title: ProteomeCommons.org JAF: reference information and tools for proteomics.
abstract: CONCLUSIONS
  Analysis of proteomics data, specifically mass spectrometry data, commonly relies on libraries of known information such as atomic masses, known stable isotopes, atomic compositions of amino acids, observed modifications of known amino acids and ion masses that directly correspond to known amino acid sequences. The Java Analysis Framework (JAF) for proteomics provides a freely usable, open-source library of Java code that abstracts all of the aforementioned data, enabling more rapid development of proteomics tools. The JAF also includes several user tools that can be run directly from a web browser.
  
  
  BACKGROUND
  The current version and an archive of all older versions of the Java Analysis Framework for Proteomics is freely available, including complete source-code, at http://www.proteomecommons.org/current/511/.
authors.affiliation: Department Biological Chemistry, University of Michigan, Ann Arbor, MI 48104, USA. jfalkner@umich.edu
authors.forename: J A
authors.initials: JA
authors.lastname: Falkner
authors.forename: J W
authors.initials: JW
authors.lastname: Falkner
authors.forename: P C
authors.initials: PC
authors.lastname: Andrews
mesh_terms: D003628:Database Management Systems; D030562:Databases, Protein; D004282:Documentation / Q000379:methods*; D010449:Peptide Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000145:classification; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins