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PubMed1999

Negative ion electrospray and tandem mass spectrometric analysis of platelet activating factor (PAF) (1-hexadecyl-2-acetyl-glycerophosphocholine).

The analysis of 1-hexadecyl-2-acetyl-glycerophosphocholine (platelet activating factor, PAF) by negative ion and normal-phase liquid chromatography/tandem mass spectrometry (LC/MS/MS) was investigated as an alternative technique to the currently used gas chromatography/MS and positive ion LC/MS/MS procedures. The positive ion [M + H]+ derived from PAF and generated by electrospray ionization is abundant, but the potential presence of isobaric 1-octadecanoyl-2-lyso-glycerophosphocholine (stearoyl-lyso-GPC) and 1-hexadecanoyl-2-formyl-glycerophosphocholine (PFPC) in biological samples limits the use of the most abundant collision-induced decomposition (CID) transition (formation of the phosphocholine ion, m/z 524-->184) if chromatographic separation is not achieved. Less abundant CID product ions, such as loss of the neutral ketene molecule derived from the respective fatty acyl groups, provide the requisite specificity, but the intensity of these transitions yields a signal-to-noise ratio that greatly diminishes the analytical sensitivity. With negative ion LC/MS/MS, however, the molecular anions [M - 15]- derived from PAF, stearoyl-lyso-GPC and PFPC decompose to the carboxylate anions at m/z 59, 283 and 255, respectively, permitting discrimination of these isobaric molecules even without chromatographic separation. In addition, the CID of [M - 15]- was favorable, yielding ion currents of sufficient intensity to permit the measurement of PAF when isolated from small quantities of biological material. With the use of a stable isotopically labeled variant of PAF and isotope dilution, negative ion LC/MS/MS was found to measure PAF reliably even in the presence of the isobaric stearoyl-lyso-GPC and permitted the use of non-chlorinated mobile phases for normal-phase high-performance LC.

Humans↗
PubMed2025

Spatiotemporally resolved GPCR interactome uncovers unique mediators of receptor agonism.

Cellular signaling by membrane G protein-coupled receptors (GPCRs) is governed by a complex and diverse array of mechanisms. The dynamics of a GPCR interactome, as it evolves over time and space in response to an agonist, provide a unique perspective on pleiotropic signaling decoding and functional selectivity at the cellular level. In this study, we utilized proximity-based APEX2 proteomics to investigate the interaction network of the luteinizing hormone receptor (LHR) on a minute-to-minute timescale. We developed an analytical approach that integrates quantitative multiplexed proteomics with temporal reference profiles, creating a platform to identify the proteomic environment of APEX2-tagged LHR at the nanometer scale. LHR activity is finely regulated spatially, leading to the identification of putative interactors, including the Ras-related GTPase RAP2B, which modulate both receptor signaling and post-endocytic trafficking. This work provides a valuable resource for spatiotemporal nanodomain mapping of LHR interactors across subcellular compartments.

Humans↗
PubMed2002

High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MS.

In this work, we describe the application of a stable isotope amino acid (lysine) labeling in conjunction with data-dependent multiplexed tandem mass spectrometry (MS/MS) to facilitate the characterization and identification of peptides from proteomic (global protein) digests. Lysine auxotrophic yeast was grown in the presence of 13C-labeled or unlabeled lysine and combined after harvesting in equal proportions. Endoproteinase LysC digestion of the cytosolic fraction produced a global proteomic sample, consisting of heavy/light labeled peptide pairs. Then data-dependent multiplexed-MS/MS was applied to simultaneously select and dissociate only labeled peptide ion pairs. The approach allows differentiation between N-terminal (e.g., b-type ions) and C-terminal fragment ions (e.g., y-type ions) in resulting tandem mass spectra, as well as the capability of differentiation between near-isobaric glutamine and lysine residues. We also describe the utility of peptide composition and fragment information to support peptide identifications and examine the potential application of lysine labeling for differential quantitative protein analysis.

Amino Acids↗
PubMed2005

Enhanced sensitivity for the determination of ambiphilic polyaromatic amines by LC-MS/MS after acetylation.

A new method for the analysis of aminonitropyrenes and diaminopyrenes was developed for urine and hemoglobin samples using LC-MS/MS. A good separation by LC was only achieved after derivatization of the amino group, which also increased sensitivity to a limit of detection (LOD) of 0.1 pg (on column) for diaminopyrene and 5 pg for aminonitropyrene using electrospray ionization (ESI). Compared to a derivatization with pentafluorobenzoyl chloride yielding only one sensitive MS/MS transition, acetylation offers the advantages of a higher selectivity with two sensitive MS/MS transitions and the possibility of a direct detection of acetylated aminonitropyrenes and diaminopyrenes formed metabolically in vivo. Acetylated diaminopyrene was detected in urine and after hydrolysis of the corresponding hemoglobin adducts followed by acetylation in blood samples of rats after administration of dinitropyrene but not in controls. A method based on GC-MS with negative chemical ionization of the electrophore labelled metabolites was non-selective since only one major ion [M - HF]- was formed and some isobaric peaks were observed preventing unequivocal analyte identification at concentrations close to the LOD.

Amines↗
PubMed1998

Measurement of sulfate concentrations and tracer/tracee ratios in biological fluids by electrospray tandem mass spectrometry.

A reproducible and very sensitive method is described for the quantitation of inorganic sulfate in biological fluids by negative electrospray ionization tandem mass spectrometry. After addition to the sample of (34)S-labeled sodium sulfate internal standard and deproteinization with methanol, interfering bicarbonate anions are removed by acidification and chloride and phosphate by means of a single filtration step. The tandem mass spectrometer is used in neutral loss mode to detect HSO(4)(-) ions free of interference from residual isobaric H(2)PO(4)(-) ions. Organic sulfates do not interfere with the measurement. Serum and urinary inorganic sulfate concentrations measured with this technique agree closely with determinations by ion-exchange chromatography with conductivity detection. Unlike the latter method, this technique does not require dedicated equipment. The method is also suitable for measuring the ratio of (34)S-labeled sulfate to unlabeled sulfate in serum and hence represents an attractive alternative for the use of the radioactive (35)S isotope in human studies of body composition and oxidation of sulfur-containing substrates to sulfate.

Chemistry Techniques, Analytical↗
PubMed1998

[Changes of the gene expression of vascular endothelial growth factor in the lung of rats with chronic hypoxic pulmonary hypertension].

To observe the effect of chronic hypoxia on the gene expression of vascular endothelial growth factor (VEGF) in rat's lung, and the role of VEGF in the pathogenesis of hypoxic pulmonary hypertension, thirteen male Wistar rats were exposed to isobaric hypoxia for 3 weeks. The pulmonary artery pressure was measured by right cardiac catheterization. The serum level of VEGF was measured by Elisa. The VEGF cRNA was labeled with digoxigenin-UTP by in vitro transcription. The expression of VEGF mRNA in the lung was examined by hybridization in situ. The pulmonary artery pressure was significantly increased after hypoxic exposure. The serum level of VEGF in rats treated with hypoxia (420.3 +/- 73.1 pg/ml) was significantly increased in comparison with that of normal rats (322.2 +/- 58.1 pg/ml). The VEGF hybridization signals on the wall of pulmonary arteriole were significantly increased in rats with pulmonary hypertension. Chronic hypoxia can markedly increase expression of VEGF mRNA in the pulmonary arteriole and hence stimulate VEGF synthesis and secretion. The increase of VEGF may play a role in the developing process of hypoxic pulmonary hypertension.

Animals↗
PubMed2006

Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry.

The detailed characterization of protein N-glycosylation is very demanding given the many different glycoforms and structural isomers that can exist on glycoproteins. Here we report a fast and sensitive method for the extensive structure elucidation of reducing-end labeled N-glycan mixtures using a combination of capillary normal-phase HPLC coupled off-line to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and TOF/TOF-MS/MS. Using this method, isobaric N-glycans released from honey bee phospholipase A2 and Arabidopsis thaliana glycoproteins were separated by normal-phase chromatography and subsequently identified by key fragment ions in the MALDI-TOF/TOF tandem mass spectra. In addition, linkage and branching information were provided by abundant cross-ring and "elimination" fragment ions in the MALDI-CID spectra that gave extensive structural information. Furthermore, the fragmentation characteristics of N-glycans reductively aminated with 2-aminobenzoic acid and 2-aminobenzamide were compared. The identification of N-glycans containing 3-linked core fucose was facilitated by distinctive ions present only in the MALDI-CID spectra of 2-aminobenzoic acid-labeled oligosaccharides. To our knowledge, this is the first MS/MS-based technique that allows confident identification of N-glycans containing 3-linked core fucose, which is a major allergenic determinant on insect and plant glycoproteins.

Amination↗
PubMed1996

Analytical instruments for stable isotopic tracers in mineral metabolism.

Thermal ionization mass spectrometry (TIMS) is the best of four currently used techniques for obtaining results of high accuracy and precision in studies of metal metabolism. TIMS is also the most general technique because it allows measurements of all the metallic elements of interest. The highest absolute sensitivity as well as the ability to determine multiple elements are simultaneously obtained with inductively coupled plasma mass spectrometry (ICP-MS). Current results with this technique show that, although element quantification may be done with acceptable accuracy and precision, use of ICP-MS in metabolic studies at low levels of isotopic labels may be limited. The most favorable elements for study using ICP-MS in metabolic studies appear to be Mg, Zn and possibly Fe. Use of this technique is limited further by isobaric interferences from plasma jet ion molecule reactions, and metabolic studies of Ca are particularly limited. Acceptable levels of accuracy and precision have been obtained from fast atom bombardment-secondary ion mass spectrometry (FAB-SIMS), which has allowed these approaches to be used in metabolic studies of ZN, Fe and Ca, but the approaches are ultimately limited by hydride isobaric interferences. Both FAB-SIMS and gas chromatography-mass spectrometry of metal chelates have the advantage of using widely available instrumentation. GC-MS of metal chelates has been shown to be useful in studies of Cr and Se metabolism and for the determination of a number of other metals. Values of accuracy and precision from use of this approach have been satisfactory.

Calcium↗
PubMed2006

A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies.

Proteomic research includes the characterization of protein mixtures in order to understand complex biological systems and determine relationships between proteins, their function, and protein-protein interactions. Often the goal of such research is to monitor changes of proteins in perturbed systems, a type of study referred to as differential expression analysis. To perform these studies requires the ability to execute some type of differential comparison of a given protein state in reference to some type of a control. The iTRAQ reagents are a set of isobaric reagents which are amine specific and allow for the identification and quantitation of up to four different samples simultaneously. The amine specificity of these reagents makes most peptides in a sample amenable to this labeling strategy with no loss of information from samples involving post-translational modifications, such as the scrutiny of signal transduction pathways that often involve phosphorylation phenomena. In addition, the multiplexing capacity of these reagents allows for information replication within certain LC-MS/MS experimental regimes, providing additional statistical validation within any given experiment. The results presented herein demonstrate a few examples of the wide variety of quantitative information that can be realized when undertaking such experimental approaches. These include temporal analysis of drug-induced-protein expression, discovery and elucidation of disease markers, and protein-protein interactions in multi-protein complexes.

Animals↗
PubMed1999

First attempt of odorant quantitation using gas chromatography-olfactometry.

An aroma compound was quantitated for the first time by GC-olfactometry (GC-O) on the basis of the detection frequency of odorants by a panel of 8-12 persons. The method was previously optimized regarding the coincidence of olfactometric peak apexes and the repeatability of peak height and area over 4 months. The number of required calibration points and the confidence interval of the curve were investigated. This technique was then tested by quantifying a model solution of 1-octen-3-one. The standard addition method was found to be unsuitable in this context, but external calibration gave excellent results in the ppt range. GC-O was then challenged using one of the most sensitive and selective methods, GC/MS, to quantitate 1-octen-3-one in coffee, a complex aroma. Results showed performances comparable to GC/MS/MS for this odorant, or even better as the latter required 75-500 times more sample to perform the quantitation. However, at such a low concentration, overestimation cannot be excluded with either technique because of possible coelution of odorants or isobaric ions, respectively. These results show that GC-olfactometry can compete with the most sensitive and selective techniques, such as MS, for determination of extremely intense odorants, because little sample preparation is required and there is no need for the synthesis of labeled compounds.

Calibration↗
PubMed2006

Identification of differentiating neural progenitor cell markers using shotgun isobaric tagging mass spectrometry.

The use of neural precursor cells (NPCs) represents a promising repair strategy for many neurological disorders. This requires an understanding of the molecular events and biological features that regulate the self-renewal of NPCs and their differentiation into neurons, astrocytes, and oligodendendrocytes. In this study, we have characterized the proteomic changes that occur upon differentiation of these cells using the novel iTRAQ labeling chemistry for quantitative mass spectrometry. In total, 55 distinct proteins underwent expression changes during NPC differentiation. This included 14 proteins that were identified by our previous two-dimensional difference gel electrophoresis (2D-DIGE) analysis of differentiating mouse neurospheres. The importance of the iTRAQ approach was demonstrated by the identification of additional proteins that were not resolved by the 2D-DIGE technology. The proteins identified by the iTRAQ approach included growth factors, signaling molecules, proliferating cell-specific proteins, heat shock proteins, and other proteins involved in the regulation of metabolism and the transcriptional and translational machinery. Further characterization of the identified proteins should provide greater insight into the mechanisms involved in regulation of neurogenesis in the adult central nervous system and potentially that of other proliferating cell types, including peripheral stem cells or cancer cells.

Amino Acid Sequence↗
PubMed2002

Global internal standard technology for comparative proteomics.

The work described in this paper tests the efficacy of a global isotope labeling (global internal standard technology, GIST) strategy for quantification in proteomics. Using GIST, overexpression of beta-galactosidase in Escherichia coli was identified and quantified. The GIST protocol involved tryptic digestion of proteins from control and experimental samples followed by differential isotopic labeling of the resulting tryptic peptides, mixing the differentially labeled control and experimental digests, fractionation of the peptide mixture by reversed-phase chromatography, and isotope ratio analysis by mass spectrometry. N-Acetoxysuccinimide and N-acetoxy-[2H3]succinimide were used to differentially derivatize primary amino groups in peptides from experimental and control samples, respectively. The relative concentration of isotopically labeled peptides was determined by isotope ratio analysis with both matrix-assisted laser desorption ionization mass spectrometry and tandem mass spectrometry (MS-MS). Peptide masses and sequences obtained by MS-MS were used to identify proteins. MS-MS was found to be uniquely suited for isobaric peptide quantification.

Amino Acid Sequence↗
PubMed2000

Development of a method for rapid quantitation of amino acids by liquid chromatography-tandem mass spectrometry (LC-MSMS) in plasma.

A new analytical method has been developed and is proposed for the rapid determination of eighteen common amino acids, including tryptophan, in plasma and dried blood spots, by liquid chromatography coupled with ionspray tandem mass spectrometry. Potentially the method can include other amino acids and can be used for the diagnosis of metabolic disease. The use of the ionspray tandem mass spectrometry approach permits extremely rapid chromatographic separation of all amino acids requiring less than four minutes for the analysis of each sample, after a simple sample preparation procedure. The chromatographic separation of the analytes was achieved using a CN normal phase column and a water/acetonitrile/trifluoroacetic acid mobile phase at flow rate of 1 ml/min. The mass spectrometer was operated in multiple reaction monitoring mode, where each analyte had its own unique precursor and product ion setting. The quantitative analysis of amino acids was achieved using as internal standards just two representative isotopically labeled amino acids: D4-Ala and D5-Phe. Calibration is made externally by using aqueous solutions with the same labelled amino acids as internal standards. The high specificity of tandem mass spectrometry coupled with a fast chromatographic process is suitable for the rapid and reliable assay of metabolically significant amino acids. The liquid chromatography-tandem mass spectrometry method is more effective than other published tandem mass spectrometry methods at distinguishing isobaric amino acids like Leu, Ile and HO-Pro and certainly far more rapid than HPLC or ion-exchange chromatographic methods.

Amino Acids↗
PubMed2006

Structure and biosynthesis of free lipid A molecules that replace lipopolysaccharide in Francisella tularensis subsp. novicida.

Francisella tularensis subsp. novicida U112 phospholipids, extracted without hydrolysis, consist mainly of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and two lipid A species, designated A1 and A2. These lipid A species, present in a ratio of 7:1, comprise 15% of the total phospholipids, as judged by 32Pi labeling. Although lipopolysaccharide is detectable in F. tularensis subsp. novicida U112, less than 5% of the total lipid A is covalently linked to it. A1 and A2 were analyzed by electrospray ionization and matrix-assisted laser desorption ionization mass spectrometry, gas chromatography/mass spectrometry, and NMR spectroscopy. Both compounds are disaccharides of glucosamine, acylated with primary 3-hydroxystearoyl chains at positions 2, 3, and 2' and a secondary palmitoyl residue at position 2'. Minor isobaric species and some lipid A molecules containing a 3-hydroxypalmitoyl chain in place of 3-hydroxystearate are also present. The 4'- and 3'-positions of A1 and A2 are not derivatized, and 3-deoxy-d-manno-octulosonic acid (Kdo) is not detectable. The 1-phosphate groups of both A1 and A2 are modified with an alpha-linked galactosamine residue, as shown by NMR spectroscopy and gas chromatography/mass spectrometry. An alpha-linked glucose moiety is attached to the 6'-position of A2. The lipid A released by mild acid hydrolysis of F. tularensis subsp. novicida lipopolysaccharide consists solely of component A1. F. tularensis subsp. novicida mutants lacking the arnT gene do not contain a galactosamine residue on their lipid A. Formation of free lipid A in F. tularensis subsp. novicida might be initiated by an unusual Kdo hydrolase present in the membranes of this organism.

Alkalies↗
PubMed2006

Relative quantification of tau-related peptides using guanidino-labeling derivatization (GLaD) with online-LC on a hybrid ion trap (IT) time-of-flight (ToF) mass spectrometer.

Development of a quantification method based on isotopic variants of O-methyl isourea (OMIU) in conjunction with reversed-phase (RP) liquid chromatography (LC) electrospray mass spectrometry is described for determining the relative quantification of tau-related peptides Ac-VQIVXK-NH2. Extracted ion chromatograms of the mass spectrometric data derived from online microcapillary LC separation identifies the retention times of the isotopically derivatized peptides together with their ion abundances. Data-dependent MSMS analysis of both derivatized variants of the same peptide provides a complementary method for identification and resolution between isobaric species. In addition, with respect to offline LC MALDI a larger number of analogues are detected and formation of amyloid is also observed for the aspartic acid and histidine-containing peptides.

Amyloid↗
PubMed2004

Normal-phase nanoscale liquid chromatography-mass spectrometry of underivatized oligosaccharides at low-femtomole sensitivity.

We here describe the online liquid chromatography (LC) electrospray ionization mass spectrometry (MS) of underivatized glycans using a nanoscale normal-phase amide column at a flow rate of 300 nL/min. Retention on the amide column is based on polar interactions of the oligosaccharide hydroxyl groups with the stationary phase, and thus, the retention time predictably increases with elongation of the oligosaccharide chain. The system is characterized by its high chromatographic resolution, which routinely allows the separation of isobaric structures. Separation of oligosaccharide mixtures over a 1-h range permits the detailed characterization of the different species by multiple ion selection and fragmentation steps using ion trap MS. The here presented miniaturization of the online-LC system to the nanoscale in combination with ion trap MS allows the detection of oligosaccharide species in a mixture at low-femtomole sensitivity. Online normal-phase nano-LC-MS of complex oligosaccharide mixtures further facilitates the sensitive and detailed structural analysis of oligosaccharides by overcoming the need for cumbersome and time-consuming derivatization procedures such as reductive amination for labeling with hydrophobic fluorophores or labeling with tritium. The method should be useful for the sensitive and quick analysis of glycosylation patterns and individual oligosaccharides from biotechnologically produced glycoproteins as well as scarcely available biological samples.

Amides↗
PubMed2002

Quantifying peptides in isotopically labeled protease digests by ion mobility/time-of-flight mass spectrometry.

Ion mobility/time-of-flight techniques have been used to analyze mixtures of isotopically labeled peptides. The isotopic labels were generated by treatment of peptides with N-acetoxysuccinimide (or the deuterated analogue), which results in acetylation (or deuterioacetylation) of the primary amines (i.e., the N-terminus and lysine residues). The relative concentrations of a peptide in each sample are determined by comparing the peak intensities for isotopic pairs. An important consideration is that as mixtures become increasingly complex, isotopic pairs of peaks may overlap with other peaks in the mass spectrum. The influence of the acetyl and deuterioacetyl groups on the mobilities of peptides is considered. The coincidence in mobilities of isotopic pairs provides a means of distinguishing isotopic pairs from other isobaric interferences.

Acetylation↗
PubMed1982

Evidence that cytoplasmic birefringence is a normal feature of rat adrenal chromaffin cells.

The rat adrenal medulla was fixed by isobaric whole-body perfusion with glutaraldehyde. Specimens treated with anisotropic stains exhibited a diffuse cytoplasmic birefringence. Evidence is presented that birefringence is not only associated with "dark" cell formation, but may be a normal feature of fixed chromaffin cells. It is suggested that the birefringence is caused by the fixed contents of the chromaffin vesicles and/or the microtrabecular lattice recently described in rat chromaffin cells.

Adrenal Medulla↗