Estimation and optimization of the peak capacity of one-dimensional gradient high performance liquid chromatography using a long monolithic silica capillary column.

An estimation of the performance and optimization of gradient HPLC conditions using various columns for maximum total peak capacity was studied for "one-shot proteomics" which involves one-dimensional gradient HPLC, connected to an electrospray ionization (ESI)-mass spectrometry (MS), using a monolithic silica-C18 capillary column (350 cm long and 100 µm internal diameter) and an over 40 h shallow gradient elution with one injection. Optimization of such special one-dimensional HPLC has been a tedious task if carried out with a trial-and-error approach due to the extremely long analysis time for each run. Here, the optimized separation conditions including the column type, either particle-packed or monolithic, and the column length with a fixed gradient time are proposed by calculating the peak capacity obtainable using a long column and a long gradient time that may promote the "one-shot proteomics" approach. For instance, conventional conditions at less than 20 MPa can be adapted for a 40 h gradient elution for the proteomics experiment, and a ca. 3 m long monolithic silica-C18 capillary column was identified as the optimized medium indicated by our model with peak capacity theory. To verify this model experimentally, the numbers of identified peptides and proteins were investigated with a nano LC/MS/MS system coupled with a 3m monolithic silica-C18 capillary column by using various elution times. The experimental results showed that the numbers of identified peptides and proteins were maximized and reached a plateau with a gradient time of several tens of hours, which indicated that our model to optimize one dimensional HPLC conditions with a long column could be verified and useful.

Identification of a new plasma biomarker of Alzheimer's disease using metabolomics technology.

We performed unbiased analysis of steroid-related compounds to identify novel Alzheimer's disease (AD) plasma biomarkers using liquid chromatography-atmospheric pressure chemical ionization-mass spectroscopy. The analysis revealed that desmosterol was found to be decreased in AD plasma versus controls. To precisely quantify variations in desmosterol, we established an analytical method to measure desmosterol and cholesterol. Using this LC-based method, we discovered that desmosterol and the desmosterol/cholesterol ratio are significantly decreased in AD. Finally, the validation of this assay using 109 clinical samples confirmed the decrease of desmosterol in AD as well as a change in the desmosterol/cholesterol ratio in AD. Interestingly, we could also observe a difference between mild cognitive impairment and control. In addition, the decrease of desmosterol was somewhat more significant in females. Receiver operating characteristic (ROC) analysis between controls and AD, using plasma desmosterol shows a score of 0.80, indicating a good discrimination power for this marker in the two reference populations and confirms the potential usefulness of measuring plasma desmosterol levels for diagnosing AD. Further analysis showed a significant correlation of plasma desmosterol with Mini-Mental State Examination scores. Although larger sample populations will be needed to confirm this diagnostic marker sensitivity, our studies demonstrate a sensitive and accurate method of detecting plasma desmosterol concentration and suggest that plasma desmosterol could become a powerful new specific biomarker for early and easy AD diagnosis.

Quantitative and wide-ranging profiling of phospholipids in human plasma by two-dimensional liquid chromatography/mass spectrometry.

Normal-phase or reverse-phase liquid chromatography has been used in phospholipidomics for lipid separation prior to mass spectrometry analysis. However, separation using a single separation mode is often inadequate, as high-abundance phospholipids can mask large numbers of low-abundance lipids of interest. In order to detect and quantify low-abundance phospholipids, we present a novel two-dimensional (2D) approach for sensitive and quantitative global analysis of phospholipids. The methodology monitors individual glycerolipids and phospholipids through the use of a new quantitative normal-phase, solid-phase extraction procedure, followed by molecular characterization and relative quantification using an ion-trap Orbitrap equipped with a reverse-phase liquid chromatograph, with data processing by MS++ software. The CV (%) of the peak area of each lipid standard was less than 15% with this extraction method. When the method was applied to a liver sample, we could detect more phosphatidylserine (PS) compared to the previous method. Finally, our developed method was applied to Alzheimer's disease (AD) plasma samples. Several hundred peaks were detected from a 60 µL plasma sample. A partial-least-squares discriminant analysis (PLS-DA) plot using peak area ratio gave a unique group of PLS scores which could distinguish plasma samples of Alzheimer's disease (AD) patients from those of age-matched healthy controls.

Ethylenediaminetetraacetic acid increases identification rate of phosphoproteomics in real biological samples.

We have developed a novel approach to enhance phosphopeptide identification in liquid chromatography/mass spectrometry (LC/MS)-based phosphoproteomics. After enrichment of phosphopeptides with immobilized metal affinity chromatography (IMAC) and titanium dioxide (TiO(2)) microcolumns, samples were coinjected with ethylenediaminetetraacetic acid (EDTA) into LC/MS. This procedure decreased the MS peak intensity of nonphosphorylated peptides, but not that of phosphopeptides, and as a result, the number of identified phosphopeptides was increased. EDTA appeared to have no effect on liquid chromatographic separation of phosphorylated and nonphosphorylated peptides. Although the mechanism of the positive effect of EDTA on identification of phosphopeptides is unknown, and we have never observed metal ion adduct peaks in LC/MS spectra, coinjection of EDTA seemed to enhance phosphopeptide recovery from the LC/MS system. This simple technique was successfully applied to the identification of phosphopeptides in mouse brain (2938 phosphopeptides), human plasma (127 phosphopetides), and human cerebrospinal fluid (CSF) (123 phosphopeptides). We also identified nonphosphopeptides in the same samples using a two-dimensional (2D) LC/MS-based shotgun approach. The results overall indicated that 20-25% of brain proteins were phosphorylated, while only 1-2% of proteins in plasma and CSF were phosphorylated. These ratios were almost constant throughout the range of protein expression levels. In addition, EDTA-enhanced phosphoproteomics could identify low-abundance proteins in the samples, because nonphosphoproteins corresponding to more than one-third of the identified phosphoproteins could not be identified by 2D-LC/MS. Finally, we were able to find that the newly developed approach was very effective for the phosphoproteome analysis in Alzheimer disease model mice brain.

Quantitative profiling of polar cationic metabolites in human cerebrospinal fluid by reversed-phase nanoliquid chromatography/mass spectrometry.

Reversed-phase (RP) nanoliquid chromatography (LC)/mass spectrometry (MS) is widely used for proteome analysis, but hydrophilic metabolites are poorly retained on RP columns. We describe here the development and application of an efficient, robust, and quantitative nano-LC/MS method for cationic metabolome analysis in the positive ionization mode without any derivatization of analytes. Various stationary phases for nano-LC, coating of the internal wall of the capillary column, and various mobile phases were evaluated in terms of separation and peak shapes for 33 hydrophilic metabolites, including nonderivatized amino acids. Polar cationic compounds were strongly bound to mixed-functional RP with cation exchange mode resin, and the best separation was obtained with hydrophilic internal wall coating and a two-step trifluoroacetic acid (TFA) gradient in methanol as the mobile phase. Simple, but optimized, sample processing and the use of a high content of methanol allowed robust nano-LC/MS analysis. Our developed method was applied for biomarker discovery in Alzheimer's disease (AD). Several hundred peaks were detected from 10 microL of cerebrospinal fluid (CSF). In a principal component analysis (PCA) plot using peak intensities without normalization, peak separation depended on the experimental date, not disease state. Therefore, constant amounts of two stable isotope-labeled amino acids, Val and Lys, were added as internal standards (ISs) to each sample before processing. These ISs were eluted in different gradient slopes in the two-step gradient, and the normalized peak ratios using the corresponding ISs gave a unique group of PCA scores which could distinguish AD CSF samples from age-matched control CSF samples.

Evaluation of comprehensive multidimensional separations using reversed-phase, reversed-phase liquid chromatography/mass spectrometry for shotgun proteomics.

Two-dimensional liquid-chromatographic (LC) separation followed by mass spectrometric (MS) analysis was examined for the identification of peptides in complex mixtures as an alternative to widely used two-dimensional gel electrophoresis followed by MS analysis for use in proteomics. The present method involves the off-line coupling of a narrow-bore, polymer-based, reversed-phase column using an acetonitrile gradient in an alkaline mobile phase in the first dimension with octadecylsilanized silica (ODS)-based nano-LC/MS in the second dimension. After the first separation, successive fractions were acidified and dried off-line, then loaded on the second dimension column. Both columns separate peptides according to hydrophobicity under different pH conditions, but more peptides were identified than with the conventional technique for shotgun proteomics, that is, the combination of a strong cation exchange column with an ODS column, and the system was robust because no salts were included in the mobile phases. The suitability of the method for proteomics measurements was evaluated.

High-speed solubility screening assay using ultra-performance liquid chromatography/mass spectrometry in drug discovery.

Ultra-performance liquid chromatography (UPLC) was investigated as an alternative to high-performance liquid chromatography (HPLC) for analyzing pharmaceutical drug candidates. We previously developed a 96-well-based high-speed solubility assay system (HSSOL) using HPLC/UV and a LogD assay system (HSLogD) using HPLC/MS [Y. Dohta, T. Yamashita, S. Horiike, T. Nakamura, T. Fukami, Anal. Chem. 79 (2007) 8312]. We have introduced the UPLC/MS system into this previously developed HSSOL system to increase throughput. Results obtained by the UPLC/MS and HPLC/UV systems showed good agreement, validating the usefulness of the UPLC/MS system. A high-speed solubility assay system was developed employing the UPLC/MS system, thereby tripling the throughput.

A system for LogD screening of 96-well plates using a water-plug aspiration/injection method combined with high-performance liquid chromatography-mass spectrometry.

A system for screening of the octanol/water distribution coefficient (LogD) using automatic sampling of 96-well plates was developed. The high-speed assay for LogD (HSLogD) screening uses a water-plug aspiration/injection method combined with high-performance liquid chromatography-mass spectrometry (HPLC-MS). The method is useful for LogD analysis of highly hydrophobic compounds, where the concentration of the compound in the octanol phase is much higher than that in the water phase. In the case of LogD analyses, the conventional shake-flask method has been widely used, but it is difficult to increase the throughput of the shake-flask method because the lower water phase is carefully separated by manual separation without contamination of the upper octanol phase. We attempted to develop an automatic sampling method instead of manual separation to increase the throughput of the measurement. In initial attempts at automatic sampling, contamination of the octanol phase occurred when sampling of the water phase was made. This was because the octanol phase entered the sampling needle as it passed through to the lower water phase. This contamination was prevented by taking up a few microliters of water into the needle as a plug before sampling of the water phase (the water-plug aspiration/injection method). LogD values of some common drugs measured using the HSLogD agreed with reported LogD values (0 < LogD < 5).

Identification of membrane-type receptor for bile acids (M-BAR).

Bile acids play an essential role in the solubilization and absorption of dietary fat and lipid-soluble vitamins. Bile acids also modulate the transcription of various genes for enzymes and transport proteins for their own and cholesterol homeostasis through binding to nuclear receptors. Here we report a novel category of bile acid receptor, a membrane-type G protein-coupled receptor (GPCR), BG37. Bile acids induced rapid and dose-dependent elevation of intracellular cAMP levels in BG37-expressing cells, but not in mock-transfected cells, independently of nuclear receptor expression. The rank order of potency of various bile acids for BG37-expressing cells was different from that for the nuclear receptor-mediated response. These observations demonstrate the presence of two independent signaling pathways for bile acids; membrane-type GPCR for rapid signaling and nuclear receptors for delayed signaling. Expression of BG37 was detected in various specific tissues, suggesting its physiological role, although it remains to be further characterized.