The elemental composition dynamics of large polyphosphate granules in Acinetobacter strain 210A

Electron microscopy and energy dispersive X-ray micro-analysis were used to examine the elemental composition of large polyphosphate granules in unfixed and unstained intact cells of Acinetobacter strain 210A. When grown in medium with butyrate, Acinetobacter strain 210A possessed 1 or 2 large granules with a diameter of 0.4 m besides a relatively large number of small granules. The large granules were composed of phosphorus, magnesium and potassium. A decrease in the Mg/Ca-ratio of the medium from 5.95 to 0.0073 resulted in a decline in the intracellular Mg/Ca-ratio from 15 to 0.56. At a high intracellular Mg/Ca-ratio, magnesium was the dominant counterion in the polyphosphate granule. Calcium became the major cation in the polyphosphate bodies at a low intracellular Mg/Ca-ratio. Omission of Ca²⁺ or modification of the K/Mg ratio in the medium did not significantly affect the cation composition of the polyphosphate granules. The dissociation constants for Mg- and Ca-polyphosphate were 9.3×10^-2 mol/l and 1.5×10^-1 mol/l, respectively.     

Quantitative metabolome analysis using capillary electrophoresis mass spectrometry

A new approach for the comprehensive and quantitative analysis of charged metabolites by capillary electrophoresis mass spectrometry (CE-MS) is proposed. Metabolites are first separated by CE based on charge and size and then selectively detected using MS by monitoring over a large range of m/z values. This method enabled the determination of 352 metabolic standards and its utility was demonstrated in the analysis of 1692 metabolites from Bacillus subtilis extracts, revealing significant changes in metabolites during B. subtilis sporulation.     

Quantitative metabolome analysis using liquid chromatography-high-resolution mass spectrometry

In this report, we introduce a liquid chromatography single-mass spectrometry method for metabolome quantification, using the LTQ Orbitrap high-resolution mass spectrometer. Analytes were separated with hydrophilic interaction liquid chromatography. At a working resolution of 30,000 (at m/z 400), the limit of detection varied from 50 fmol to 5 pmol for 25 metabolites tested. In terms of metabolite concentration, the linearity was about 2 to 3 orders of magnitude for most compounds (R² > 0.99). To determine the accuracy of the system in complex sample matrices, the isotope dilution method was evaluated from mixtures of pure compounds and uniformly ¹³C-labeled cell extracts. With the application of this method, quantification was possible within single runs even when the pool sizes of individual metabolites varied from 0.13 to 55.6 μM. As a case study, intracellular concentrations of central metabolites were determined for Methylobacterium extorquens AM1 during growth on two different carbon sources, methanol and succinate. Reproducible results from technical and biological repetitions were obtained that revealed significant variations of intracellular metabolite pool sizes, depending on the carbon source. The LTQ Obitrap offers new perspectives and strategies for metabolome quantification.     

Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry

A main objective of proteomics research is to systematically identify and quantify proteins in a given proteome (cells, subcellular fractions, protein complexes, tissues or body fluids). Protein labeling with isotope-coded affinity tags (ICAT) followed by tandem mass spectrometry allows sequence identification and accurate quantification of proteins in complex mixtures, and has been applied to the analysis of global protein expression changes, protein changes in subcellular fractions, components of protein complexes, protein secretion and body fluids. This protocol describes protein-sample labeling with ICAT reagents, chromatographic fractionation of the ICAT-labeled tryptic peptides, and protein identification and quantification using tandem mass spectrometry. The method is suitable for both large-scale analysis of complex samples including whole proteomes and small-scale analysis of subproteomes, and allows quantitative analysis of proteins, including those that are difficult to analyze by gel-based proteomics technology.     

Determination of the elemental composition of mature wheat grain using a modified secondary ion mass spectrometer (SIMS)

An imaging secondary ion mass spectrometry system has been developed that allows the distribution of elements or ions to be superimposed on an image of the plant cell or tissue generated by ion-induced secondary electrons. This system has been evaluated by analysing the aleurone and sub-aleurone cells of mature wheat grain, showing high spatial resolution (100-200 nm) images of O-, PO(2)-, Mg+, Ca+, Na+ and K+ within the phytate granules of the aleurone, with CN- being diagnostic for proteins and C(2)- being diagnostic for starch in the starchy endosperm cells. This system should provide improved localization of elements in a range of other plant systems.     

Preparation and analysis of Pseudomonas putida cells for elemental composition

A series of procedures including cultivation, harvesting, washing, drying, ashing, and chemical preparation were developed for the analysis of the elemental composition of Pseudomonas putida cells. The composition of P. putida grown in continuous culture in five separate experiments at 30°C, pH 7.5, in 0.1% peptone‐yeast extract medium adjusted to a salinity of 26.5 g/L was averaged in μg/g for 50 subsamples: C, 521,000 ± 10,200; N, 143,000 ± 2,100; H, 73,600 ± 2,000; P, 17,600 ± 4,600; S, 5,200 ± 200; Mg, 3,970 ± 1,360; Na, 2,730 ± 1,160; Ca, 2,560 ± 700; K, 2,400 ± 630; Fe, 170 ± 55; Zn, 97 ± 34; and Cu, 28 ± 7.

The critical steps in the procedure were washing three times with “pure”; 4°C water using mechanical agitation and homogenization of the dried cells with an agate mortar and pestle.     

Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry

Pooling of DNA samples before genotyping is a valuable means of streamlining large-scale genotyping efforts in disease association studies, single-nucleotide polymorphism (SNP) validation or mutant allele screening programs. In this report, we explore the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to quantitative analysis of SNPs. The measurements are based on MALDI-TOF MS analysis of primer extension assays performed on standard mixtures of pooled PCR products at several test loci. The inherent high molecular weight resolution of MALDI-TOF MS conveys high specificity and good signal-to-noise ratio for performing accurate quantitation. The methods described maximize the sensitivity and quantitative capacity of MALDI-TOF MS while preserving the throughput and economic advantages of the MALDI-TOF platform. Using the format described, we demonstrate that allele frequencies as low as 5% can be detected quantitatively and unambiguously.     

Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry

We present a robust and general method for the identification and relative quantification of phosphorylation sites in complex protein mixtures. It is based on a new chemical derivatization strategy using a dendrimer as a soluble polymer support and tandem mass spectrometry (MS/MS). In a single step, phosphorylated peptides are covalently conjugated to a dendrimer in a reaction catalyzed by carbodiimide and imidazole. Modified phosphopeptides are released from the dendrimer via acid hydrolysis and analyzed by MS/MS. When coupled with an initial antiphosphotyrosine protein immunoprecipitation step and stable-isotope labeling, in a single experiment, we identified all known tyrosine phosphorylation sites within the immunoreceptor tyrosine-based activation motifs (ITAM) of the T-cell receptor (TCR) CD3 chains, and previously unknown phosphorylation sites on total 97 tyrosine phosphoproteins and their interacting partners in human T cells. The dynamic changes in phosphorylation were quantified in these proteins.     

Rapid isolation and characterization of bacterial lipopeptides using liquid chromatography and mass spectrometry analysis

The structural analysis of post‐translational modifications (PTMs) of lipoproteins is difficult due to the hydrophobic properties of their fatty acid moieties. At the present time, the relative positions of fatty acid components on the N‐acyl‐S‐diacylglycerylcysteine core structure has not been specifically identified in any natural or bacterial expressed recombinant lipoproteins. In this study, we describe a rapid solid‐phase extraction using acetonitrile and isopropanol method that can be performed manually to isolate large amounts of relatively pure lipopeptides generated by the limited tryptic‐digestion of recombinant lipoproteins. Using these lipopeptides and LC/MS mass spectra analysis, two groups of N‐terminal lipidated (diacyl or triacyl) molecules that differ by one fatty acid unit were successfully identified. This LC/MS method also provided the separation of lipopeptides differing by 14 Da for the on‐line MS identification. Multiple‐stage fragmentation analyses of the di‐ and triacyl lipopeptides using both the positive and negative ion modes enabled to identify the putative structure of the N‐acyl‐S‐diacylglycerylcysteine containing an amide bond to palmitic acid at the N‐terminal cysteine, a palmitic acid at sn1 position, and an unsaturated fatty acid of either hexadecenoic acid, cyclopropaneoctanoic acid, oleic acid and nonadecenoic acid at sn2 position of diacylglycerol residue through ester bonding. For diacyl lipoprotein, the saturated palmitoyl fatty acid group is absent at sn1 position of glycerol‐derived lipid residue of lipopeptide.     

Quantitative analysis of the protein composition of yeast ribosomes

The molecular weights of the individual yeast ribosomal proteins were determined. The ribosomal proteins from the 40-S subunit have molecular weights ranging from 11 800 to 31 000 (average molecular weight = 21 300). The molecular weights of the 60-S subunit proteins range from 10 000 to 48 400 (average molecular weight = 21 800). Stoichiometric measurements, performed by densitometric scanning on ribosomal proteins extracted from high-salt dissociated subunits revealed that isolated ribosomal subunits contain, besides some protein species occurring in submolar amounts, a number of protein species which are present in multiple copies: S13, S27, L22, L31, L33, L34 and L39. The mass fractions of the ribosomal proteins which were found to be present on isolated ribosomes in non-unimolar amounts, were re-examined by using an isotope dilution technique. Applying this method to proteins extracted from mildely isolated 80-S ribosomes, we found that some protein species such as S32, S34 and L43 still are present in submolar amounts. On the other hand, however, we conclude that some other ribosomal proteins, in particular the strongly acidic proteins L44 and L45 get partially lost during ribosome dissociation. Proteins L44/L45 appears to be present on 80-S ribosomes in three copies.     

Quantitative analysis of the kinetics of phospholipase A2 using fast atom bombardment mass spectrometry

Fast atom bombardment mass spectrometry that can directly analyze lysophospholipids was used to quantitatively determine the kinetics of phospholipase A2. This method is 1250 times more sensitive than the colorimetric assay.     

Exploring ocean biogeochemistry by single-cell microprobe analysis of protist elemental composition

The biogeochemical cycles of many elements in the ocean are linked by their simultaneous incorporation into protists. In order to understand these elemental interactions and their implications for global biogeochemical cycles, accurate measures of cellular element stoichiometries are needed. Bulk analysis of size-fractionated particulate material obscures the unique biogeochemical roles of different functional groups such as diatoms, calcifying protists, and diazotrophs. Elemental analysis of individual protist cells can be performed using electron, proton, and synchrotron X-ray microprobes. Here we review the capabilities and limitations of each approach and the application of these advanced techniques to cells collected from natural communities. Particular attention is paid to recent studies of plankton biogeochemistry in low-iron waters of the Southern Ocean. Single-cell analyses have revealed significant inter-taxa differences in phosphorus, iron, and nickel quotas. Differences in the response of autotrophs and heterotrophs to iron fertilization were also observed. Two-dimensional sub-cellular mapping indicates the importance of iron to photosynthetic machinery and of zinc to nuclear organelles. Observed changes in diatom silicification and cytoplasm content following iron fertilization modify our understanding of the relationship between iron availability and silicification. These examples demonstrate the advantages of studying ocean biogeochemistry at the level of individual cells.     

Quantitative analysis of lysophosphatidic acid by time-of-flight mass spectrometry using a phosphate-capture molecule

Lysophosphatidic acid (LPA) is a lipid mediator that may play an important role in wound healing, embryonic development, and progression of cancer. Here, we report a procedure for the quantification of LPA by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The method is based on a characteristic mass shift with total charge change (from -2 to +1) of the phosphate species due to 1:1 complexation of LPA(2-) with a dinuclear zinc (II) complex [1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-olato dizinc(II) complex; Zn(2)L(3+)] at physiological pH. The monocationic complex [LPA(2-)-Zn(2)L(3+)](+) was detected in the positive mode, in which no other signal of cation adducts of LPA(2-) was observed. The detection limit of 18:1 LPA by this method was 0.1 pmol on a sample plate. The intensity ratio of [LPA(2-)-Zn(2)L(3+)](+) against an internal standard [17:0 LPA(2-)-Zn(2)L(3+)](+) increased linearly with their molar ratio. Based on the relative intensities of complex ions, we determined the amounts of LPA homologs in an egg white by this method; the results obtained were in good agreement with those by gas liquid chromatography. This sensitive and convenient procedure for LPA-specific detection is useful for the quantification of LPA homologs occurring in biological materials.     

Quantitative analysis of tissue folate using ultra high-performance liquid chromatography tandem mass spectrometry

The tissue distribution of folate in its numerous coenzyme forms may influence the development of disease at different sites. For instance, the susceptibility of human colonic mucosa to localized folate deficiency may predispose to the development of colorectal cancer. We report a sensitive and robust ultra high-performance liquid chromatography (UHPLC) tandem mass spectrometry method for quantifying tissue H₄folate, 5-CH₃-H₄folate, 5-CHO-H₄folate, folic acid, and 5,10-CH⁺-H₄folate concentration. Human colonic mucosa (20–100 mg) was extracted using lipase and conjugase enzyme digestion. Rapid separation of analytes was achieved on a UHPLC 1.9-μm C18 column over 7 min. Accurate quantitation was performed using stable isotopically labeled (¹³C₅) internal standards. The instrument response was linear over physiological concentrations of tissue folate (R² > 0.99). Limits of detection and quantitation were less than 20 and 30 fmol on column, respectively, and within- and between-run imprecision values were 6–16%. In colonic mucosal samples from 73 individuals, the average molar distribution of folate coenzymes was 58% 5-CH₃-H₄folate, 20% H₄folate, 18% formyl-H₄folate (sum of 5-CHO-H₄folate and 5,10-CH⁺-H₄folate), and 4% folic acid. This assay would be useful in characterizing folate distribution in human and animal tissues as well as the role of deregulated folate homeostasis on disease pathogenesis.     

Quantitative urine amino acid analysis using liquid chromatography tandem mass spectrometry and aTRAQ reagents

Ion-exchange chromatography (IEC) is the most widely used method for amino acid analysis in physiological fluids because it provides excellent separation and reproducibility, with minimal sample preparation. The disadvantage, however, is the long analysis time needed to chromatographically resolve all the amino acids. To overcome this limitation, we evaluated a novel liquid chromatography tandem mass spectrometry (LC-MS/MS) method, which utilizes aTRAQ reagents, for amino acid analysis in urine. aTRAQ reagents tag the primary and secondary amino groups of amino acids. Internal standards for each amino acid are also labeled with a modified aTRAQ tag and are used for quantification. Separation and identification of the amino acids is achieved by liquid chromatography tandem mass spectrometry using retention times and mass transitions, unique to each amino acid, as identifiers. The run time, injection-to-injection, is 25 min, with all amino acids eluting within the first 12 min. This method has a limit of quantification (LOQ) of 1 μmol/L, and is linear up to 1000 μmol/L for most amino acids. The Coefficient of Variation (CV) was less than 20% for all amino acids throughout the linear range. Method comparison demonstrated concordance between IEC and LC-MS/MS and clinical performance was assessed by analysis of samples from patients with known conditions affecting urinary amino acid excretion. Reference intervals established for this method were also concordant with reference intervals obtained with IEC. Overall, aTRAQ reagents used in conjunction with LC-MS/MS should be considered a comparable alternative to IEC. The most attractive features of this methodology are the decreased run time and increased specificity.     

Quantitative analysis of amyloid-beta peptides in cerebrospinal fluid using immunoprecipitation and MALDI-Tof mass spectrometry.

Immunoprecipitation (IP) combined with matrix-assisted laser desorption ionization (MALDI) time of flight (Tof) mass spectrometry has been used to develop quantitative assays for amyloid-beta (Abeta) peptides in cerebrospinal fluid (CSF). Inclusion of (15)N labelled standard peptides allows for absolute quantification of multiple Abeta isoforms in individual samples. Characterization of variability associated with all steps of the assay indicated that the IP step is the single largest contributor to overall variability. Optimization of the assay resulted in overall coefficient of variation 相似文献   

Quantitative analysis of the composition of the native and scrambled ribonuclease A

Reversible conversion between the native and scrambled proteins can be applied to analyze the denaturation curve of a disulfide-containing protein. In the case of RNase A, scrambled species could not be well separated from the native species by HPLC to permit precise quantitative analysis of the extent of denaturation. Methods are developed here to overcome this problem. The methods exploit the difference of conformational stability between the native and scrambled RNase A. When a sample of partially denatured RNase A was placed under mild reducing conditions (0.2-1 mM dithiothreitol for 10 min), the disulfide bonds of the native RNase A remain intact, whereas those of scrambled isomers become fully reduced. The native and fully reduced species of RNase A can be completely separated by HPLC. Alternatively, a mixture of partially denatured RNase A can be treated with mild concentration of proteolytic enzymes (trypsin or thermolysin). In this approach, scrambled isomers of RNase A were totally fragmented and readily separated from the native RNase A. These methods allow analysis and construction of the denaturation curves of RNase A in the presence of urea, GdmCl and GdmSCN.