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Start Over Descriptor "Enrichment methods" Journal journal of separation science
4 results on '"Enrichment methods"'

1. An overview on enrichment methods for cell surface proteome profiling.

Author

Li, Yanan, Qin, Hongqiang, and Ye, Mingliang

Subjects
*CELL membranes, *GLYCANS, *MASS analysis (Spectrometry), *CELL communication, *FREE groups, *CARBOXYL group
Abstract

Cell surface proteins are essential for many important biological processes, including cell–cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface‐exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction‐based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling. [ABSTRACT FROM AUTHOR]

Published
2020
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2. Recent advances in methods for the analysis of protein o‐glycosylation at proteome level.

Author

You, Xin, Qin, Hongqiang, and Ye, Mingliang

Subjects
*GLYCOSYLATION, *PROTEOMICS, *LECTINS, *ENZYMATIC analysis, *HYDRAZIDES
Abstract

Abstract: O‐Glycosylation, which refers to the glycosylation of the hydroxyl group of side chains of Serine/Threonine/Tyrosine residues, is one of the most common post‐translational modifications. Compared with N‐linked glycosylation, O‐glycosylation is less explored because of its complex structure and relatively low abundance. Recently, O‐glycosylation has drawn more and more attention for its various functions in many sophisticated biological processes. To obtain a deep understanding of O‐glycosylation, many efforts have been devoted to develop effective strategies to analyze the two most abundant types of O‐glycosylation, i.e. O‐N‐acetylgalactosamine and O‐N‐acetylglucosamine glycosylation. In this review, we summarize the proteomics workflows to analyze these two types of O‐glycosylation. For the large‐scale analysis of mucin‐type glycosylation, the glycan simplification strategies including the ‘‘SimpleCell’’ technology were introduced. A variety of enrichment methods including lectin affinity chromatography, hydrophilic interaction chromatography, hydrazide chemistry, and chemoenzymatic method were introduced for the proteomics analysis of O‐N‐acetylgalactosamine and O‐N‐acetylglucosamine glycosylation. [ABSTRACT FROM AUTHOR]

Published
2018
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3. Affinity and chemical enrichment strategies for mapping low‐abundance protein modifications and protein‐interaction networks

Author

Aurchie Rahman, Akash Talukder, Sharel Cornelius, Adway O. Zacharias, Saiful M. Chowdhury, and Zixiang Fang

Subjects
0301 basic medicine, Chemistry, Research areas, 010401 analytical chemistry, Proteins, Filtration and Separation, Computational biology, Arginine, Proteomics, 01 natural sciences, Enrichment methods, 0104 chemical sciences, Analytical Chemistry, Protein–protein interaction, 03 medical and health sciences, 030104 developmental biology, Protein structure, Affinity chromatography, Interaction network, Protein Interaction Networks, Protein Interaction Maps, Protein Processing, Post-Translational
Abstract

Protein post-translational modifications and protein interactions are the central research areas in mass-spectrometry-based proteomics. Protein post-translational modifications affect protein structures, stabilities, activities, and all cellular processes are achieved by interactions among proteins and protein complexes. With the continuing advancements of mass spectrometry instrumentations of better sensitivity, speed, and performance, selective enrichment of modifications/interactions of interest from complex cellular matrices during the sample preparation has become the overwhelming bottleneck in the proteomics workflow. Therefore, many strategies have been developed to address this issue by targeting specific modifications/interactions based on their physical properties or chemical reactivities, but only a few have been successfully applied for systematic proteome-wide study. In this review, we summarized the highlights of recent developments in the affinity enrichment methods focusing mainly on low stoichiometric protein lipidations. Besides, to identify potential glyoxal modified arginines, a small part was added for profiling reactive arginine sites using an enrichment reagent. A detailed section was provided for the enrichment of protein interactions by affinity purification and chemical cross-linking, to shed light on the potentials of different enrichment strategies, along with the unique challenges in investigating individual protein post-translational modification or protein interaction network.

Published
2020

4. Unraveling the different proteomic platforms

Author

Federica Iavarone, Andrea Urbani, Massimo Castagnola, Federica Vincenzoni, Tiziana Cabras, and Irene Messana

Subjects
biology, Computer science, Systems biology, Absolute quantification, Filtration and Separation, Nanotechnology, Computational biology, Mass spectrometry, Proteomics, Enrichment methods, Analytical Chemistry, Targeted proteomics, Histone, Ubiquitin, Functional proteomics, Proteins metabolism, biology.protein, Structural proteomics
Abstract

This review is addressed to scientists working outside the field of proteomics and wishes to shed a light on the possibility offered by the latest proteomics strategies. Bottom-up and top-down platforms are critically examined outlining advantages and limitations of their application to qualitative and quantitative investigations. Discovery, directed and targeted proteomics as different options for the management of the MS instrument are defined emphasizing their integration in the experimental plan to accomplish meaningful results. The issue of data validation is analyzed and discussed. The most common qualitative proteomic platforms are described, with a particular emphasis on enrichment methods to elucidate PTMs codes (i.e. ubiquitin and histone codes). Label-free and labeled methods for relative and absolute quantification are critically compared. The possible contribution of proteomics platforms to the transition from structural proteomics to functional proteomics (study of the functional connections between different proteins) and to the challenging system biology (integrated study of all the functional cellular functions) is also briefly discussed.

Published
2012

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