Identification of Post-Translational Modifications by Mass Spectrometry

2013 ◽  
Vol 66 (7) ◽  
pp. 734 ◽  
Author(s):  
Armand G. Ngounou Wetie ◽  
Izabela Sokolowska ◽  
Alisa G. Woods ◽  
Costel C. Darie
Keyword(s):  
Mass Spectrometry ◽  
Structure Stability ◽  
Biological Processes ◽  
Protein Activity ◽  
Post Translational Modifications ◽  
Protein Modifications ◽  
Effector Molecules ◽  
Pathological Conditions ◽  
Activity Structure

Proteins are the effector molecules of many cellular and biological processes and are thus very dynamic and flexible. Regulation of protein activity, structure, stability, and turnover is in part controlled by their post-translational modifications (PTMs). Common PTMs of proteins include phosphorylation, glycosylation, methylation, ubiquitination, acetylation, and oxidation. Understanding the biology of protein PTMs can help elucidate the mechanisms of many pathological conditions and provide opportunities for prevention, diagnostics, and treatment of these disorders. Prior to the era of proteomics, it was standard to use chemistry methods for the identification of protein modifications. With advancements in proteomic technologies, mass spectrometry has become the method of choice for the analysis of protein PTMs. In this brief review, we will highlight the biochemistry of PTMs with an emphasis on mass spectrometry.

scholarly journals Identification, Characterization, and Regulatory Mechanisms of a Novel EGR1 Splicing Isoform

2019 ◽  
Vol 20 (7) ◽  
pp. 1548 ◽  
Author(s):  
Vincenza Aliperti ◽  
Giulia Sgueglia ◽  
Francesco Aniello ◽  
Emilia Vitale ◽  
Laura Fucci ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Cell Types ◽  
Regulatory Mechanisms ◽  
Brain Diseases ◽  
Regulation Of Transcription ◽  
Biological Processes ◽  
Activation Domain ◽  
Post Translational Modifications ◽  
Pathological Conditions ◽  
Proliferation And Apoptosis

EGR1 is a transcription factor expressed in many cell types that regulates genes involved in different biological processes including growth, proliferation, and apoptosis. Dysregulation of EGR1 expression has been associated with many pathological conditions such as tumors and brain diseases. Known molecular mechanisms underlying the control of EGR1 function include regulation of transcription, mRNA and protein stability, and post-translational modifications. Here we describe the identification of a splicing isoform for the human EGR1 gene. The newly identified splicing transcript encodes a shorter protein compared to the canonical EGR1. This isoform lacks a region belonging to the N-terminal activation domain and although it is capable of entering the nucleus, it is unable to activate transcription fully relative to the canonical isoform.

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 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.

The role of mass spectrometry analysis in bacterial effector characterization

2017 ◽  
Vol 474 (16) ◽  
pp. 2779-2784 ◽  
Author(s):  
Nichollas E. Scott ◽  
Elizabeth L. Hartland
Keyword(s):  
Mass Spectrometry ◽  
Cell Biology ◽  
Critical Role ◽  
Effector Proteins ◽  
Mass Spectrometry Analysis ◽  
Protein Activity ◽  
Post Translational Modifications ◽  
Spectrometry Analysis ◽  
New Generation

Many secreted bacterial effector proteins play a critical role in host–pathogen interactions by mediating a variety of post-translational modifications, some of which do not occur natively within the eukaryotic proteome. The characterization of bacterial effector protein activity remains an important step to understanding the subversion of host cell biology during pathogen infection and although molecular biology and immunochemistry remain critical tools for gaining insights into bacterial effector functions, increasingly mass spectrometry (MS) and proteomic approaches are also playing an indispensable role. The focus of this editorial is to highlight the strengths of specific MS approaches and their utility for the characterization of bacterial effector activity. With the capability of new generation MS instrumentation, MS-based technologies can provide information that is inaccessible using traditional molecular or immunochemical approaches.

Dicarbonyl derived post-translational modifications: chemistry bridging biology and aging-related disease

2020 ◽  
Vol 64 (1) ◽  
pp. 97-110
Author(s):  
Christian Sibbersen ◽  
Mogens Johannsen
Keyword(s):  
Mass Spectrometry ◽  
Future Research ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Dicarbonyl Compounds ◽  
Protein Targets ◽  
Post Translational Modifications ◽  
Reactive Protein ◽  
Glycation End Products ◽  
Direct Mass Spectrometry

Abstract In living systems, nucleophilic amino acid residues are prone to non-enzymatic post-translational modification by electrophiles. α-Dicarbonyl compounds are a special type of electrophiles that can react irreversibly with lysine, arginine, and cysteine residues via complex mechanisms to form post-translational modifications known as advanced glycation end-products (AGEs). Glyoxal, methylglyoxal, and 3-deoxyglucosone are the major endogenous dicarbonyls, with methylglyoxal being the most well-studied. There are several routes that lead to the formation of dicarbonyl compounds, most originating from glucose and glucose metabolism, such as the non-enzymatic decomposition of glycolytic intermediates and fructosyl amines. Although dicarbonyls are removed continuously mainly via the glyoxalase system, several conditions lead to an increase in dicarbonyl concentration and thereby AGE formation. AGEs have been implicated in diabetes and aging-related diseases, and for this reason the elucidation of their structure as well as protein targets is of great interest. Though the dicarbonyls and reactive protein side chains are of relatively simple nature, the structures of the adducts as well as their mechanism of formation are not that trivial. Furthermore, detection of sites of modification can be demanding and current best practices rely on either direct mass spectrometry or various methods of enrichment based on antibodies or click chemistry followed by mass spectrometry. Future research into the structure of these adducts and protein targets of dicarbonyl compounds may improve the understanding of how the mechanisms of diabetes and aging-related physiological damage occur.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

Unrestrictive protein modification localization and quality control for open search of mass spectra

2018 ◽  
Author(s):  
Zhiwu An ◽  
Fuzhou Gong ◽  
Yan Fu
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Tandem Mass Spectrometry ◽  
Mass Spectra ◽  
Protein Modification ◽  
Software Tool ◽  
Tandem Mass ◽  
Simulation Data ◽  
Post Translational Modifications

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br>

scholarly journals FOXC1 in cancer development and therapy: deciphering its emerging and divergent roles

2017 ◽  
Vol 9 (12) ◽  
pp. 797-816 ◽  
Author(s):  
Zhi Yang ◽  
Shuai Jiang ◽  
Yicheng Cheng ◽  
Tian Li ◽  
Wei Hu ◽  
...  
Keyword(s):  
Transcriptional Regulator ◽  
Cancer Development ◽  
Protein Activity ◽  
Stem Cell Maintenance ◽  
Cancer Migration ◽  
Forkhead Box ◽  
Pathological Conditions ◽  
Clinical Biomarker ◽  
Abnormal Cell Proliferation ◽  
Cell Maintenance

Forkhead box C1 (FOXC1) is an essential member of the forkhead box transcription factors and has been highlighted as an important transcriptional regulator of crucial proteins associated with a wide variety of carcinomas. FOXC1 regulates tumor-associated genes and is regulated by multiple pathways that control its mRNA expression and protein activity. Aberrant FOXC1 expression is involved in diverse tumorigenic processes, such as abnormal cell proliferation, cancer stem cell maintenance, cancer migration, and angiogenesis. Herein, we review the correlation between the expression of FOXC1 and tumor behaviors. We also summarize the mechanisms of the regulation of FOXC1 expression and activity in physiological and pathological conditions. In particular, we focus on the pathological processes of cancer targeted by FOXC1 and discuss whether FOXC1 is good or detrimental during tumor progression. Moreover, FOXC1 is highlighted as a clinical biomarker for diagnosis or prognosis in various human cancers. The information reviewed here should assist in experimental designs and emphasize the potential of FOXC1 as a therapeutic target for cancer.

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