|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.
|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.
|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.
|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).
|Software for Automated Differential Expression Using 2D and 3D Representations of LC-MS Data Interactive Confirmation of Results|
Lennart Björkesten, Anders Kaplan, Malin Söderström, Harald Pettersen, Staffan Lindqvist, John Flensburg and David Fenyo
DeCyder™ MS is a novel software program for fully automated differential expression analysis based on LC-MS/MS data including detection, quantitation, sample to sample comparison and statistical data evaluation. Results can be interactively confirmed against original raw data through 2D and 3D data visualizations.
|The Use of Software Visualization Tools for the Identification of PTM Patterns and Artefacts in LC-MS Experiments|
Harald Pettersen Lennart Björkesten and Matthias Berg
By representing LC-MS data as a 2D-image as demonstrated in the novel DeCyder™ MS software, it is possible to identify phenomena, which are very difficult to recognize using conventional LC-MS data representation.
|Sensitive Identification of Phosphopeptides in Brain Tissue using 2D-NanoLC-ESI-MSn|
Jenny Samskog, Henrik Wadensten, and John Flensburg
In this work, a biocompatible nano liquid chromatography (LC) system, Ettan™ MDLC, was used for separating tryptic peptides from brain tissue by cation exchange (SCX) to enrich the phosphopeptides followed by reversed-phase chromatography (RPC). The phosphopeptides were detected by neutral loss MS.
|IGF1 Biomarker Assay Validation|
Michael Robinson, Urban A. Kiernan, Dobrin Nedelkov, Kemmons A. Tubbs, Eric E. Niederkofler, Randall W. Nelson
This work demonstrates the development and validation of a novel clinical proteomics approach in which specific protein targets can be expeditiously and selectively isolated from acomplex biological fluid for MS characterization.
|Addressing the Repoducibility Aspect of LC-MS Based Protein Identification |
Jenny Samskog, Henrik Wadensten, and John Flensburg, GE Healthcare/ Amersham Biosciences AB, Uppsala, Sweden
By using the detection, matching, and visualization approach ofDeCyder™ MS were retention time, precursor mass, and the topology of the intensity profile is utilized in combination with the matching of tandem mass spectra, it is possible to achieve repeat analysis with a very high reproducibility.
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