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Mass Spectrometry Data (mass + spectrometry_data)
Selected AbstractsDetection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualizationRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 10 2006Matthias Berg We demonstrate how visualization of liquid chromatography/mass spectrometry data as a two-dimensional signal intensity map can be used to assess the overall quality of the data, for the identification of polymer contaminants and artifacts, as well as for the confirmation of post-translational modifications. Copyright © 2006 John Wiley & Sons, Ltd. [source] BIOACTIVE POLAR LIPIDS IN OLIVE OIL, POMACE AND WASTE BYPRODUCTSJOURNAL OF FOOD BIOCHEMISTRY, Issue 4 2008HARALABOS C. KARANTONIS ABSTRACT Olive oil protects against atherosclerosis because of biologically active microconstituents. In this study, total polar lipids from olive oil, pomace, pomace oil and waste byproducts were extracted, fractionated by thin layer chromatography and tested for their bioactivity. The most active ones were further purified on high-performance liquid chromatography, and the resulting lipid fractions were tested for their bioactivity. Bioactive compounds were determined in all samples with the exception of olive pomace oil. These lipids inhibited platelet-activating factor (PAF)-induced platelet aggregation and also induced platelet aggregation. The bioactive compound from olive pomace has been chemically characterized as a glycerylether-sn-2-acetyl glycolipid based on mass spectra. Chemical determinations and mass spectrometry data reinforce the assumption that these active microconstituents share both similar bioactivity and common structural features. The existence of PAF antagonists in polar lipid extracts from olive oil waste by-products render them biologically valuable materials for the food industry that could be used for the production of functional foods. PRACTICAL APPLICATIONS Isolated bioactive polar lipids from waste by-products of the olive oil industry that act as inhibitors of platelet-activating factor (PAF) may be used for enrichment and production of foods with higher nutritional value, as PAF plays a major role in inflammatory disorders, including atherosclerosis development. [source] A new pathway for the synthesis of ,-ribazole-phosphate in Listeria innocuaMOLECULAR MICROBIOLOGY, Issue 6 2010Michael J. Gray Summary The genomes of Listeria spp. encode all but one of 25 enzymes required for the biosynthesis of adenosylcobalamin (AdoCbl; coenzyme B12). Notably, all Listeria genomes lack CobT, the nicotinamide mononucleotide:5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (EC 2.4.2.21) enzyme that synthesizes the unique ,-linked nucleotide N1 -(5-phospho-,- d -ribosyl)-DMB (,-ribazole-5,-P, ,-RP), a precursor of AdoCbl. We have uncovered a new pathway for the synthesis of ,-RP in Listeria innocua that circumvents the lack of CobT. The cblT and cblS genes (locus tags lin1153 and lin1110) of L. innocua encode an ,-ribazole (,-R) transporter and an ,-R kinase respectively. Results from in vivo experiments indicate that L. innocua depends on CblT and CblS activities to salvage exogenous ,-R, allowing conversion of the incomplete corrinoid cobinamide (Cbi) into AdoCbl. Expression of the L. innocua cblT and cblS genes restored AdoCbl synthesis from Cbi and ,-R in a Salmonella enterica cobT strain. LinCblT transported ,-R across the cell membrane, but not ,-RP or DMB. UV-visible spectroscopy and mass spectrometry data identified ,-RP as the product of the ATP-dependent ,-R kinase activity of LinCblS. Bioinformatics analyses suggest that ,-R salvaging occurs in important Gram-positive human pathogens. [source] A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noisePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 15 2008Deukwoo Kwon Dr. Abstract In recent years there has been an increased interest in using protein mass spectroscopy to discriminate diseased from healthy individuals with the aim of discovering molecular markers for disease. A crucial step before any statistical analysis is the pre-processing of the mass spectrometry data. Statistical results are typically strongly affected by the specific pre-processing techniques used. One important pre-processing step is the removal of chemical and instrumental noise from the mass spectra. Wavelet denoising techniques are a standard method for denoising. Existing techniques, however, do not accommodate errors that vary across the mass spectrum, but instead assume a homogeneous error structure. In this paper we propose a novel wavelet denoising approach that deals with heterogeneous errors by incorporating a variance change point detection method in the thresholding procedure. We study our method on real and simulated mass specrometry data and show that it improves on performances of peak detection methods. [source] Multiple approaches to data-mining of proteomic data based on statistical and pattern classification methodsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 9 2003Jacob W. Tatay Abstract The data-mining challenge presented is composed of two fundamental problems. Problem one is the separation of forty-one subjects into two classifications based on the data produced by the mass spectrometry of protein samples from each subject. Problem two is to find the specific differences between protein expression data of two sets of subjects. In each problem, one group of subjects has a disease, while the other group is nondiseased. Each problem was approached with the intent to introduce a new and potentially useful tool to analyze protein expression from mass spectrometry data. A variety of methodologies, both conventional and nonconventional were used in the analysis of these problems. The results presented show both overlap and discrepancies. What is important is the breadth of the techniques and the future direction this analysis will create. [source] Popitam: Towards new heuristic strategies to improve protein identification from tandem mass spectrometry dataPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2003Patricia Hernandez Abstract In recent years, proteomics research has gained importance due to increasingly powerful techniques in protein purification, mass spectrometry and identification, and due to the development of extensive protein and DNA databases from various organisms. Nevertheless, current identification methods from spectrometric data have difficulties in handling modifications or mutations in the source peptide. Moreover, they have low performance when run on large databases (such as genomic databases), or with low quality data, for example due to bad calibration or low fragmentation of the source peptide. We present a new algorithm dedicated to automated protein identification from tandem mass spectrometry (MS/MS) data by searching a peptide sequence database. Our identification approach shows promising properties for solving the specific difficulties enumerated above. It consists of matching theoretical peptide sequences issued from a database with a structured representation of the source MS/MS spectrum. The representation is similar to the spectrum graphs commonly used by de novo sequencing software. The identification process involves the parsing of the graph in order to emphazise relevant sections for each theoretical sequence, and leads to a list of peptides ranked by a correlation score. The parsing of the graph, which can be a highly combinatorial task, is performed by a bio-inspired algorithm called Ant Colony Optimization algorithm. [source] Correcting mass isotopomer distributions for naturally occurring isotopesBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2002Wouter A. Van Winden In one method of metabolic flux analysis, simulated mass spectrometry data is fitted to measured mass distributions of metabolites that are isolated from cultures with defined feeding of 13C-labeled substrates. Doing so, simulated mass distributions must be corrected for the presence of naturally occurring isotopes. A method that was recently introduced for this purpose consists of consecutive correction steps for each isotope of each element in the considered compound. Here we show that all isotopes of each individual element must, however, be corrected in one single step. Furthermore, it is shown that the source of information with respect to isotopic compositions of the elements needs to be chosen with care. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 477,479, 2002. [source] | |||||||||||||