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IsobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins.

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Title: IsobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins.
Authors: Breitwieser, Florian P.1, Colinge, Jacques1 jcolinge@cemm.oeaw.ac.at
Source: Journal of Proteomics. Sep2013, Vol. 90, p77-84. 8p.
Subjects: Computer software, Post-translational modification, Proteomics, Phosphorylation, Acetylation, Tandem mass spectrometry
Abstract: Abstract: The establishment of extremely powerful proteomics platforms able to map thousands of modification sites, e.g. phosphorylations or acetylations, over entire proteomes calls for equally powerful software tools to effectively extract useful and reliable information from such complex datasets. We present a new quantitative PTM analysis platform aimed at processing iTRAQ or Tandem Mass Tags (TMT) labeled peptides. It covers a broad range of needs associated with proper PTM ratio analysis such as PTM localization validation, robust ratio computation and statistical assessment, and navigable user report generation. IsobarPTM is made available as an R Bioconductor package and it can be run from the command line by non R specialists. Biological significance: “IsobarPTM is a new software tool facilitating the quantitative analysis of protein modification regulation streamlining important issues related to PTM localization and statistical modeling. Users are provided with a navigable spreadsheet report, which also annotate already public modification sites.” This article is part of a Special Issue entitled: From Genome to Proteome: Open Innovations. [Copyright &y& Elsevier]
Copyright of Journal of Proteomics is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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DbLabel: Engineering Source
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PubType: Academic Journal
PubTypeId: academicJournal
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  Data: <searchLink fieldCode="AR" term="%22Breitwieser%2C+Florian+P%2E%22">Breitwieser, Florian P.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Colinge%2C+Jacques%22">Colinge, Jacques</searchLink><relatesTo>1</relatesTo><i> jcolinge@cemm.oeaw.ac.at</i>
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  Data: <searchLink fieldCode="JN" term="%22Journal+of+Proteomics%22">Journal of Proteomics</searchLink>. Sep2013, Vol. 90, p77-84. 8p.
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  Data: <searchLink fieldCode="DE" term="%22Computer+software%22">Computer software</searchLink><br /><searchLink fieldCode="DE" term="%22Post-translational+modification%22">Post-translational modification</searchLink><br /><searchLink fieldCode="DE" term="%22Proteomics%22">Proteomics</searchLink><br /><searchLink fieldCode="DE" term="%22Phosphorylation%22">Phosphorylation</searchLink><br /><searchLink fieldCode="DE" term="%22Acetylation%22">Acetylation</searchLink><br /><searchLink fieldCode="DE" term="%22Tandem+mass+spectrometry%22">Tandem mass spectrometry</searchLink>
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  Data: Abstract: The establishment of extremely powerful proteomics platforms able to map thousands of modification sites, e.g. phosphorylations or acetylations, over entire proteomes calls for equally powerful software tools to effectively extract useful and reliable information from such complex datasets. We present a new quantitative PTM analysis platform aimed at processing iTRAQ or Tandem Mass Tags (TMT) labeled peptides. It covers a broad range of needs associated with proper PTM ratio analysis such as PTM localization validation, robust ratio computation and statistical assessment, and navigable user report generation. IsobarPTM is made available as an R Bioconductor package and it can be run from the command line by non R specialists. Biological significance: “IsobarPTM is a new software tool facilitating the quantitative analysis of protein modification regulation streamlining important issues related to PTM localization and statistical modeling. Users are provided with a navigable spreadsheet report, which also annotate already public modification sites.” This article is part of a Special Issue entitled: From Genome to Proteome: Open Innovations. [Copyright &y& Elsevier]
– Name: AbstractSuppliedCopyright
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  Data: <i>Copyright of Journal of Proteomics is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1016/j.jprot.2013.02.022
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      – Code: eng
        Text: English
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        PageCount: 8
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      – SubjectFull: Computer software
        Type: general
      – SubjectFull: Post-translational modification
        Type: general
      – SubjectFull: Proteomics
        Type: general
      – SubjectFull: Phosphorylation
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      – SubjectFull: Acetylation
        Type: general
      – SubjectFull: Tandem mass spectrometry
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              M: 09
              Text: Sep2013
              Type: published
              Y: 2013
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