Comparison of the performance of 1D SDS-PAGE with nondenaturing 2DE on the analysis of proteins from human bronchial smooth muscle cells using quantitative LC-MS/MS

Jin, Ya; Zhang, Jun; Manabe, Takashi; Tan, Wen

doi:10.1016/j.jchromb.2018.12.025

Cited by 8 publications

(3 citation statements)

References 20 publications

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“…The sequential loss of a methyl radical and CO is the characteristic fragmentation pathway of protoberberine alkaloids 18 . As an example, palmatine was identified by comparison of the retention time and MS/MS data of the corresponding standard and previous literature 19,20 . The proposed fragmentation pathway is shown in Figure 3A.…”

Section: Resultsmentioning

confidence: 99%

An integrated strategy for the establishment of a protoberberine alkaloid profile: Exploration of the differences in composition between Tinosporae radix and Fibraurea caulis

Zhao

Zhang

Wang³

et al. 2021

Phytochemical Analysis

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Introduction Accurate species and content identification of major active components in herbals are the guarantee of the safety and effectiveness for medical and commodity purposes. Objectives In this study, an integrated strategy used to establish the protoberberine alkaloid profile was applied to explore the differences in composition between the pieces of Tinosporae radix and Fibraurea caulis, both of which had morphological similarities. Materials and methods First, an in‐house library including possible protoberberine alkaloids based on different substituents was predicted by systematic literature survey. Meanwhile, diagnostic fragments of protoberberine alkaloids were investigated using the corresponding standards. Second, ultra‐performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry (UPLC‐QTOF‐MS/MS) was used to obtain multidimensional mass spectral data. Then, the identifications were confirmed by targeted filter of the acquired data based on the library. Results As a result, 10 protoberberine alkaloid molecules including 46 isomers were identified or characterised. The qualitative distribution and relative content of protoberberine alkaloids revealed the fundamental difference between Tinosporae radix and Fibraurea caulis. 25 alkaloids were present in both herbals, while five compounds were detected only in Tinosporae radix. Furthermore, the contents of four alkaloids in Tinosporae radix were significantly higher than those in its adulterant, Fibraurea caulis. Conclusion The five unique ingredients in Tinosporae radix can be used as a better indicator for distinguishing the pieces of Tinosporae radix and Fibraurea caulis. The protoberberine alkaloid profile established in this study can be applied to quality evaluation of the two herbals or other herbals containing major protoberberine alkaloids.

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Section: Resultsmentioning

confidence: 99%

An integrated strategy for the establishment of a protoberberine alkaloid profile: Exploration of the differences in composition between Tinosporae radix and Fibraurea caulis

Zhao

Zhang

Wang³

et al. 2021

Phytochemical Analysis

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“…However, this method is rarely used on its own. It is coupled with other techniques, such as the Enzyme-mediated activation of radical sources (EMARS) reaction which found host cell membrane proteins near the spike protein attachment site of SARS-CoV-2 [31] and mass spectrometry for the study of membrane protein present in the extracellular vesicles of carbapenem-resistant Klebsiella pneumoniae [32], and in complementarity with Two-dimensional gel electrophoresis coupled to mass spectrometry (2DE-MS) [33].…”

Section: Techniques and Methods Used For Protein Analysismentioning

confidence: 99%

Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics

Boulos,

Jabbour,

Khoury

et al. 2023

Molecules

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In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.

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“…Previously, we have reported on MS-based profiling of proteins on nondenaturing 1DE or 2DE gels. By combining lane slicing or grid cutting and quantitative LC–MS/MS, gel distributions could be reconstructed for all the identified proteins, and the analysis based on pattern correlation and bioinformatics provided abundant information on complex formation and subunit structures. − Compared with nondenaturing gel electrophoresis, SDS-PAGE provides better analysis for insoluble proteins, and also the dissociated polypeptides could be directly correlated with gene products and their proteoforms. Therefore, in this work, we aimed to examine if a method coupling SDS-PAGE with systematic LC–MS/MS could provide extra information that correlates with proteoforms.…”

Section: Introductionmentioning

confidence: 99%

1DE-MS Profiling for Proteoform-Correlated Proteomic Analysis, by Combining SDS-PAGE, Whole-Gel Slicing, Quantitative LC–MS/MS, and Reconstruction of Gel Distributions of Several Thousands of Proteins

2022

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SDS-PAGE has often been used in proteomic analysis, but generally for sample prefractionation although the technique separates proteins by molecular masses (M w s) and the information would contribute to proteoform-level analysis. Here, we report a method that combines SDS-PAGE, whole-gel slicing, and quantitative LC− MS/MS for establishing gel distributions of several thousand proteins in a proteome. A previously obtained data set on rat cerebral cortex with cerebral ischemia-reperfusion injury 1 was analyzed, and the gel distributions of 5906 proteins were reconstructed. These distributions, referred to as 1DE-MS profiles, revealed that about 30% of the proteins had more than one proteoform detected in the gels. The profiles were categorized into six types by distribution (narrow, dispersed, or broad) and relative deviations between the abundance-peak apparent M w s and calculated M w s. Only 56% of the proteins showed narrow distributions and matched M w s, while the others had rather complex profiles. Bioinformatic analysis on example profiles showed the resolved proteoforms involved alternative splicing, proteolytic processing, glycosylation and ubiquitination, fragmentation, and probably transmembrane structures. Profile-based differential analysis revealed that many of the disease-caused changes were proteoform dependent. This work provided a proteome-scale view of protein distributions in SDS-PAGE gels, and the method would be useful to obtain proteoform-correlated information for in-depth proteomics.

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Comparison of the performance of 1D SDS-PAGE with nondenaturing 2DE on the analysis of proteins from human bronchial smooth muscle cells using quantitative LC-MS/MS

Cited by 8 publications

References 20 publications

An integrated strategy for the establishment of a protoberberine alkaloid profile: Exploration of the differences in composition between Tinosporae radix and Fibraurea caulis

An integrated strategy for the establishment of a protoberberine alkaloid profile: Exploration of the differences in composition between Tinosporae radix and Fibraurea caulis

Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics

1DE-MS Profiling for Proteoform-Correlated Proteomic Analysis, by Combining SDS-PAGE, Whole-Gel Slicing, Quantitative LC–MS/MS, and Reconstruction of Gel Distributions of Several Thousands of Proteins

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