Modificomics: Posttranslational modifications beyond protein phosphorylation and glycosylation

Reinders, Jörg; Sickmann, Albert

doi:10.1016/j.bioeng.2007.03.002

Cited by 69 publications

(55 citation statements)

References 81 publications

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“…In 2007, modificomics was advocated as a prominent and independent extension of proteomics (49), with the aim of exploring the language of post-translational modifications at the "omics" level and interpreting phenotype in the context of PTMs (39). To aid modificomics research, we have developed SysPTM, which integrates a data repository with powerful information extraction tools.…”

Section: Discussionmentioning

confidence: 99%

SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications

Xing

Ding

et al. 2009

Molecular & Cellular Proteomics

113

100

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With the rapid expansion of protein post-translational modification (PTM) research based on large-scale proteomic work, there is an increasing demand for a suitable repository to analyze PTM data. Here we present a curated, web-accessible PTM data base, SysPTM. SysPTM provides a systematic and sophisticated platform for proteomic PTM research equipped not only with a knowledge base of manually curated multi-type modification data but also with four fully developed, in-depth data mining tools. Currently, SysPTM contains data detailing 117,349 experimentally determined PTM sites on 33,421 proteins involving nearly 50 PTM types, curated from public resources including five data bases and four web servers and more than one hundred peer-reviewed mass spectrometry papers. Protein annotations including Pfam domains, KEGG pathways, GO functional classification, and ortholog groups are integrated into the data base. Four online tools have been developed and incorporated, including PTMBlast, to compare a user's PTM dataset with PTM data in SysPTM; PTMPathway, to map PTM proteins to KEGG pathways; PTMPhylog, to discover potentially conserved PTM sites; and PTMCluster, to find clusters of multi-site modifications. Post-translational modifications (PTMs)1 are various processing events that change the maturity, activity, and/or turnover of proteins. More than 200 different types of PTMs have been found, with new ones still being reported (1). PTMs not only change the physicochemical properties of proteins (2) but also dynamically regulate various biological events such as protein degradation, subcellular localization, conformational change, protein-protein interaction, and signal transduction (3-5). Previous studies have revealed the central roles of PTMs in human health and disease. For example, phosphorylation of pRB1 has been associated with tumorigenesis through controlling cell division (6); S-nitrosylation of parkin regulates its E3 ligase activity, resulting in protein accumulation in sporadic Parkinson disease (7); and defects in protein glycosylation have been related to several forms of congenital muscular dystrophy (8). Given this important role in health and disease, PTMs have been regarded as potential disease biomarkers or therapeutic targets. For example, Erlotinib (Tarceva), an inhibitor of epidermal growth factor receptor tyrosine kinase, has been approved by the Food and Drug Administration to treat non-small cell lung cancer (9); and histone deacetylase inhibitors have been demonstrated to have a potential therapeutic role in Huntington disease (10). The broad range of important roles played by PTMs in physiological and pathological processes has made PTM research an active field in recent years. Yet we remain limited in our knowledge of the full scope of PTM distribution on proteins and the precise location of PTM sites.There are two major kinds of experimental methods to identify PTMs: 1) traditional biological experiments such as radiolabeling PTM proteins (11), Western analysis with antibodies against ...

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Section: Discussionmentioning

confidence: 99%

SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications

Xing

Ding

et al. 2009

Molecular & Cellular Proteomics

113

100

View full text Add to dashboard Cite

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“…Studies have shown that glycosylation and phosphorylation, the major PTMs in proteins, are usually altered in many diseases states (for recent review [133]). The extension and distribution of aberrant phospho-and glyco-proteins in biological systems can be detected on 2-DE gels.…”

Section: Post-translational Modificationmentioning

confidence: 99%

Two‐dimensional gel electrophoresis and mass spectrometry for biomarker discovery

Penque

2009

Proteomics Clinical Apps

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The proteome project, initiated in 1995, was made possible by 2-DE combined with MS. The project main objective was and remains the identification of all proteins expressed by a cell, tissue or organism in a given time and condition. Following this objective, the global profiling of proteins in health versus pathological state by the 2-DE/MS-based proteomic approach has contributed to the elucidation of the basic mechanisms of disease by discovering candidate disease biomarkers and disease targets for new drug development. This review will briefly summarize the historical evolution of 2-DE up to today, and review 2-DE/MS technology and its specific methods of study of immunoresponse (immunoproteomics), PTM of proteins, complex proteinprotein interactions (interactome), the proteome of cell membrane and intracellular proteome turnover in disease biomarker discovery. 2-DE historical evolutionGlobal profiling of proteins in healthy versus pathological states is a strategy to discover biomarkers for early diagnostics, disease progression, treatment response and novel targets for therapeutic drugs development. The idea of making an inventory of all the proteins in a cell, tissue or organism with normal or abnormal physiology, was (re)initiated in the middle of the 1990s with the proteome project [1]. Since then, many technologies to make the analysis of the proteome a reality have been united.The perfect technological 'marriage' that made the proteome project feasible was between high resolution 2-DE for separation of large numbers of proteins and MS for identification and characterization of the proteins displayed on this gel [2]. However, before this happy union occured, science and technology devoted to protein study had a long journey until 2-DE and MS combination was possible (Fig. 1). It started in the last century, in 1937, when Tiselius [3] introduced electrophoresis technique as a modification of Reiner's early concept (1927) [4] to analyse a complex mixture of proteins such as serum proteins. Only 20 years later, in 1959, electrophoresis on a gel support formed by crosslinked polymerization of Cyanogum 41, a commercial name for two organic monomers, acrylamide and the crosslinking agent, N,N1-methylenebisacrylamide, was shown to be useful and was named PAGE by Raymond and Weintraub [5]. The adaptation of polyacrylamide gel to IEF in a stable pH gradient, developed by Svensson in 1962 [6], was possible by the end of the 1960s [7][8][9]. About this time, the 2-D by combining IEF to separate undenatured proteins according to their charge and gradient SDS-PAGE for a second separation, according to their molecular mass, was for the first time introduced by Kenrick and Margolis (1970) [10]. Only in 1975, was IEF in denaturing conditions, as known today, used to follow the 2-D PAGE and it was described in three independent works [11][12][13]. The most powerful demonstraCorrespondence: Dr. Deborah Penque, Laboratório de Proteó-mica, Departamento de Genética, Instituto Nacional de Saúde, Dr. Ricardo Jorge, I.P., A...

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“…Nevertheless, the identification and location of PTMs remains a challenge in routine analysis [125]. In the specific context of oxidative modifications, two major difficulties arise due to heterogeneity of possible modifications; first, whereas MS/MS is perfectly suited to the detection and identification of chemical modifications on amino acid side chains, the number of possible modifications (such as the different oxidation states of cysteine or methionine, the presence of nitrotyrosine, to name only the most standard ones) as well as the possibility of non specific peptide cleavages dramatically increase the search space when trying to match tandem mass spectra to peptide sequences in the queried database.…”

Section: Mass Spectrometric and Bioinformatics Challengesmentioning

confidence: 99%

Oxidation of proteins: Basic principles and perspectives for blood proteomics

Barelli

Canellini

Thadikkaran

et al. 2008

Proteomics Clinical Apps

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Protein oxidation mechanisms result in a wide array of modifications, from backbone cleavage or protein crosslinking to more subtle modifications such as side chain oxidations. Protein oxidation occurs as part of normal regulatory processes, as a defence mechanism against oxidative stress, or as a deleterious processes when antioxidant defences are overcome. Because blood is continually exposed to reactive oxygen and nitrogen species, blood proteomics should inherently adopt redox proteomic strategies. In this review, we recall the biochemical basis of protein oxidation, review the proteomic methodologies applied to analyse redox modifications, and highlight some physiological and in vitro responses to oxidative stress of various blood components.

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Modificomics: Posttranslational modifications beyond protein phosphorylation and glycosylation

Cited by 69 publications

References 81 publications

SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications

SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications

Two‐dimensional gel electrophoresis and mass spectrometry for biomarker discovery

Oxidation of proteins: Basic principles and perspectives for blood proteomics

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