical ionization mass spectrometric detection. Sorbent tubes were packed with Tenax TA and sorbent particles prepared in-house by the sol-gel process. Thermal desorption was performed within a split/splitless injection port with minimal instrument modification. Performance was characterized by relative thermal desorption recovery, precision (reproducibility), linearity of the calibration, and method detection limits. Method validation was performed with a series of dinitrotoluenes, dinitrobenzene, trinitrotoluene, trinitrobenzene, two aminodinitrotoluenes, three nitroesters, and two nitramines. The performance of Tenax TA and the sol-gel sorbents is evaluated based on the method validation data. The method was applied to the analysis of trace explosive vapor collected and concentrated with sol-gel solid sorbent traps from the headspace of a smokeless gunpowder sample.     

Extraction chromatographic methods in the sample preparation sequence for thermal ionization mass spectrometric analysis of plutonium isotopes

A sample preparation sequence for actinide isotopic analysis by thermal ionization mass spectrometry (TIMS) is described that includes column-based extraction chromatography as the first separation step, followed by anion-exchange column separations. The sequence is designed to include a wet ashing step after the extraction chromatography to prevent any leached extractant or oxalic acid eluent reagents from interfering with subsequent separations, source preparation, or TIMS ionization. TEVA resin and DGA resin materials, containing extractants that consist only of C, N, O, and H atoms, were investigated for isolation of plutonium. Radiotracer level studies confirmed expected high yields from column-based separation procedures. Femtogram-level studies were carried out with TIMS detection, using multiple monoisotopic spikes applied sequentially throughout the separation sequence. Pu recoveries were 87% and 86% for TEVA and DGA resin separations, respectively. The Pu recoveries from 400 μL anion-exchange column separation sequences were 89% and 93% for trial sequences incorporating TEVA and DGA resin. Thus, a prior extraction chromatography step in the sequence did not interfere with the subsequent anion-exchange separation when a simple wet ash step was carried out in between these column separations. The average measurement efficiency for Pu, encompassing the chemical separation recoveries and the TIMS ionization efficiency, was 2.73% ± 0.77% (2σ) for the DGA resin trials and 2.67% ± 0.54% for the TEVA resin trials, compared to 3.41% and 2.37% (average 2.89%) for two control trials. These compare with an average measurement efficiency of 2.78% ± 1.70%, n = 33 from process benchmark analyses using Pu spikes processed through a sequence of oxalate precipitation, wet ash, iron hydroxide precipitation, and anion-exchange column separations. We conclude that extraction chromatography can be a viable separation procedure as part of a multistep sequence for TIMS sample preparation.     

Picogram level quantitation of 2,3,7,8-tetrachlorodibenzo-p-dioxin in fish extracts by capillary gas chromatography/matrix isolation/Fourier transform infrared spectrometry

For the first time, gas chromatography/matrix isolation/Fourier transform infrared spectrometry (GC/MI/FTIR) has been reported to confirm the identity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (2378-TCDD) and to quantify its level in fish extracts in the 170-220 pg range "on disk". When expressed on a fish tissue basis, analyte levels ranged from 15 to 45 pg/g. Spectroscopic identification was based on the position and relative intensity of seven absorption bands. Optical alignment as well as performance evaluation and optimization of the GC/MI/FTIR system are described. The use of [13C12]2378-TCDD as an internal standard was essential for quantitation, and quality assurance controls were used to verify system performance. GC/MI/FTIR quantitation of 2378-TCDD was compared with that independently found by GC with electron capture detection. Recovery of 2378-TCDD averaged 52% (n = 8, 30% relative standard deviation) for fish extracts.     

Improved tert-butyldimethylsilylation gas chromatographic/mass spectrometric detection of nerve gas hydrolysis products from soils by pretreatment of aqueous alkaline extraction and strong anion-exchange solid-phase extraction

In the analysis of tert-butyldimethylsilyl derivatives (IBDMS) of alkyl methylphosphonic acids (RMPA) and methylphosphonic acid (MPA), from soils by gas chromatography/mass spectrometry (GC/MS), the detection yields are generally low, due to the suppression of TBDMS derivatization by the soil matrix components and the adsorption of RMPA and MPA to the soils. An ion-exchange pretreatment of the aqueous soil extract can be used to overcome the former factor by removing interfering compounds. A pretreatment method is described for improving the detection yields due to the latter factor, using an alkaline extraction procedure. The recovery was estimated quantitatively using capillary electrophoresis. The soil samples tested included volcanogenous immature soils and showed a low aqueous extraction recovery and GC/MS detection yields. The inclusion of sodium hydroxide in the extraction solvent dramatically increased the recovery. Using a 0.1 M sodium hydroxide solution, the recovery was in excess of 68%. Interfering components were removed from the alkaline soil extract by solid-phase extraction of the acids on a silica-based strong anion exchanger. The alkaline soil extract was neutralized with hydrofluoric acid and applied to the cartridge in the fluoride form. After washing with water, MPA and RMPA could be eluted with methanolic ammonia nearly quantitatively. Using the established pretreatment method, MPA and RMPA were detected from all the soil samples in more than 67% yield.     

Determination of polybrominated diphenyl ethers and polychlorinated biphenyls in human adipose tissue by large-volume injection-narrow-bore capillary gas chromatography/electron impact low-resolution mass spectrometry

A new analytical method has been developed for the quantification of polybrominated diphenyl ethers (PBDEs) in human adipose tissue samples. After Soxhlet extraction and a cleanup procedure using two successive solid-phase extraction cartridges containing acid silica and acid silica: neutral silica:deactivated basic alumina (from top to bottom), detection can been achieved by narrow-bore (0.10-mm i.d.) capillary gas chromatography/electron impact low-resolution mass spectrometry using a large-volume injection technique. Using narrow-bore capillaries, it is possible to analyze complex mixtures in a short time (up to 10 min), saving 50% or more of the analysis time of conventional columns while maintaining a similar resolution power. The method allows the determination of five major PBDE congeners (BDE 28, 47, 99, 100, and 153) at concentrations below 1 ng/g lipid weight. Detection limits in the selected ion mode varied between 0.05 and 0.30 ng/g lipid weight, depending on the degree of bromination. The sensitivity of this method can compete with low-resolution mass spectrometry with electron capture ionization, while a much better selectivity is obtained. Levels of PBDEs in 20 Belgian human adipose tissue samples ranged between 2.18 and 11.70 ng/g lipid weight and were similar to previously reported values from Europe.     

Software tools for analysis of mass spectrometric lipidome data

New software tools for quantitative analysis of mass spectrometric lipidome data have been developed. The LIMSA tool finds and integrates peaks in a mass spectrum, matches the peaks with a user-supplied list of expected lipids, corrects for overlap in their isotopic patterns, and quantifies the identified lipid species according to internal standards. Three different algorithms for isotopic correction (deconvolution) were implemented and compared. LIMSA has a convenient user interface and can be applied on any type of MS spectrum. Typically, analysis of one spectrum takes only a few seconds. The SECD tool, designed for analysis of LC-MS data sets, provides an intuitive and informative display of MS chromatograms as two-dimensional "maps" for visual inspection of the data and allows the user to extract mass spectra, to be further analyzed with LIMSA, from arbitrary regions of these maps. More reliable analysis of complex lipidome data with improved signal-to-noise ratio is obtained when compared to standard time-range averaged spectra. The functionality of these tools is demonstrated by analysis of standard mixtures as well as complex biological samples. The tools described here make accurate, high-throughput analysis of extensive sample sets feasible and are made available to the scientific community free of charge.     

Sample handling for mass spectrometric proteomic investigations of human sera

Proteomic investigations of sera are potentially of value for diagnosis, prognosis, choice of therapy, and disease activity assessment by virtue of discovering new biomarkers and biomarker patterns. Much debate focuses on the biological relevance and the need for identification of such biomarkers while less effort has been invested in devising standard procedures for sample preparation and storage in relation to model building based on complex sets of mass spectrometric (MS) data. Thus, development of standardized methods for collection and storage of patient samples together with standards for transportation and handling of samples are needed. This requires knowledge about how sample processing affects MS-based proteome analyses and thereby how nonbiological biased classification errors are avoided. In this study, we characterize the effects of sample handling, including clotting conditions, storage temperature, storage time, and freeze/thaw cycles, on MS-based proteomics of human serum by using principal components analysis, support vector machine learning, and clustering methods based on genetic algorithms as class modeling and prediction methods. Using spiking to artificially create differentiable sample groups, this integrated approach yields data that--even when working with sample groups that differ more than may be expected in biological studies--clearly demonstrate the need for comparable sampling conditions for samples used for modeling and for the samples that are going into the test set group. Also, the study emphasizes the difference between class prediction and class comparison studies as well as the advantages and disadvantages of different modeling methods.