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At least 235 records · Page 13Linked to original sources
PubMed2004

A new technique (COMSPARI) to facilitate the identification of minor compounds in complex mixtures by GC/MS and LC/MS: tools for the visualization of matched datasets.

In the rapidly growing field of metabolomics, it is common to analyze complex biological samples by chromatography coupled to mass spectrometry. While several techniques are available for the detection of significant peaks in individual samples, it is still difficult to determine small differences between similar samples. Using conventional software, visual inspections of individual chromatograms or individual mass spectra are often of little use because the differences in the composition of small molecules are too small to be recognizable. Thus, we developed a new approach to visualizing mass spectral datasets using a tool that allows one to easily detect these small differences between mass spectra and chromatograms derived from matched samples. Using these tools on extracts from wild-type and methyltransferase knockout strains of the yeast Saccharomyces cerevisiae, we were able to readily identify those mass spectra in our data sets that were different between the wild-type and the knockout extracts and to identify the molecules involved. The software was also successfully applied to a set of LC/MS data from peptide digests that were performed with identical substrates but different enzymes. We have named this visualization tool COMSPARI (COMparision of SPectrAl Retention Information) and are making the software publicly available via Internet at.

Cell Extracts↗
PubMed1990

Peripheral mechanisms of olfactory discrimination of complex mixtures by the spiny lobster: no cell types for mixtures but different contributions of the cells to the across neuron patterns.

Toward understanding mechanisms of olfactory discrimination, we have examined the existence of cell types and the role of cells in the coding of odorant quality in the olfactory organ of the spiny lobster. The results consisted of responses of 30 antennular chemoreceptor cells to 8 behaviorally discriminable complex stimuli--4 natural extracts and 4 artificial mixtures, each at 3 concentrations. Multidimensional scaling and cluster analysis failed to identify unequivocal cell types, but rather suggested a continuum of cellular response profiles. The lack of cell types suggests that the code for the quality of natural odorants in this system is a population code. The distribution of cells along the response continuum was based on any of many features of their response profiles. The most effective stimulus (= best stimulus) and the least effective stimulus (= least stimulus), two features of the response profiles, could only partially explain the differences in response profiles of cells. Nonetheless, cells with different response profiles were shown to have different functions in odorant coding. Most cells contribute to some degree to the discrimination of any two stimuli, but a cell's contribution to the discrimination of two stimuli is usually disproportionally robust when those two stimuli produce very different responses in that cell.

Action Potentials↗
PubMed1983

Pulmonary function in normal and elastase-treated hamsters exposed to a complex mixture of olefin-ozone-sulfur dioxide reaction products.

An elastase-induced emphysema model was utilized to determine if hamsters with preexisting lung disease were more susceptible to lung damage from air pollutant exposure. Male golden hamsters, divided into two treatment groups, were given a single intratracheal injection of either 6 units of porcine pancreatic elastase (EMP) or buffer (CNT). After a 4-week recovery period, equal numbers of each group were exposed 23 hr/day X 28 day to filtered air (AIR) or to the complex by-products from a dark phase reaction mixture of trans-2-butene, ozone, and sulfur dioxide (MIX). Lung function measurements on the elastase-treated groups showed changes consistent with mild emphysema. There were no significant differences in lung volumes or lung compliance between the AIR- and MIX-exposed animals. However, the nitrogen washout slope decreased (P less than 0.05), and the diffusing capacity for carbon monoxide increased (P less than 0.05) in both the CNT and EMP hamsters exposed to the MIX. The change in diffusing capacity was greater (P less than 0.05) in normal hamsters than in hamsters with emphysema, and it is hypothesized that animals with impaired lung function had a decreased ability to respond to a pulmonary insult from the mix.

Air Pollutants↗
PubMed1988

[Effect of a complex mixture of plasma proteins with heparin on the anticoagulation and fibrinolytic activity of the blood plasma in animals following intravenous administration of tissue thromboplastin].

The i.v. administration of 1.5 ml of the heparin complexes with plasma proteins prior to the injection of tissue thromboplastin induced a stronger neutralization of formed thrombin in the blood and higher anticoagulating and fibrinolytic activities in albino rats as compared to the injection of tissue thromboplastin alone.

Animals↗
PubMed2002

Fast, high-sensitivity, multipesticide analysis of complex mixtures with supersonic gas chromatography-mass spectrometry.

We developed a new instrumental approach, termed Supersonic GC-MS, which achieves fast, sensitive, confirmatory and quantitative analysis of a broad range of pesticides in complex agricultural matrices. Our Supersonic GC-MS system is a modification of a bench-top Agilent 6890 GC+5972 MSD with a supersonic molecular beam (SMB) interface and fly-through EI ion source. One of the main advantages of Supersonic GC-MS is an enhanced molecular ion (M+) in the resulting mass spectra. For example, the M+ was observed in all 88 pesticides that we studied using the Supersonic GC-MS whereas only 36 of 63 (57%) pesticides that we investigated in standard GC-MS exhibited a M+. We also found that the degree of matrix interference is exponentially reduced with the fragment mass by about 20-fold per 100 amu increasing mass. The enhancement of the M+ combined with the reduction in matrix background noise permit rapid full scan analysis of a potentially unlimited number of pesticides, unlike selected ion monitoring or MS-MS in which specific conditions are required in segments for targeted pesticides. Furthermore, unlike the case with chemical ionization, EI-SMB-MS spectra still give accurate identification of compounds using common mass spectral libraries. In practice,we found thatlibraries favor mass spectra in which the M+ appears, thus Supersonic GC-MS produced better spectra for compound identification than standard GC-MS. To achieve even lower identification limits, the M+ plus a second major ion (still using full scan data) gives higher signal-to-chemical noise ratios than the traditional 3-ion approach. The replacement of two low-mass ions with the M+ (supersonic two-ions method) results in a significant reduction of matrix interference by a factor of up to 90. Another main advantage of Supersonic GC-MS is its exceptional suitability for fast GC-MS with high carrier gas flow-rate. Fast Supersonic GC-MS was able to analyze thermally labile pesticides, such as carbamates, that are difficult or impossible to analyze in standard GC-MS. Large volume injection using a ChromatoProbe was also demonstrated, in the 6 min analysis of pesticides at 20 ng/g in a spice matrix.

Gas Chromatography-Mass Spectrometry↗
PubMed1975

Application of open-tubular column/gas-liquid chromatography to the analysis of complex mixtures of branched-chain fatty acids.

Methyl and butyl esters of branched-chain fatty acids of subcutaneous triacylgycerols from barley-fed lambs were subjected to urea-adduction and the resulting fractions were analyzed as methyl esters by gas-liquid chromatography on wall-coated open-tubular columns. The chromatogram of each fraction was less complex than that of the original and there was evidence to suggest that, in the original mixture of branched-chain acids, components resistant to urea-adduction were present, but their occurrence was obscured in chromatograms by the presence of monomethyl-substituted acids.

Chromatography, Gas↗
PubMed1988

Assessment of a complex mixture of interacting proteins in the coagulant active venom from Agkistrodon contortrix contortrix.

The crude venom of Agkistrodon contortrix contortrix was characterized by means of 2D-PAGE (using various separation principles in the respective directions) and high performance gel filtration chromatography. It was found that the venom presents a rich and remarkably stable mixture of proteins, mostly glycoproteins, which may interact each other. High stability of the venom in spite of the presence of many proteolytic enzymes, must most likely be attributed to the sugar moieties of venom proteins. Carbohydrate composition also causes considerable heterogeneity in charge and the presence of wide range of charge isomers. The intricate complexity of the venom makes it a real difficult-to-separate mixture.

Animals↗
PubMed2005

Active-site peptide "fingerprinting" of glycosidases in complex mixtures by mass spectrometry. Discovery of a novel retaining beta-1,4-glycanase in Cellulomonas fimi.

New proteomics methods are required for targeting and identification of subsets of a proteome in an activity-based fashion. Here, we report the first gel-free, mass spectrometry-based strategy for mechanism-based profiling of retaining beta-endoglycosidases in complex proteomes. Using a biotinylated, cleavable 2-deoxy-2-fluoroxylobioside inactivator, we have isolated and identified the active-site peptides of target retaining beta-1,4-glycanases in systems of increasing complexity: pure enzymes, artificial proteomes, and the secreted proteome of the aerobic mesophilic soil bacterium Cellulomonas fimi. The active-site peptide of a new C. fimi beta-1,4-glycanase was identified in this manner, and the peptide sequence, which includes the catalytic nucleophile, is highly conserved among glycosidase family 10 members. The glycanase gene (GenBank accession number DQ146941) was cloned using inverse PCR techniques, and the protein was found to comprise a catalytic domain that shares approximately 70% sequence identity with those of xylanases from Streptomyces sp. and a family 2b carbohydrate-binding module. The new glycanase hydrolyzes natural and artificial xylo-configured substrates more efficiently than their cello-configured counterparts. It has a pH dependence very similar to that of known C. fimi retaining glycanases.

Amino Acid Sequence↗
PubMed2005

X-Hitting: an algorithm for novelty detection and dereplication by UV spectra of complex mixtures of natural products.

A major challenge in lead discovery is to detect well-known and trivial compounds rapidly, a process known as dereplication, so that isolation, structure elucidation, and pharmacological investigations can be focused on novel compounds. In this paper, we present a new algorithm, X-hitting, based on cross sample comparison of full UV spectra from HPLC analysis of highly complex natural product extracts/samples. X-Hitting allows automatic identification of known compounds but more important also allows finding of potentially new or similar compounds. We demonstrate this new algorithm by automatic identification of known structures, a task we call cross-hitting, and tentative identification of potentially new bioactive compounds, a task we call new-hitting, in HPLC data from analysis of fungal extracts. Both tasks are illustrated using 18 important reference compounds and complex fungal extracts obtained from isolates in the IBT Culture Collection held at BioCentrum-DTU, Technical University of Denmark. The receiver operating characteristics statistic is used to evaluate the performance of the compound predictor, and it was found that compounds could be identified with high confidence (AUC approximately 0.98). Based on high confidence in retrieving identical spectra, the method is extended to include similar but still different spectra.

Algorithms↗
PubMed1995

Two-dimensional DNA typing: A cost-effective way of analyzing complex mixtures of DNA fragments for sequence variations.

By two-dimensional (2D) DNA typing, multiple DNA fragments can be analyzed in parallel for all possible sequence variations. The method involves electrophoretic separation in polyacrylamide gels, first by size and subsequently on the basis of basepair sequence in a denaturing gradient. The system has been automated partly and a dedicated image analysis system for rapid interpretation of the often complex spot patterns was developed. In this review, the basic principles of 2D DNA typing, its methodology, and some major applications in genetic studies of animals, plants, and microorganisms will be discussed, with the emphasis on human genetics.

Cost-Benefit Analysis↗
PubMed2005

Protein "fingerprinting" in complex mixtures with peptoid microarrays.

We report here that microarrays comprised of several thousand peptoids (oligo-N-substituted glycines) are useful tools for the identification of proteins via a "fingerprinting" approach. By using maltose-binding protein, glutathione S-transferase, and ubiquitin, a specific and highly reproducible pattern of binding was observed when fluorescently labeled protein was hybridized to the array. A similar pattern was obtained when binding of an unlabeled protein to the array was visualized by secondary hybridization of a labeled antibody against that protein, showing that native proteins can be identified without the requirement for prior chemical labeling. This work suggests that small-molecule microarrays might be used for more complex fingerprinting assays of potential diagnostic value.

Antibodies↗
PubMed2004

Metalworking fluid--the toxicity of a complex mixture.

Various chemicals are used in the manufacture of cooling and lubricating fluids and fall into the classes of straight, soluble, semisynthetic, and synthetic metalworking fluids. The diversity of chemicals and in-use contaminants makes the risk assessment of metalworking fluids quite difficult. Toxicologists have used a number of methods to evaluate the component(s) responsible for the adverse pulmonary effects of metal working fluid aerosols encountered in the workplace. Although investigators have studied the adverse effects of metalworking fluid chemicals alone and in combination, the majority of evidence strongly suggests that the microbial changes that occur in fluid composition, during use and storage in the workplace, are responsible for the pulmonary effects reported for workers exposed to metalworking fluid aerosols. This review discusses the methodologies used to examine the toxicity of the complex nature of modern metalworking fluids and the findings that point toward bacterial endotoxin as a major contributor to their adverse effects.

Aerosols↗
PubMed2001

Towards defining the urinary proteome using liquid chromatography-tandem mass spectrometry. II. Limitations of complex mixture analyses.

With an emphasis on obtaining a multitude of high quality tandem mass spectrometry spectra for protein identification, instrumental parameters are described for the liquid chromatography-tandem mass spectrometry analysis of trypsin digested unfractionated urine using a hybrid quadrupole-time-of-flight (Q-TOF) mass spectrometer. Precursor acquisition rates of up to 20 distinct precursors/minute in a single analysis were obtained through the use of parallel precursor selection (four precursors/survey period) and variable collision induced dissociation integration time (1 to 6 periods summed). Maximal exploitation of the gas phase fractionated ions was obtained through the use of narrow survey scans and iterative data-dependent analyses incorporating dynamic exclusion. The impact on data fidelity as a product of data-dependent selection of precursor ions from a dynamically excluded field is discussed with regards to sample complexity, precursor selection rates, survey scan range and facile chemical modifications. Operational and post-analysis strategies are presented to restore data confidence and reconcile the greatest number of matched spectra.

Amino Acid Sequence↗
PubMed2006

Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins.

The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 'computational secretome,' 43% showed no significant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed significant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identified in culture filtrates by mass spectrometry (LS-MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identified in carbon-starved cultures. Beyond proteases and M6Pase, 28 specific gene products were identified including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium's extracellular enzyme systems.

Carboxylic Ester Hydrolases↗
PubMed1991

Complex mixtures in industrial workspaces: lessons for indoor air quality evaluations.

Acceptable occupational exposure levels for hundreds of airborne concentrations of dusts, vapors, fumes, and gases have been set by consensus organizations and regulatory bodies for decades. These levels have established tremendous precedent and are tempting reference values in the relatively new field of indoor air quality evaluations where validated criteria are greatly needed. The American Conference of Government Industrial Hygienists (ACGIH) has been the most visible and productive group setting these guidelines for industrial exposure. The ACGIH Chemical Substances Committee has published an annual list of threshold limit values (TLVs) for more than 40 years. Currently the list covers more than 400 substances. In 1989, the Occupational Safety and Health Administration (OSHA) published updated permissible exposure limits (PELs) for approximately 600 substances. Most PELs before this update were adopted from the 1968 ACGIH list of TLVs and consensus standards of the American Standards Association. This OSHA update has resulted in reductions of 212 PELs and the addition of 164 new levels. The magnitude of the problem of protecting workers can be seen by the small fraction that the OSHA PELs represent of the more than 60,000 entries in the National Institute for Occupational Safety and Health's Registry of Toxic Effects of Chemical Substances. None of these levels, whether guidelines or regulatory requirements, are established based on any possible synergistic effect with other chemicals. The only guidance given by the ACGIH for synergistic effects is that such cases must be determined individually. Clearly, there are major drawbacks in using occupational standards and guidelines for evaluating the health effects of chemical agents that can be found in office settings, often in concentrations orders of magnitude less than what is routinely measured in the workplace. These guidelines are even less valuable when the concern is the complex mixing of chemicals in nonoccupational environments.

Air Pollutants, Occupational↗