111 Result(s)
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English
Bioinformatics
Cell Biology
Proteomics
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Protocol
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Proteomic Data Exchange and Storage
The ever increasing volumes of proteomic data now being produced by laboratories across the world have resulted in major issues in data storage and accessibility. The further demands of multilaboratory initiat...
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Assaying Calpain Activity
The calpains represent a well-conserved family of intracellular proteases that exhibit broad substrate specificity and consequently influence many cellular processes. Calpain activity regulates the turnover of...
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Sequence Handling by Sequence Analysis Toolbox v1.0
The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that...
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Useful Mass Spectrometry Programs Freely Available on the Internet
The intention with this chapter is to give an overview of a broad range of freely available programs on the internet which are useful for analyses of mass spectrometry data. The list is by no means a full list...
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Organization of Proteomics Data With YassDB
In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for...
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Interpretation of Collision-Induced Fragmentation Tandem Mass Spectra of Posttranslationally Modified Peptides
Tandem collision-induced dissociation (CID) mass spectrometry (MS) provides a sensitive means of analyzing the amino acid sequence of peptides. Modern MS instrumentation is capable of rapidly generating many t...
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Extracting Monoisotopic Single-Charge Peaks From Liquid Chromatography-Electrospray Ionization-Mass Spectrometry
Peak extraction from raw data is the first step in analysis of mass spectrometry (MS) data. The quality of this procedure is very important because it affects the quality of all subsequent analysis, such as da...
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Separation of Cell-Cell Adhesion Complexes by Differential Centrifugation
The number of proteins found associated with cell-cell adhesion substructures is growing rapidly. Based on potential protein-protein interactions, complex protein networks at cell-cell contacts can be modeled....
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Quantitative Proteomics by Stable Isotope Labeling and Mass Spectrometry
The goal of quantitative proteomics is to systematically study static state or perturbation-induced changes in protein profile. Most of the recently developed mass spectrometry (MS)-based quantitative proteomi...
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Analysis of Focal Adhesions and Cytoskeleton by Custom Microarray
Focal adhesions and the cell cytoskeleton (intermediate filaments, microfilaments, microtubules) are involved in mechanotransduction—both direct (transduction of mechanical forces to the nucleus) and indirect ...
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Analysis of Leukocyte Migration Through Monolayers of Cultured Endothelial Cells
In this chapter methods are described for analyzing the adhesion and migration of isolated leukocytes on endothelial cell monolayers that have been cultured on different substrates and treated with cytokines. ...
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Bioinformatic Analysis of Adhesion Proteins
Proteins that mediate cell-cell and cell-extracellular matrix (ECM) adhesion have been fundamental in the evolution of multicellular animals. Fibrillar collagens, proteoglycans, integrins, and cadherins are pr...
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Dynamic Assessment of Cell-Matrix Mechanical Interactions in Three-Dimensional Culture
Cell-matrix mechanical interactions play a defining role in a range of biological processes such as developmental morphogenesis and wound healing. Despite current agreement that fibroblasts exert mechanical fo...
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Analysis of Carbohydrates by Mass Spectrometry
The analysis method described in this chapter demonstrates the structural characterization of carbohydrates based on their molecular mass, as well as the mass of their respective fragment ions using mass spect...
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Double-Hydrogel Substrate as a Model System for Three-Dimensional Cell Culture
When cultured on two-dimensional surfaces, most adherent cells show profound differences from those in their native habitats. In addition to chemical factors, it is likely that both physical parameters, such a...
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Using RNA Interference to Knock Down the Adhesion Protein TES
RNA interference (RNAi) is a specific and efficient method to knock down protein levels using small interfering RNAs (siRNAs), which target mRNA degradation. RNAi can be used in mammalian cell culture systems ...
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Calibration of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Peptide Mass Fingerprinting Spectra
This chapter describes a number of aspects important for calibration of matrix-assisted laser desorption/ionization time-of-flight spectra prior to peptide mass fingerprinting searches. Both multipoint interna...
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Quantitative Proteomics for Two-Dimensional Gels Using Difference Gel Electrophoresis
Difference gel electrophoresis (DIGE) technology provides a powerful quantitative component to proteomics experiments involving two-dimensional (2D) gel electrophoresis. DIGE allows for the detection of subtle...
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Introduction to Proteomics
Mass spectrometry (MS) has recently become one of the most informative methods for studying proteins. Albiet, MS cannot compete with the detailed structural information obtained by methods such as nuclear magn...
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Virtual Expert Mass Spectrometrist v3.0
The number of tools described in the literature for analysis of proteome data is growing fast. However, most tools are not able to communicate or exchange data with other tools. In Virtual Expert Mass Spectrom...
