title: POTAMOS mass spectrometry calculator: computer aided mass spectrometry to the post-translational modifications of proteins. A focus on histones.
abstract: Mass spectrometry is a widely used technique for protein identification and it has also become the method of choice in order to detect and characterize the post-translational modifications (PTMs) of proteins. Many software tools have been developed to deal with this complication. In this paper we introduce a new, free and user friendly online software tool, named POTAMOS Mass Spectrometry Calculator, which was developed in the open source application framework Ruby on Rails. It can provide calculated mass spectrometry data in a time saving manner, independently of instrumentation. In this web application we have focused on a well known protein family of histones whose PTMs are believed to play a crucial role in gene regulation, as suggested by the so called "histone code" hypothesis. The PTMs implemented in this software are: methylations of arginines and lysines, acetylations of lysines and phosphorylations of serines and threonines. The application is able to calculate the kind, the number and the combinations of the possible PTMs corresponding to a given peptide sequence and a given mass along with the full set of the unique primary structures produced by the possible distributions along the amino acid sequence. It can also calculate the masses and charges of a fragmented histone variant, which carries predefined modifications already implemented. Additional functionality is provided by the calculation of the masses of fragments produced upon protein cleavage by the proteolytic enzymes that are most widely used in proteomics studies.
authors.affiliation: Department of Informatics & Telecommunications Technology, Technological Educational Institute of Epirus, Kostakioi, Arta, Greece.
authors.forename: A
authors.initials: A
authors.lastname: Vlachopanos
authors.affiliation: Laboratory of Biological Chemistry, Medical School, University of Ioannina, Greece; Foundation for Research and Technology, Hellas-Biomedical Research Institute, Ioannina, Greece.
authors.forename: E
authors.initials: E
authors.lastname: Soupsana
authors.affiliation: Laboratory of Biological Chemistry, Medical School, University of Ioannina, Greece; Foundation for Research and Technology, Hellas-Biomedical Research Institute, Ioannina, Greece.
authors.forename: A S
authors.initials: AS
authors.lastname: Politou
authors.affiliation: Department of Informatics & Telecommunications Technology, Technological Educational Institute of Epirus, Kostakioi, Arta, Greece; Laboratory of Biological Chemistry, Medical School, University of Ioannina, Greece; Foundation for Research and Technology, Hellas-Biomedical Research Institute, Ioannina, Greece; Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA. Electronic address: gpapamokos@seas.harvard.edu.
authors.forename: G V
authors.initials: GV
authors.lastname: Papamokos
mesh_terms: D006657:Histones / Q000737:chemistry*; D006801:Humans; D020407:Internet; D013058:Mass Spectrometry / Q000379:methods*; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D006657:Histones
keywords: Bioinformatics; Histones; Mass spectrometry; POTAMOS mass spectrometry calculator; Post-translational modifications; Protein cleavage; Proteomics; Ruby on rails; SQLite