Isobar(PTM): A software tool for the quantitative analysis of post-translationally modified proteins()

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. Isobar(PTM) 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.