Search

The article focuses on the reasons why the author has spent nine years pursuing a map of the 450-protein nuclear pore complex (NPC). His fascination by how things move in and about the cell's nucleus contribute with his determination to mapping huge complexes. The author, together with his colleagues, has generated proteomics, biochemical and mass spectrometry data for all NPC proteins. Fitting each protein's volume into its hotspot gives a physical map of the pore. It is considered that this serves as a powerful approach to solve large assemblies.

Proteomic tools—in particular, mass spectrometry (MS)—have advanced significantly in recent years, and the identification of proteins within complex mixtures is now a routine procedure. Quantitative methods of analysis are less well advanced and continue to develop. These include the use of stable isotope ratio approaches, isotopically labeled peptide standards, and nonlabeling methods. This paper summarizes the use of MS as a proteomics tool to identify and semiquantify proteins and their modified forms by using examples of relevance to the Maillard reaction. Finally, some challenges for the future are presented. [ABSTRACT FROM AUTHOR]

Increasing attention has been focused on the study of protein–metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely short-lived, which requires very high resolution in order to detect them. As in the case of protein–protein interactions, protein–metabolite interactions are still not clearly defined. Existing assays for detecting protein–metabolite interactions have an additional limitation in the form of a limited capacity to identify interacting metabolites. Thus, although recent advances in mass spectrometry allow the routine identification and quantification of thousands of proteins and metabolites today, they still need to be improved to provide a complete inventory of biological molecules, as well as all interactions between them. Multiomic studies aimed at deciphering the implementation of genetic information often end with the analysis of changes in metabolic pathways, as they constitute one of the most informative phenotypic layers. In this approach, the quantity and quality of knowledge about PMIs become vital to establishing the full scope of crosstalk between the proteome and the metabolome in a biological object of interest. In this review, we analyze the current state of investigation into the detection and annotation of protein–metabolite interactions, describe the recent progress in developing associated research methods, and attempt to deconstruct the very term "interaction" to advance the field of interactomics further. [ABSTRACT FROM AUTHOR]

Abstract: In this paper we describe a combination of the mass spectrometric techniques MALDI–TOF/TOF and MALDI–FTMS to identify proteins in complex samples using prespotted MALDI target plates. By this procedure accurate FTMS mass measurements and TOF/TOF data are obtained from the same spot. We have found that this combination of techniques leads to more reliable identification of peptides. [Copyright &y& Elsevier]

Motivation: High-throughput protein identification experiments based on tandem mass spectrometry (MS/MS) often suffer from low sensitivity and low-confidence protein identifications. In a typical shotgun proteomics experiment, it is assumed that all proteins are equally likely to be present. However, there is often other evidence to suggest that a protein is present and confidence in individual protein identification can be updated accordingly. [ABSTRACT FROM PUBLISHER]

Over the last 20 years, mass spectrometrybased proteomics has become an indispensable tool in the cellular and molecular life sciences. This has been enabled by the ‘soft ionisation’ techniques of electrospray and matrix-assisted laser desorption-ionisation, which allow the gentle ionisation and vaporisation of large, thermally labile biomolecules. Innovative instrumentation designs and biochemical strategies have brought success in the large-scale identification and quantification of proteins, as well as the characterisation of their complexes and post-translational modifications. This review describes the instrumentation used for proteomics research. It presents an overview of the current applications of mass spectrometry-based proteomics to the cellular and molecular life sciences, and discusses challenges that exist for research in the future. [ABSTRACT FROM AUTHOR]