Fully automated online multi-dimensional protein profiling system for complex mixtures

For high throughput proteome analysis of highly complex protein mixtures, we have constructed a fully automated online system for multi-dimensional protein profiling, which utilizes a combination of two-dimensional liquid chromatography and tandem mass spectrometry (2D-LC-MS-MS), based on our well-established offline system described previously [K. Fujii, T. Nakano, T. Kawamura, F. Usui, Y. Bando, R. Wang, T. Nishimura, J. Proteome Res. 3 (2004) 712]. A two-valve switching system on a programmable auto sample injector is utilized for online two-dimensional chromatography with strong cation-exchange (SCX) and reversed-phase (RP) separations. The SCX separation is carried out during the equilibration of RP chromatography and the entire sequence of analysis was performed under fully automated conditions within 4 h, based on six SCX fractionations, and 40 min running time for the two-dimensional RP chromatography. In order to evaluate its performance in the detection and identification of proteins, digests of six standard proteins and yeast 20S proteasome have been analyzed and their results were compared to those obtained by the one-dimensional reversed-phase chromatography system (ID-LC-MS-MS). The 2D-LC-MS-MS system demonstrated that both the number of peptide fragments detected and the protein coverage had more than doubled. Furthermore, this multi-dimensional protein profiling system was also applied to the human 26S proteasome, which is one of the highly complex protein mixtures. Consequently, 723 peptide fragments were identified as 31 proteasome components, together with other coexisting proteins in the sample. The identification could be comprehensively performed with a 63% sequence coverage on an average, and additionally, with modifications at the N-terminus. These results indicated that the online 2D-LC-MS-MS system being described here is capable of analyzing highly complex protein mixtures in a high throughput manner, and that it would be applicable to dynamic proteomics.     

Application of high performance liquid chromatography for the profiling of complex chemical mixtures with the aid of chemometrics

In this paper, chemometrics methods were applied to resolve the high performance liquid chromatography (HPLC) fingerprints of complex, many-component substances to compare samples from a batch from a given manufacturer, or from those of different producers. As an example of such complex substances, we used a common Chinese traditional medicine, Huoxiang Zhengqi Tincture (HZT) for this research. Twenty-one samples, each representing a separate HZT production batch from one of three manufacturers were analyzed by HPLC with the aid of a diode array detector (DAD). An Agilent Zorbax Eclipse XDB-C18 column with an Agilent Zorbax high pressure reliance cartridge guard-column were used. The mobile phase consisted of water (A) and methanol (B) with a gradient program of 25-65% (v/v, B) during 0-30 min, 65-55% (v/v, B) during 30-35 min and 55-100% (v/v, B) during 35-60 min (flow rate, 1.0 ml min⁻¹; injection volume, 20 μl; and column temperature-ambient). The detection wavelength was adjusted for maximum sensitivity at different time periods. A peak area matrix with 21 objects × 14 HPLC variables was obtained by sampling each chromatogram at 14 common retention times. Similarities were then calculated to discriminate the batch-to-batch samples and also, a more informative multi-criteria decision making methodology (MCDM), PROMETHEE and GAIA, was applied to obtain more information from the chromatograms in order to rank and compare the complex HZT profiles. The results showed that with the MCDM analysis, it was possible to match and discriminate correctly the batch samples from the three different manufacturers. Fourier transform infrared (FT-IR) spectra taken from samples from several batches were compared by the common similarity method with the HPLC results. It was found that the FT-IR spectra did not discriminate the samples from the different batches.     

Protein abundance quantification in embryonic stem cells using incomplete metabolic labelling with 15N amino acids,matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry,and analysis of relative isotopologue abundances of peptides

An isotope dilution method for protein quantification is presented in the context of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) and mass fingerprinting experiments, revealing an unappreciated high reproducibility and accuracy of relative peak intensity measurements. Labelled proteins were generated by growing cells in a medium containing (15)N-enriched amino acids, and were mixed with proteins of natural isotopic composition from control cells in ratios of approximately 0:1, 1:7, 1:2, 2:1, 7:1, and 1:0 (labelled/unlabelled). Mixtures were separated by two-dimensional gel electrophoresis and analysed by MALDI-TOFMS using typical experimental conditions. A linear relationship is demonstrated between the relative isotopologue abundances (RIA values) for particular peaks in the isotopic distribution of tryptic peptide fragments of the proteins, and the mole fractions of labelled proteins in the mixture. Analysis of RIA values (ARIA quantification) for peptides of six typical silver-stained protein spots for the various mixtures could reproduce the experimentally contrived ratios with approximate errors between 4% (2:1 mixture) and about 18% (1:7 mixture). A consideration of error and its propagation is discussed. ARIA does not require complete separation of the isotope patterns of labelled and unlabelled peptides, and is therefore advantageous in combination with all kinds of labelling experiments in biological systems, because it is compatible with minimal metabolic incorporation of labelling reagent. Simulations indicate that the minimum required (15)N enrichment of the total amino acid pool sufficient for ARIA is less than 4%. In an accompanying paper in this issue, we apply ARIA to proteins differentially labelled with isotope-coded alkylation reagents.     

Infrared spectra and relative stability of the F3CH/NH3 H-bonded complex in liquefied Xe

FTIR spectra of mixtures of fluoroform (F3CH) and ammonia (NH3), have been studied in liquid xenon between 5400 and 500 cm-1. Spectroscopic evidence for the formation of a hydrogen bonded complex has been found and the complexation enthalpy Delta(LXe)H degrees in the temperature interval between 173 and 215 K, was determined to be 14.4 (7) kJ mol-1. The parallel fundamentals nu1 and nu2 of ammonia reveal a strong narrowing effect upon complex formation, whereas the perpendicular fundamentals nu3 and nu4 show a modest decrease of their width. CP corrected ab initio calculations at the MP2(FULL)/6-311++G(3df,2pd) level predict a linear geometry for the complex, characterized by a small red shift of the CH stretch frequency of fluoroform. The ab initio interaction energy was found to be compatible with the isolated molecule complexation energy extrapolated from the experimental Delta(LXe)H degrees .     

Linking protein fractionation with multidimensional monolithic reversed-phase peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins

Recently, multidimensional shotgun proteomics has proven to be an alternative technology able to identify hundreds of proteins from single samples. Two major limitations of the technology are the presence of high abundance proteins (e.g. RUBISCO in plant leaf tissue) and the enormous number of co-eluting peptides that overstrain the loading and resolving capacity of conventional particle-packed columns as well as the capacity of electrospray ionisation due to ion suppression. Here, the coupling of fast performance liquid chromatography (FPLC) pre-fractionation of an Arabidopsis leaf protein extract and subsequent two-dimensional liquid chromatography/mass spectrometry with improved resolution using a monolithic silica C18 capillary column allowed the identification of 1032 unique proteins in a single 4 mg total protein plant leaf tissue sample. The reassignment of peptide IDs to distinct FPLC protein fractions enhances the identification procedure, especially in the case of present protein isoforms. The proposed strategy is useful to detect proteins otherwise not seen in conventional multidimensional chromatography/mass spectrometry approaches.     

Host/guest complex of β-cyclodextrin/5-thia pentacene-14-one for photoinitiated polymerization of acrylamide in water

β-Cyclodextrin (β-CD) was used to complex the photoinitiator, 5-thia pentacene-14-one (TX-A), yielding a water-soluble host/guest complex. IR, UV–Vis and fluorescence spectroscopy were employed to characterize complexed β-CD/TX-A. Photoinitiated polymerization of acrylamide in water was achieved with β-CD/TX-A in the presence of N-methyldiethanolamine (MDEA). Excellent polymerization yields were observed in air saturated solutions when MDEA was added.     

N-3 alkylation of uracils with unprotected amino alcohols using the Mitsunobu reaction

During our search for novel CGRP antagonists, we had great difficulty in accessing one of our key motifs. Herein, we communicate how we solved the problem by an unprecedented Mitsunobu alkylation using unprotected amino alcohols.     

Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: an analytical challenge for studying complex protein mixtures

The large-gel two-dimensional electrophoresis (2-DE) technique, developed by Klose and co-workers over the past 25 years, provides the resolving power necessary to separate crude proteome extracts of higher eukaryotes. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) provides the sample throughput necessary to identify thousands of different protein species in an adequate time period. Spot excision, in situ proteolysis, and extraction of the cleavage products from the gel matrix, peptide purification and concentration as well as the mass spectrometric sample preparation are the crucial steps that interface the two analytical techniques. Today, these routines and not the mass spectrometric instrumentation determine how many protein digests can be analyzed per day per instrument. The present paper focuses on this analytical interface and reports on an integrated protocol and technology developed in our laboratory. Automated identification of proteins in sequence databases by mass spectrometric peptide mapping requires a powerful search engine that makes full use of the information contained in the experimental data, and scores the search results accordingly. This challenge is heading a second part of the paper.     

Carrier ampholyte-free solution isoelectric focusing as a prefractionation method for the proteomic analysis of complex protein mixtures

The field of proteomics requires methods that offer high sensitivity and wide dynamic range. One of the strategies used to improve the dynamic range is sample prefractionation, such as microsolution isoelectric focusing (IEF). We have modified a commercial solution IEF instrument, the Rotofor, to prefractionate protein mixtures by carrier ampholyte-free solution IEF. The focusing chamber of the Rotofor was divided into several compartments by polyacrylamide membranes with imbedded Immobiline mixtures of specific pH values. When an electric field is applied, each protein migrates to the compartment confined by membranes with pH values flanking its isoelectric point. The approach was demonstrated for the focusing of myoglobin into a predicted compartment, as well as the separation of a complex soluble yeast protein mixture into several distinct fractions. The proteins were dissolved in water or 30% isopropanol. The method is applicable to both gel-based and solution-phase protein identification methods, without the need for further sample preparation.     

Analysis of complex mixtures by capillary gas chromatography with statistical estimation of the number of components

Evaluation of the number of components by the Davis-Giddings single chromatogram method is applied to capillary gas chromatograms of a dichloromethane extract of camomile. Various runs with OV-1 or Carbowax 20M as the stationary phase were done under different experimental conditions (column temperature programming rate and column length). The results showed that the number of components obtained by this statistical procedure does not depend greatly on the nature of the stationary phase or on the experimental conditions. The component number of the camomile extract was about 200 and the stand-alone probability at unit resolution was 0.2–0.3.     

Resolving the problem of chromatographic overlap by 3D cross correlation (3DCC) processing of LC, MS and NMR data for characterization of complex glycan mixtures

Chromatographic overlap is a common problem in the analysis of complex mixtures. As a result, it is not possible to identify the components because each resulting NMR or MS spectrum contains multiple components. We introduce three-dimensional cross correlation (3DCC) that dissects NMR spectra of a mixture into spectra of the individual components without actually separating them. Correlation of peaks from MS and NMR profiles along a common LC time domain yields 3DCC NMR spectra of pure components correlated with a mass and a retention time. The method requires an LC run followed by fractionation and recording of MS and NMR spectra. The method is applicable to mixtures of any classes of molecules. Here, we demonstrate its application to a mixture of complex glycans obtained from a glycoprotein. Fourteen glycans eluting within only 3 min showed heavy overlap in the chromatographic run. 3DCC allowed their direct characterization without separation. Some of these structures from the glycoprotein bovine fibrinogen had not previously been described. The 3DCC procedure has been implemented in standard software. Actually, 3DCC can be used for any combination of separation techniques, like LC or GC, combined with two characterization methods like UV, IR, Raman, NMR or MS.     

Application of a flow-tunable, serially coupled gas chromatographic capillary column system for the analysis of complex mixtures

Summary A capillary column gas chromatographic system employing two serially coupled fused-silica columns and a simple coupling element is described. The system is operated in flow-tunable mode (flow-tunable tandem system). The very fact of continuous tuning over a large polarity (selectivity) range, ultimately determined by the two constituent columns, offers several possibilities in the analysis of complex mixtures. In this paper two applications are discussed in detail: optimization of peak separation and peak identification. For these applications it is feasible to use, retention data collected from experiments on the tandem system, and empirical formulas. A relatively simple theoretical mathematical model valid for the flow-tunable tandem system, however, furnishes an easy way of calculating retention data on the system from data collected from the individual single columns, thus, creating a new possibility for optimization and peak identification. Optimization and peak identification processes using the empirical and theoretical models are both demonstrated by analysis of solvent mixtures. Dedicated to the memory of Dr. Tibor Tóth Presented at Balaton Symposium on High-Performance Separation Methods, Siófok, Hungary, September 1–3, 1999     

Phase complex of the CsCl-Cs2MoO4-MoO3 system

Phase relationships in the CsCl-Cs₂MoO₄-MoO₃ system and its boundary elements were studied by thermal analysis and X-ray powder diffraction. Phase diagrams were constructed, phase crystallization fields were demarcated, and parameters of invariant point were revealed.     

Gas chromatography and gas chromatography/mass spectrometry for the characterization of complex mixtures of large oligosaccharides

High temperature gas chromatography and gas chromatography/mass spectrometry are used in the characterization of complex natural mixtures of permethylated oligosaccharides released from proteins or lipids. The high resolution allows separation of isomeric compounds and the mass range extends to oligosac-charides around molecular mass 2000 daltons or 10 sugar residues for isomalto-oligosaccharides. The mass spectra of permethylated oligosaccharide alditols from mucin glycopeptides are very informative and the approach allows a simple and rapid characterization of these complex components.     

Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data

In many cases of protein structure determination by NMR a high-quality structure is required. An important contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists. Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and used on NMR data of alpha-helical and beta-sheet proteins using homology models and/or X-ray structures. The program produced no erroneous stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar coupling information is available.     

液相色谱/质谱联机研究还原烷基化合成3-(β-羟乙基砜基)N-乙基苯胺的反应历程

 3 (β 羟乙基砜基 )苯胺在催化剂镍的存在下与醛发生加氢反应 ,可直接制得 3 (β 羟乙基砜基 )N 乙基苯胺。运用高效液相色谱 /质谱联机系统对反应生成的中间产物进行分析 ,研究了加氢还原烷基化反应的历程。