title: LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.
abstract: We present LuciPHOr2, a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data. As an extension of the original LuciPHOr (version 1) for phosphorylation site localization, the new software provides a site-level localization score for generic PTMs and associated false discovery rate called the false localization rate. We describe several novel features such as operating system independence and reduced computation time through multiple threading. We also discuss optimal parameters for different types of data and illustrate the new tool on a human skeletal muscle dataset for lysine-acetylation.
  
  
  METHODS
  The software is freely available on the SourceForge website http://luciphor2.sourceforge.net.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Damian
authors.initials: D
authors.lastname: Fermin
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Avtonomov
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Hyungwon
authors.initials: H
authors.lastname: Choi
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA, Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
mesh_terms: D000107:Acetylation; D000465:Algorithms; D006801:Humans; D008239:Lysine / Q000737:chemistry / Q000378:metabolism; D009124:Muscle Proteins / Q000737:chemistry / Q000378:metabolism*; D018482:Muscle, Skeletal; D010446:Peptide Fragments / Q000032:analysis; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D009124:Muscle Proteins; D010446:Peptide Fragments; D008239:Lysine