Is there a unifying mechanism for protein folding

The ability to rapidly and efficiently digest and identify an unknown protein is of great utility for proteome studies. Identification of proteins via peptide mapping is generally accomplished through proteolytic digestion with enzymes such as trypsin. Limitations of this approach consist in manual sample manipulation steps and extended reaction times for proteolytic digestion. The use of immobilized trypsin for cleavage of proteins is advantageous in comparison with application of its soluble form. Enzymes can be immobilized on different supports and used in flow systems such as immobilized enzyme reactors (IMERs). This review reports applications of immobilized trypsin reactors in which the IMER has been integrated into separation systems such as reversed-phase liquid chromatography or capillary electrophoresis, prior to MS analysis. Immobilization procedures including supports, mode of integration into separation systems, and methods are described.

Immobilized trypsin systems coupled on-line to separation methods: recent developments and analytical applications.

Data analysis—the Achilles heel of proteomics

The present invention features mass spectrometry data analysis techniques that can be employed to selectively identify analytes differing in abundance between different sample sets. The employed techniques determine the statistical significance of changes to signals associated with mass-to-charge ratios (“m/z intensity pairs”) between individual samples and sample sets. Based on the statistical significance, changes likely to indicate analyte level differences are identified. Based on intensities of the signals, ratios of analyte abundances can be determined.

Mass spectrometry data analysis techniques

Electron capture dissociation (ECD) represents one of the most recent and significant advancements in tandem mass spectrometry (MS/MS) for the identification and characterization of polypeptides. In comparison with the conventional fragmentation techniques, such as collisionally activated dissociation (CAD), ECD provides more extensive sequence fragments, while allowing the labile modifications to remain intact during backbone fragmentation—an important attribute for characterizing post-translational modifications. Herein, we present a brief overview of the ECD technique as well as selected applications in characterization of peptides and proteins. Case studies including characterization and localization of amino acid glycosylation, methionine oxidation, acylation, and “top–down” protein mass spectrometry using ECD will be presented. A recent technique, coined as electron transfer dissociation (ETD), will be also discussed briefly.

Electron capture dissociation mass spectrometry in characterization of peptides and proteins.

Proteomics: drug target discovery on an industrial scale

The targets of the majority of drugs on the market and in development are proteins, and the efficient analysis of these molecules is critical to defining targets for better therapeutic intervention. Mass spectrometry is currently the key technology for parallel protein analysis (also referred to as proteomics). In this review we will describe recent advances in mass spectrometry instrumentation, methods and applications that are likely to impact drug discovery.

Enabling parallel protein analysis through mass spectrometry.

The present invention provides a method for enriching cell surface proteins by oxidizing glycosylated protein with periodate. The present invention further provides that the cell surface proteins are obtained from intact cells either from cell lines or from tissues. The present invention provides a method not only capable of obtaining increased quantities of the cell surface proteins, but also capable of obtaining a wide ranges of proteins that are not detectable by other means.

Selective capture and enrichment of proteins expressed on the cell surface

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Proteomics: drug target discovery on an industrial scale

Enabling parallel protein analysis through mass spectrometry.

Selective capture and enrichment of proteins expressed on the cell surface