title: Command line tool for calculating theoretical MS spectra for given sequences.
abstract: Scientists usually want to verify the ion matching process of algorithms that look up peptide sequences in DNA or protein databases. The verification step is often done numerically or visually. Not all search algorithms present the appropriate theoretical spectrum information within their results. Thus, the theoretical spectrum for each result should be calculated from the sequence of the matched peptide. We present an operating-system-independent command line tool for this purpose that can be integrated easily into complex as well as existing environments, and can be used to present the theoretical spectrum to the user in either graphical or tabular format by third party products.
  
  
  BACKGROUND
  The code is available via the website http://www.protein-ms.de
authors.affiliation: Protein Mass Spectrometry and Functional Proteomics Group, Rudolf-Virchow-Center for Experimental Biomedicine, Universitaet Wuerzburg, Versbacher Strasse 9, D-97078 Wuerzburg, Germany.
authors.forename: Andreas M
authors.initials: AM
authors.lastname: Boehm
authors.forename: Florian
authors.initials: F
authors.lastname: Grosse-Coosmann
authors.forename: Albert
authors.initials: A
authors.lastname: Sickmann
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D013058:Mass Spectrometry / Q000379:methods*; D008956:Models, Chemical; D009862:Online Systems; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins