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Thursday, July 31, 2014
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Evaluation of Different Interpretation Strategies to Discover PTM in MS/MS Peptide Fragmentation Data
Daniel Chamrad, Gerhard Korting, Ken Fantom, Andy West, Klaus Schneider, Ulrike Schweiger-Hufagel, Herbert Thiele and Martin Bluggel

The phenomenon of acquired high quality MS/MS spectra that can not be explained within typical sequence database searches is well known. Although protein identification was successful it is manually very laborious and in most cases even impossible to match these spectra with any suggested protein sequence. The procedure of second pass searches has been developed to overcome this problem. Here we report from our in house developed tool PTM-Explorer.

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Towards Understanding of Ryegrass-Endophyte Symbiosis through Data Integration of Transcriptome and Metabolome
Mingshu Cao, Linda Johnson, Albert Koulman, Geoff Lane and Susanne Rasmussen

Combined with extensive bioinformatics analyses, our joint analysis of transcriptomics and metabolomics data has generated interesting findings which led to further laboratory verification, such as potential genes associated with alkaloid production.

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Herbal Metabolic Profiling of Raw and Steamed Panax notoginseng
Eric C.Y. Chan, Swee-Lee Yap, Aik-Jiang Lau, Pay-Chin Leow, Ding-Fung Toh, and Hwee-Ling Koh

At present, metabolite profiling is of growing importance in herbal medicine fields such as breeding, formulation, quality control and clinical trials. Herbal metabolic profiling allows direct detection of down-stream derivatives of metabolites, arising from herbal formulation process, using metabolite profiling ultra performance liquid chromatography time-of-flight mass spectrometry.

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Metabolic Profiling of Human Blood Plasma by Combined Ultra Performance Liquid Chromatography / Mass Spectrometry
Steve Bruce, Pär Jonsson, Henrik Antti, Olivier Cloarec, Stefan Marklund and Thomas Moritz

Metabolic profiling is concerned with the analysis of low molecular weight compounds present in complex samples such as plasma. Analytical techniques such as UPLC/MS are proving to be powerful tools for metabolic profiling on complex samples such as plasma. Here we describe a protocol of metabolic profiling analysis on plasma by UPLC/MS.

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Effective Fishing of Characteristic Proteome Fractions and Identification of Biomarkers Therein: Application of VisualCockpit to Multidimensional Chromatogram and MS Data
S. Kreusch, M. Nagel, R. Janetzko, G. A. Cumme, A. Winter, M. Pohl, A. Meier-Hellmann and H. Rhode

Characteristic 2D fractions are rapidly identified among thousands using interactive visualization, filtering and data mining with VisualCockpit. Biomarker candidates are found therein after identifying proteins from sequence tags. VisualCockpit correlates their concentrations, reflected by normalized MS peptide peak height sum, enzyme activity and immunoreactivity, to donor conditions.

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Automated Profiling and Identification of Endogenous Peptidomic Markers in Human Plasma
T. Richmond, M. Askenazi, J. Sutton and L. Bonilla

Development of robust methods that include the accurate identification of the relevant components of the peptidome is critical not only to our understanding of the biology of disease states, but also to our ability to discover markers for these states.

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Differential Expression Analysis using an Unlabelled Approach and a New Software for Relative Quantification of LC-MS Data
John Flensburg, Carolina Johansson and Lars Sundstrom

DeCyder™ MS Differential Analysis Software (DeCyder MS) is a new tool for visualization, detection, identification and label-free relative quantification of LC-MS and LC-MS/MS data.

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KingFisher - A Multifunctional Tool for Proteomics
Mehto, M., Walker, E., Maggott, K., Richmond, T., Partanen, M., Kymalainen, V., Lamberg, A.

In the proteomics area with the increasing capacity of the mass spectrometers, sample preparation is becoming a limiting step for protein identification. Magnetic particle based technology provides a rapid and easy solution for automation of the sample preparation step.

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Metabonomics for MolPAGE Discovering Diabetes Biomarkers
K. Magnus Åberg, Mark Jairaj, Henrik Toft Pedersen, Dorrit Baunsgaard

MolPAGE (Molecular Phenotyping to Accelerate Genomic Epidemiology) is an EU consortium with almost twenty collaborating universities and companies throughout Europe. One of the aims of MolPAGE is to find early onset biomarkersfor type 2 diabetes (T2DM) and cardio-vascular diseases(CVD).

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Showing Results 71 - 80 of 84
Scientific News
Mass Spec-Based Metabolomics Workflows to Evaluate Plant Immunity
This article reviews metabolomics studies used to evaluate plant immunity with an emphasis on mass spectrometry in its many forms.
Using LC-MS to Analyse Sulfonamides in Food Grade Honey
Sulfonamides are one of a number of groups of chemicals whose presence in honey is limited by international regulations.
Reimagining UHPLC
To learn more about the new Vanquish UHPLC system from Thermo Fisher Scientific we spoke to Wulff Niedner, Director of HPLC Product Marketing.
Mass Spec Predicts Improved Response to Anti-HER2 Therapy in Breast Cancer
Immunohistochemistry is the standard technique for detecting HER2 protein expression, it does not provide absolute quantification of this receptor and is prone to false-positives.
Mass Spectrometry Tool Helps Guide Brain Cancer Surgery
A tool to help brain surgeons test and more precisely remove cancerous tissue was successfully used during surgery, according to a Purdue University and Brigham and Women's Hospital study.
Evaluating Acute Hydrogen Sulfide Poisoning in Rats through Serum Metabolomics
Through the use of GC/MS-based metabolomics, researchers have evaluated the effect of acute hydrogen sulfide poisoning on the metabolic profiles of rats.
Simultaneous Determination of Free Urinary Steroids
Researchers have described an LC–MS/MS method that accurate, precise and is in accordance with FDA guidelines.
Human Proteome Project Uncovers 193 Proteins Not Known to Exist
The team of international researchers reports the identification of 193 novel proteins that came from regions of the genome not predicted to code for proteins.
Comparison of Pesticide Residues in Surface and Ground Water
Measurement of pesticide residues can be used as baseline levels to monitor the future changes and to predict their future impact on the population of the area.
New Innovation in Food Safety Testing
Researchers have used MALDI-TOF MS as a tool to detect Listeria contamination in food.
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