Liquid chromatography mass spectrometry profiling of histones

Here we describe the use of reverse-phase liquid chromatography mass spectrometry (RPLC-MS) to simultaneously characterize variants and post-translationally modified isoforms for each histone. The analysis of intact proteins significantly reduces the time of sample preparation and simplifies data interpretation. LC-MS analysis and peptide mass mapping have previously been applied to identify histone proteins and to characterize their post-translational modifications. However, these studies provided limited characterization of both linker histones and core histones. The current LC-MS analysis allows for the simultaneous observation of all histone PTMs and variants (both replacement and bulk histones) without further enrichment, which will be valuable in comparative studies. Protein identities were verified by the analysis of histone H2A species using RPLC fractionation, AU-PAGE separation and nano-LC-MS/MS.     

Simultaneous profiling of N-glycans and proteins from human serum using a parallel-column system directly coupled to mass spectrometry

A method for the rapid identification of proteins and their N-glycans was developed through the use of two parallel columns directly connected to a mass spectrometer. Both porous graphitic carbon (PGC) and C18 capillary columns were connected in parallel with two switching valves for the simultaneous analysis of glycans and peptides, respectively. To verify the efficiency of the analytical system, profiling of N-glycans and proteins from human serum was demonstrated. This method is suitable for high-throughput analysis and automation, is contamination-free for the identification of N-glycans and proteins in a complex biological sample, and can be applied to glycomics and proteomics.     

Metabolic profiling by ion mobility mass spectrometry (IMMS)

Ion Mobility Mass Spectrometry (IMMS) was evaluated as an analytical method for metabolic profiling. The specific instrument used in these studies was a direct infusion (DI)-electrospray ionization (ESI)—ambient pressure ion mobility spectrometer (APIMS) coupled to a time-of-flight mass spectrometer (TOFMS). The addition of an ion mobility spectrometer to a mass spectrometer had several advantages over direct infusion electrospray mass spectrometry alone. This tandem instrument (ESI-IMMS) added a rapid separation step with high-resolution prior to mass spectrometric analysis of metabolite mixtures without extending sample preparation time or reducing the high through put potential of direct mass spectrometry. Further, IMMS also reduced the baseline noise common with ESI-MS analyses of complex samples and enabled rapid separation of isobaric metabolites. IMMS was used to analyze the metabolome of Escherichia coli (E. coli), containing a collection of extremely diverse chemical compounds including hydrophobic lipids, inorganic ions, volatile alcohols and ketones, amino and non-amino organic acids, and hydrophilic carbohydrates. IMMS data were collected as two-dimensional spectra showing both mobility and mass of each ion detected. Using direct infusion ESI-IMMS of a non-derivatized methanol extract of an E. coli culture, more than 500 features were detected, of which over 200 intracellular metabolites were tentatively assigned as E. coli metabolites. This analytical method also allowed simultaneous separation of isomeric metabolic features.     

Metabolic profiling of flavonoids in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry

Flavonoids detected from a model legume plant, Lotus japonicus accessions Miyakojima MG-20 and Gifu B-129, were profiled using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR/MS). Five flavonols and two anthocyanidins were detected as aglycones. LC-FTICR/MS facilitated simultaneous detection of 61 flavonoids including compounds that have not been reported previously. Chemical information of the peaks such as retention time, lambdamax, m/z value of the quasi-molecular ion, m/z value of MS/MS fragment ions, and relative intensity of MS/MS fragments was obtained, along with the molecular formulas and conjugate structures. Fourteen were completely identified by comparison with authentic compounds. The high accuracy of m/z values, being 0.081 ppm between observed and theoretical values, allowed prediction of molecular formulas of unknown compounds with the help of isotope peak information for determination of chemical composition. Based on a predicted elemental composition, the presence of a novel nitrogen-containing flavonoid was proposed. A comparison of flavonoid profiles in flowers, stems, and leaves demonstrated that the flowers yielded the most complex profile, containing 30 flower-specific flavonoids including gossypetin glycosides and isorhamnetin glycosides. A comparison of flavonoid profiles between MG-20 and B-129 grown under the same conditions revealed that the accumulation of anthocyanins was higher in B-129 than MG-20, particularly in the stem. Developmental changes in the flavonoid profiles demonstrated that kaempferol glycosides increased promptly after germination. In contrast, quercetin glycosides, predominant flavonoids in the seeds, were not detectable in growing leaves.     

Metabolic profiling of 3-nitropropionic acid early-stage Huntington's disease rat model using gas chromatography time-of-flight mass spectrometry

3-Nitropropionic acid (3-NP), a potent irreversible inhibitor of mitochondrial complex II enzyme, leads to mitochondrial dysfunction and oxidative stress in Huntington's disease (HD) rat model. In this study, biochemical assays were used to demonstrate the presence of oxidative stress and mitochondrial dysfunction in 3-NP early stage HD rat models. Gas chromatography time-of-flight mass spectrometry (GC/TOFMS) was applied to analyze metabolites in brain and plasma of 3-NP-treated and vehicle-dosed rats. The orthogonal partial least-squares discriminant analysis (OPLS-DA) model generated using brain metabolic profiles robustly differentiated the 3-NP early stage HD rat model from the control. Metabonomic characterization of the 3-NP HD rat model facilitated the detection of biomarkers that define the physiopathological phenotype of early stage HD and elucidated the treatment effect of galantamine. Brain marker metabolites that were identified based on the OPLS-DA model were associated with altered glutathione metabolism, oxidative stress, and impaired energy metabolism. The treatment effect of galantamine in early stage HD could not be concluded mechanistically using the brain metabotype. Our study confirmed that GC/TOFMS is a strategic and complementary platform for the metabonomic characterization of 3-NP induced neurotoxicity in the early stage HD rat model.     

High-throughput,Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography

The bacterial cell wall is a network of glycan strands cross-linked by short peptides (peptidoglycan); it is responsible for the mechanical integrity of the cell and shape determination. Liquid chromatography can be used to measure the abundance of the muropeptide subunits composing the cell wall. Characteristics such as the degree of cross-linking and average glycan strand length are known to vary across species. However, a systematic comparison among strains of a given species has yet to be undertaken, making it difficult to assess the origins of variability in peptidoglycan composition. We present a protocol for muropeptide analysis using ultra performance liquid chromatography (UPLC) and demonstrate that UPLC achieves resolution comparable with that of HPLC while requiring orders of magnitude less injection volume and a fraction of the elution time. We also developed a software platform to automate the identification and quantification of chromatographic peaks, which we demonstrate has improved accuracy relative to other software. This combined experimental and computational methodology revealed that peptidoglycan composition was approximately maintained across strains from three Gram-negative species despite taxonomical and morphological differences. Peptidoglycan composition and density were maintained after we systematically altered cell size in Escherichia coli using the antibiotic A22, indicating that cell shape is largely decoupled from the biochemistry of peptidoglycan synthesis. High-throughput, sensitive UPLC combined with our automated software for chromatographic analysis will accelerate the discovery of peptidoglycan composition and the molecular mechanisms of cell wall structure determination.     

Liquid chromatography high‐resolution mass spectrometry for fatty acid profiling

Quantification of fatty acids has been crucial to elucidate lipid biosynthesis pathways in plants. To date, fatty acid identification and quantification has relied mainly on gas chromatography (GC) coupled to flame ionization detection (FID) or mass spectrometry (MS), which requires the derivatization of samples and the use of chemical standards for annotation. Here we present an alternative method based on a simple procedure for the hydrolysis of lipids, so that fatty acids can be quantified by liquid chromatography mass spectrometry (LC‐MS) analysis. Proper peak annotation of the fatty acids in the LC‐MS‐based methods has been achieved by LC‐MS measurements of authentic standard compounds and elemental formula annotation supported by ¹³C isotope‐labeled Arabidopsis. As a proof of concept, we have compared the analysis by LC‐MS and GC‐FID of two previously characterized Arabidopsis thaliana knock‐out mutants for FAD6 and FAD7 desaturase genes. These results are discussed in light of lipidomic profiles obtained from the same samples. In addition, we performed untargeted LC‐MS analysis to determine the fatty acid content of two diatom species. Our results indicate that both LC‐MS and GC‐FID analyses are comparable, but that because of higher sensitivity and selectivity the LC‐MS‐based method allows for a broader coverage and determination of novel fatty acids.     

Isolation and Preparation of Bacterial Cell Walls for Compositional Analysis by Ultra Performance Liquid Chromatography

The bacterial cell wall is critical for the determination of cell shape during growth and division, and maintains the mechanical integrity of cells in the face of turgor pressures several atmospheres in magnitude. Across the diverse shapes and sizes of the bacterial kingdom, the cell wall is composed of peptidoglycan, a macromolecular network of sugar strands crosslinked by short peptides. Peptidoglycan’s central importance to bacterial physiology underlies its use as an antibiotic target and has motivated genetic, structural, and cell biological studies of how it is robustly assembled during growth and division. Nonetheless, extensive investigations are still required to fully characterize the key enzymatic activities in peptidoglycan synthesis and the chemical composition of bacterial cell walls. High Performance Liquid Chromatography (HPLC) is a powerful analytical method for quantifying differences in the chemical composition of the walls of bacteria grown under a variety of environmental and genetic conditions, but its throughput is often limited. Here, we present a straightforward procedure for the isolation and preparation of bacterial cell walls for biological analyses of peptidoglycan via HPLC and Ultra Performance Liquid Chromatography (UPLC), an extension of HPLC that utilizes pumps to deliver ultra-high pressures of up to 15,000 psi, compared with 6,000 psi for HPLC. In combination with the preparation of bacterial cell walls presented here, the low-volume sample injectors, detectors with high sampling rates, smaller sample volumes, and shorter run times of UPLC will enable high resolution and throughput for novel discoveries of peptidoglycan composition and fundamental bacterial cell biology in most biological laboratories with access to an ultracentrifuge and UPLC.     

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography-mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying gas chromatography-MS (GC-MS) and ultraperformance liquid chromatography-MS (UPLC-MS) are described. These include biofluid collection, sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control-based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described.     

Metabolomic profiling of Drosophila using liquid chromatography Fourier transform mass spectrometry

Hydrophilic interaction chromatography (HILIC) interfaced with an Orbitrap Fourier transform mass spectrometer (FT-MS) was used to carry out metabolomic profiling of the classical Drosophila mutation, rosy (ry). This gene encodes a xanthine oxidase/dehydrogenase. In addition to validating the technology by detecting the same changes in xanthine, hypoxanthine, urate and allantoin that have been reported classically, completely unsuspected changes were detected in each of the tryptophan, arginine, pyrimidine and glycerophospholipid metabolism pathways. The rosy mutation thus ramifies far more widely than previously detected.     

利用超高效液相色谱和离子色谱法测定注射用磷酸川芎嗪的含量

目的:建立超高效液相色谱法(UPLC)和离子色谱法(IC)测定磷酸川芎嗪中川芎嗪和磷酸的含量,为质量评价提供依据。方法:UPLC测定川芎嗪的色谱柱为Waters Acquity BEH C18 (2.1 mm×50 mm,1.7μm);检测波长:300 nm检测川芎嗪,274 nm检测有关物质邻苯二甲酸二甲酯;流动相为0.1%甲酸水溶液(A)-0.1%甲酸乙腈(B),梯度洗脱(0.0～0.8 min,10%B→90%B;0.8～0.81 min,90%B→10%B;0.81～1.00 min,10%B),流速:0.7 m L/min。IC测定磷酸的离子交换色谱柱为Dionex IonPac AS11-HC-4μm (4×250 mm),流动相为30 mmol/L KOH溶液等度洗脱15 min,流速1.0 m L/min,柱温35℃;电导检测器;抑制器电流为50 m A。结果:川芎嗪和磷酸在10～100 g/m L内具有良好的线性关系,相关系数均为1.0,UPLC法测定川芎嗪的回收率为102.0%。IC测定磷酸的回收率为99.8%。7个公司生产的注射剂中川芎嗪的含量均在药典规定的范围90%～110%内。但是其中3个公司生产的注射剂磷酸超出药典规定范围90%～110%。结论:与常规HPLC/UPLC测定磷酸川芎嗪含量方法比较,本文所用方法测定结果更加准确、全面、且重复性好,能够真实反应注射用磷酸川芎嗪的实际含量,对于注射用磷酸川芎嗪的安全性和有效性评估提供了一定的依据。     

Liquid chromatography-tandem mass spectrometry assay for human serum testosterone and trideuterated testosterone

A liquid chromatography tandem mass spectrometry assay for serum testosterone (T) and trideuterated testosterone (d(3)T) was developed in order to support clinical research studies that determine the pharmacokinetics, production rate, and clearance of testosterone by administration of trideuterated testosterone. After adding 19-nortestosterone as the internal standard (I.S.), sodium acetate buffer, and ether, to a serum aliquot, the mixture was shaken and centrifuged, and the ether was dried. The extract was reconstituted in methanol and 15 microl was injected into a liquid chromatograph equipped with an autosampler and Applied Biosystems-Sciex API 300 triple quadrupole mass spectrometer operated in the positive ion mode. T, d(3)T, and I.S. were monitored with transitions m/z 289 to m/z 97, m/z 292 to m/z 97, and m/z 275 to m/z 109, respectively. The two calibration curves were linear over the entire measurement range of 0-20 ng/ml for T and 0-2.0 ng/ml for d(3)T. The LOQs for T and d(3)T were 0.5 ng/ml and 0.05 ng/ml. The recoveries for T and d(3)T were 91.5 and 96.4%. For T at 1.25 ng/ml and 4.0 ng/ml, the intra-day precision (RSD, %) was 3.9 and 4.3% and intra-day accuracy 0.01 and 4.5%, respectively. The inter-day precision at these levels was 5.3 and 5.4% and inter-day accuracy was 1.9 and 0.3%. For d(3)T at 0.125 ng/ml and 0.4 ng/ml, the intra-day precision (RSD, %) was 2.8 and 8.3% and intra-day accuracy was 1.8 and 5.6%. The inter-day precision at these levels was 10.0 and 7.6% and inter-day accuracy was 5.7 and 3.4%. The concentrations of T in the 38 healthy subjects ranged from 2.5 to 14.0 ng/ml (mean 6.2 ng/ml).     

Phosphoinositide profiling in complex lipid mixtures using electrospray ionization mass spectrometry

Phosphoinositides (phosphorylated derivatives of phosphatidylinositol, PI) are versatile intracellular signaling lipids whose occurrence in low concentrations complicates direct mass measurements. Here we present a sensitive method to detect, identify and quantify phosphatidylinositol phosphate (PIP) and phosphatidylinositol bisphosphate (PIP(2)) with different fatty acid compositions (phosphoinositide profiles) in total lipid extracts by electrospray ionization mass spectrometry (ESI-MS). Using this method, we detected elevated concentrations of PIP2 in human fibroblasts from patients with Lowe syndrome, a genetic disorder that affects phosphoinositide metabolism. Saccharomyces cerevisiae cells deficient in enzymes involved in PIP metabolism--Sac1p, a phosphoinositide phosphatase, and Vps34p and Pik1p, a PI 3-kinase and PI 4-kinase, respectively--showed not only different PIP concentrations but also differential changes in PIP profiles indicating metabolic and/or subcellular pooling. Mass spectrometric analysis of phosphoinositides offers unique advantages over existing approaches and may represent a powerful diagnostic tool for human diseases that involve defective phosphoinositide metabolism.     

Integrated multi-level quality control for proteomic profiling studies using mass spectrometry

Background

Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential.

Results

We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons.

Conclusion

Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.     

UPLC-MS/MS法同时测定益气养血口服液中的5种有效成分

建立了同时测定益气养血口服液中的淫羊藿苷、黄芪甲苷、黄芪皂苷域、五味子醇甲和麦冬皂苷D5种有效成分含量的超高效液相色谱-串联质谱(UPLC-MS/MS)分析方法,用Agilent Zorbax RRHD Eclipse Plus C18(50 mm×2.1 mm,1.8滋m)色谱柱,流动相：A相为乙腈溶液,B相为含0.2%甲酸的水溶液,流速为0.35 mL/min。在电喷雾电离(ESI)正离子模式下,采用的是多重反应监测模式(MRM)进行检测。结果表明,黄芪甲苷、黄芪皂苷域、淫羊藿苷、五味子醇甲和麦冬皂苷D的线性范围分别为0.003~12 mg/L、0.3~12 mg/L、0.009~18 mg/L、0.006~1.2 mg/L、0.003~3.0 mg/L;检出限分别为1滋g/L、1滋g/L、3滋g/L、2滋g/L、1滋g/L;5种成分的加样回收率为75.9%~104%;相对标准偏差均不大于3.8%。该方法简便、准确、快速、高灵敏度,已成功地用于实际的样品分析。     

Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry

An approach to the systematic identification and quantification of the proteins contained in the microsomal fraction of cells is described. It consists of three steps: (1) preparation of microsomal fractions from cells or tissues representing different states; (2) covalent tagging of the proteins with isotope-coded affinity tag (ICAT) reagents followed by proteolysis of the combined labeled protein samples; and (3) isolation, identification, and quantification of the tagged peptides by multidimensional chromatography, automated tandem mass spectrometry, and computational analysis of the obtained data. The method was used to identify and determine the ratios of abundance of each of 491 proteins contained in the microsomal fractions of na?ve and in vitro- differentiated human myeloid leukemia (HL-60) cells. The method and the new software tools to support it are well suited to the large-scale, quantitative analysis of membrane proteins and other classes of proteins that have been refractory to standard proteomics technology.     

Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry

The objective of this study was to determine if liquid chromatography mass spectrometry (LC/MS) data of tryptic digests of proteins can be used for quantitation. In theory, the peak area of peptides should correlate to their concentration; hence, the peak areas of peptides from one protein should correlate to the concentration of that particular protein. To evaluate this hypothesis, different amounts of tryptic digests of myoglobin were analyzed by LC/MS in a wide range between 10 fmol and 100 pmol. The results show that the peak areas from liquid chromatography mass spectrometry correlate linearly to the concentration of the protein (r2 = 0.991). The method was further evaluated by adding two different concentrations of horse myoglobin to human serum. The results confirm that the quantitation method can also be used for quantitative profiling of proteins in complex mixtures such as human sera. Expected and calculated protein ratios differ by no more than 16%. We describe a new method combining protein identification with accurate profiling of individual proteins. This approach should provide a widely applicable means to compare global protein expression in biological samples.     

大苞藤黄化学成分研究及其互变异构体超高效液相色谱质谱联用分析

从大苞藤黄枝叶的混合粉碎物中分离到11个化合物,运用光谱手段分别鉴定为neobractatin(1),brasixanthone B (2),5-O-methylxanthone V1 (3),10-O-methylmacluraxanthone (4),isobractatin (5),xanthone V1(6),xerophenone A (7),xerophenone B (8),bractatin (9),macluraxanthone (10)和3-O-methylneobractatin (11).本文首次应用超高效液相色谱-质谱联用技术分离了异构体7和8并测定了其精确分子量.其中化合物6～8为首次从该植物中发现.     

Metabolic profiling of fifteen amino acids in serum of chemical-induced liver injured rats by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry

Amino acids (AA) play a crucial role in the metabolic process of animals, plants and microbial cells, which are useful for the diagnosis, follow-up and prognostics of liver disorders affecting AA metabolism. A rapid, simple and sensitive analytical method is in urgent need to investigate the intact metabolic profile and to simultaneously determine individual AA in biological samples. Here, a hydrophilic interaction liquid chromatography (HILIC) coupled with tandem mass spectrometry (MS/MS) analytical method was developed and validated for simultaneous quantification of 15 AA in rat serum using isotope stable-labeled phenylalanine and alanine as internal standards. The 15 AA without derivatization were separated on a hydrophilic interaction silica column (TSK-GEL AMIDE-80), the total analytical time was within 8?min, and the concentrations of the 15 AA were determined using a multiple reaction monitoring (MRM) mode. Limits of detection (LOD) ranged from 0.01 to 0.05???g/ml, and the calibration curve was linear in the range of 0.05?C10???g/ml (r?>?0.99). The HILIC-MS method was employed to the analysis of AA in serum samples obtained from N-acetyl-p-amino-phenol (APAP)- and chloropromazine hydrochloride (CH)- induced liver injured rats. The concentrations of each AA ranged from the low quantification value up to 10???g/ml. Based on metabolic profile of AA, multivariate statistics using principal component analysis (PCA) and partial least squares discriminate analysis (PLS-DA) could differentiate two distinct groups corresponding to APAP-induced and CH-induced rats. This novel metabolic profile study of AA based on the HILIC-MS analysis and chemometric analysis provided not only an accurate quantitative assay of the serum concentrations of biomarkers, but also a promising methodology for evaluation of chemical-induced hepatotoxicity in reflecting AA metabolic pathway.     

Salivary protein profiling in type I diabetes using two-dimensional electrophoresis and mass spectrometry

Owing to its noninvasive collection, saliva is considered as a potent diagnostic fluid. The goal of this study was to investigate the modification of the salivary proteome occurring in type 1 diabetes to highlight potential biomarkers of the pathology. High-resolution two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were combined to perform a largescale analysis. The proteomic comparison of saliva samples from healthy subjects and poorly controlled type 1 diabetes patients revealed a modulation of 23 proteins. Fourteen isoforms of α-amylase, one prolactin inducible protein, three isoforms of salivary acidic protein-1, and three isoforms of salivary cystatins SA-1 were detected as under expressed, whereas two isoforms of serotransferrin were over expressed in the pathological condition. The proteins under expressed were all known to be implicated in the oral anti-inflammatory process, suggesting that the pathology induced a decrease of non-immunological defense of oral cavity. As only particular isoforms of proteins were modulated, type 1 diabetes seemed to differentially affect posttranslational modification. Authors have contributed equally to this work.