title: TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.
abstract: Top-down mass spectrometry enables the observation of whole complex proteoforms in biological samples and provides crucial information complementary to bottom-up mass spectrometry. Because of the complexity of top-down mass spectra and proteoforms, it is a challenging problem to efficiently interpret top-down tandem mass spectra in high-throughput proteome-level proteomics studies. We present TopPIC, a tool that efficiently identifies and characterizes complex proteoforms with unknown primary structure alterations, such as amino acid mutations and post-translational modifications, by searching top-down tandem mass spectra against a protein database.
  
  
  
  http://proteomics.informatics.iupui.edu/software/toppic/ CONTACT: xwliu@iupui.eduSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Kou
authors.affiliation: Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.
authors.forename: Likun
authors.initials: L
authors.lastname: Xun
authors.affiliation: Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.|Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
mesh_terms: D000818:Animals; D006801:Humans; D011499:Protein Processing, Post-Translational; D020543:Proteome; D040901:Proteomics; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome