scholarly journals Mass spectrometry-based analysis of glycoproteins and its clinical applications in cancer biomarker discovery

2017 ◽  
Vol 4 (7) ◽  
pp. 203-215
Author(s):  
Farid Abu Shammala
Keyword(s):  
Mass Spectrometry ◽  
Posttranslational Modifications ◽  
Biomarker Discovery ◽  
Global Analysis ◽  
Structural Identification ◽  
Clinical Applications ◽  
Biological Processes ◽  
Complex Sample ◽  
Systematic Identification ◽  
Glycoprotein Glycosylation

Most proteins are glycosylated, glycosylation is one of the most important posttranslational modifications of proteins and plays essential roles in various biological processes. Aberration in the glycan moieties of glycoproteins is associated with many diseases. It is especially critical to develop the rapid and sensitive methods for analysis of aberrant glycoproteins associated with diseases. With recent advances in proteomics, analytical and computational technologies, glycoproteomics, the global analysis of glycoproteins, is rapidly emerging as a subfield of proteomics with high biological and clinical relevance. Glycoproteomics integrates glycoprotein enrichment and proteomics technologies to support the systematic identification and quantification of glycoproteins in a complex sample. It is especially critical to develop the rapid and sensitive methods for analysis of aberrant glycoproteins associated with diseases. Mass spectrometry (MS) has become a powerful tool for mapping glycoprotein glycosylation and detailed glycan structural determination. Especially, tandem mass spectrometry can provide highly informative fragments for structural identification of glycoproteins. This review provides an overview of the development of MS technologies and their applications in identification of abnormal glycoproteins and glycans in human serum to screen cancer biomarkers in recent years.

scholarly journals Mass spectrometry-based analysis of glycoproteins and its clinical applications in cancer biomarker discovery

2014 ◽  
Vol 11 (1) ◽  
pp. 14 ◽  
Author(s):  
Huan Liu ◽  
Ningbo Zhang ◽  
Debin Wan ◽  
Meng Cui ◽  
Zhiqiang Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biomarker Discovery ◽  
Clinical Applications ◽  
Cancer Biomarker

scholarly journals Enabling global analysis of protein citrullination and homocitrullination via biotin thiol tag-assisted mass spectrometry

2021 ◽  
Author(s):  
Lingjun Li ◽  
Yatao Shi ◽  
Zihui Li ◽  
Bin Wang ◽  
Xudong Shi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Global Analysis ◽  
Protein Structures ◽  
Isotopic Labeling ◽  
Underlying Mechanism ◽  
Biological Processes ◽  
Disease Pathogenesis ◽  
Post Translational Modifications ◽  
Mouse Tissues ◽  
Global Mapping

Abstract Citrullination and homocitrullination are key post-translational modifications (PTMs) that affect protein structures and functions. Although they have been linked to various biological processes and disease pathogenesis, the underlying mechanism remains poorly understood due to a lack of effective tools to enrich, detect, and localize these PTMs. Herein, we report the design and development of a biotin thiol tag that enables derivatization, enrichment, and confident identification of these two PTMs simultaneously via mass spectrometry. We perform global mapping of the citrullination and homocitrullination proteomes of mouse tissues. In total, we identify 1,198 citrullination sites and 108 homocitrullination sites from 619 and 79 proteins, respectively, representing the largest datasets to date. We discover novel distribution and functions of these two PTMs. We also perform multiplexing quantitative analysis via isotopic labeling techniques. This study depicts a landscape of protein citrullination and homocitrullination and lays the foundation to further decipher their physiological and pathological roles.

scholarly journals Data mining in mass spectrometry-based proteomics studies

2020 ◽  
Vol 2 (4) ◽  
pp. 258-276
Author(s):  
Vu Anh Le ◽  
Cam Quyen Thi Phan ◽  
Thuy Huong Nguyen
Keyword(s):  
Mass Spectrometry ◽  
Data Mining ◽  
Biomedical Research ◽  
Protein Level ◽  
Protein Identification ◽  
Biomarker Discovery ◽  
Data Sets ◽  
Biological Processes ◽  
Data Mining Techniques ◽  
Analytical Technique

The post-genomic era consists of experimental and computational efforts to meet the challenge of clarifying and understanding the function of genes and their products. Proteomic studies play a key role in this endeavour by complementing other functional genomics approaches, encompasses the large-scale analysis of complex mixtures, including the identification and quantification of proteins expressed under different conditions, the determination of their properties, modifications and functions. Understanding how biological processes are regulated at the protein level is crucial to understanding the molecular basis of diseases and often highlights the prevention, diagnosis and treatment of diseases. High-throughput technologies are widely used in proteomics to perform the analysis of thousands of proteins. Specifically, mass spectrometry (MS) is an analytical technique for characterizing biological samples and is increasingly used in protein studies because of its targeted, nontargeted, and high performance abilities. However, as large data sets are created, computational methods such as data mining techniques are required to analyze and interpret the relevant data. More specifically, the application of data mining techniques in large proteomic data sets can assist in many interpretations of data; it can reveal protein-protein interactions, improve protein identification, evaluate the experimental methods used and facilitate the diagnosis and biomarker discovery. With the rapid advances in mass spectrometry devices and experimental methodologies, MS-based proteomics has become a reliable and necessary tool for elucidating biological processes at the protein level. Over the past decade, we have witnessed a great expansion of our knowledge of human diseases with the adoption of proteomic technologies based on MS, which leads to many interesting discoveries. Here, we review recent advances of data mining in MS-based proteomics in biomedical research. Recent research in many fields shows that proteomics goes beyond the simple classification of proteins in biological systems and finally reaches its initial potential – as an essential tool to aid related disciplines, notably biomedical research. From here, there is great potential for data mining in MS-based proteomics to move beyond basic research, into clinical research and diagnostics.

Global analysis of protein expression in muscle tissues of dermatomyositis/polymyosisits patients demonstrated an association between dysferlin and human leucocyte antigen A

Rheumatology ◽  
2019 ◽  
Vol 58 (8) ◽  
pp. 1474-1484 ◽  
Author(s):  
Yizhi Xiao ◽  
Honglin Zhu ◽  
Liya Li ◽  
Siming Gao ◽  
Di Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Muscle Tissue ◽  
Inflammatory Cell ◽  
Global Analysis ◽  
Inflammatory Cell Infiltration ◽  
Cell Infiltration ◽  
Biological Processes ◽  
Monocyte Chemoattractant Protein 1 ◽  
Transmembrane Glycoprotein ◽  
Muscle Tissues

Abstract Objectives DM and PM are characterized by myofibre damage with inflammatory cell infiltration due to the strong expressions of MHC class I HLA-A and monocyte chemoattractant protein-1 (MCP-1). Dysferlin (DYSF) is a transmembrane glycoprotein that anchors in the sarcolemma of myofibres. DYSF mutation is closely associated with inherited myopathies. This study aimed to determine the role of DYSF in the development of DM/PM. Methods Mass spectrometry was performed in muscle tissues from DM/PM patients and controls. The DYSF levels in muscle tissue, peripheral blood cells and serum were detected by Western blotting, IF, flow cytometry or ELISA. Double IF and co-immunoprecipitation were used to investigate the relationship between DYSF and HLA-A. Results Mass spectrometry and bioinformatics analysis findings suggested the dysregulated proteins in DM/PM patients participated in common biological processes and pathways, such as the generation of precursor metabolites and energy. DYSF was upregulated in the muscle tissue and serum of DM/PM patients. DYSF was mainly expressed in myofibres and co-localized with HLA-A and MCP-1. DYSF and HLA-A expressions were elevated in myocytes and endothelial cells after being stimulated by patient serum and IFN-β. However, no direct interactions were found between DYSF and HLA-A by co-immunoprecipitation. Conclusion Our study revealed the dysregulated proteins involved in common and specific biological processes in DM/PM patient samples. DYSF is upregulated and exhibits a potential role along with that of HLA-A and MCP-1 in inflammatory cell infiltration and muscle damage during the development of DM/PM.

scholarly journals Enabling global analysis of protein citrullination and homocitrullination via biotin thiol tag-assisted mass spectrometry

2022 ◽  
Author(s):  
Lingjun Li ◽  
Yatao Shi ◽  
Zihui Li ◽  
Bin Wang ◽  
Xudong Shi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Global Analysis ◽  
Protein Structures ◽  
Isotopic Labeling ◽  
Underlying Mechanism ◽  
Biological Processes ◽  
Disease Pathogenesis ◽  
Post Translational Modifications ◽  
Mouse Tissues ◽  
Global Mapping

Abstract Citrullination and homocitrullination are key post-translational modifications (PTMs) that affect protein structures and functions. Although they have been linked to various biological processes and disease pathogenesis, the underlying mechanism remains poorly understood due to a lack of effective tools to enrich, detect, and localize these PTMs. Herein, we report the design and development of a biotin thiol tag that enables derivatization, enrichment, and confident identification of these two PTMs simultaneously via mass spectrometry. We perform global mapping of the citrullination and homocitrullination proteomes of mouse tissues. In total, we identify 691 citrullination sites and 81 homocitrullination sites from 432 and 63 proteins, respectively, representing the largest datasets to date. We discover novel distribution and functions of these two PTMs. We also perform multiplexing quantitative analysis via isotopic labeling techniques. This study depicts a landscape of protein citrullination and homocitrullination and lays the foundation for further deciphering their physiological and pathological roles.

scholarly journals Global Analysis of Protein Sumoylation inSaccharomyces cerevisiae

2004 ◽  
Vol 279 (44) ◽  
pp. 45662-45668 ◽  
Author(s):  
James A. Wohlschlegel ◽  
Erica S. Johnson ◽  
Steven I. Reed ◽  
John R. Yates
Keyword(s):  
Mass Spectrometry ◽  
Chromatin Remodeling ◽  
Global Analysis ◽  
Eukaryotic Cells ◽  
Transcriptional Elongation ◽  
Biological Processes ◽  
Pol Ii ◽  
Macromolecular Complexes ◽  
Cellular Factors ◽  
Biological Patterns

Although the modification of cellular factors by SUMO is an essential process inSaccharomyces cerevisiae, the identities of the substrates remain largely unknown. Using a mass spectrometry-based approach, we have identified 271 new SUMO targets. These substrates play roles in a diverse set of biological processes and greatly expand the scope of SUMO regulation in eukaryotic cells. Transcription appears to be the most prevalent process associated with sumoylation with novel SUMO substrates found in basal transcription machinery for RNA polymerases I, II, and III, pol II transcriptional elongation complexes, and a variety of chromatin remodeling, chromatin modifying, and chromatin silencing complexes. Additionally, our global analysis has revealed a number of interesting biological patterns in the list of SUMO targets including a clustering of sumoylation targets within macromolecular complexes.

Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS): basics and clinical applications

2020 ◽  
Vol 58 (6) ◽  
pp. 883-896 ◽  
Author(s):  
Muhammad Zubair Israr ◽  
Dennis Bernieh ◽  
Andrea Salzano ◽  
Shabana Cassambai ◽  
Yoshiyuki Yazaki ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Laser Desorption ◽  
Maldi Mass Spectrometry ◽  
Clinical Applications ◽  
Clinical Diagnostics ◽  
Maldi Ms ◽  
Therapeutic Drug ◽  
The Impact ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

AbstractBackgroundMatrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS) has been used for more than 30 years. Compared with other analytical techniques, it offers ease of use, high throughput, robustness, cost-effectiveness, rapid analysis and sensitivity. As advantages, current clinical techniques (e.g. immunoassays) are unable to directly measure the biomarker; rather, they measure secondary signals. MALDI-MS has been extensively researched for clinical applications, and it is set for a breakthrough as a routine tool for clinical diagnostics.ContentThis review reports on the principles of MALDI-MS and discusses current clinical applications and the future clinical prospects for MALDI-MS. Furthermore, the review assesses the limitations currently experienced in clinical assays, the advantages and the impact of MALDI-MS to transform clinical laboratories.SummaryMALDI-MS is widely used in clinical microbiology for the screening of microbial isolates; however, there is scope to apply MALDI-MS in the diagnosis, prognosis, therapeutic drug monitoring and biopsy imaging in many diseases.OutlookThere is considerable potential for MALDI-MS in clinic as a tool for screening, profiling and imaging because of its high sensitivity and specificity over alternative techniques.

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