title: Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets.
abstract: BACKGROUND
  Two-dimensional differential gel electrophoresis (2D-DIGE) provides a powerful technique to separate proteins on their isoelectric point and apparent molecular mass and quantify changes in protein expression. Abundantly available proteins in spots can be identified using mass spectrometry-based approaches. However, identification is often not possible for low-abundant proteins.
  
  
  RESULTS
  We present a novel computational approach to prioritize candidate proteins for unidentified spots. Our approach exploits noisy information on the isoelectric point and apparent molecular mass of a protein spot in combination with functional similarities of candidate proteins to already identified proteins to select and rank candidates. We evaluated our method on a 2D-DIGE dataset comparing protein expression in uninfected and HIV-1 infected T-cells. Using leave-one-out cross-validation, we show that the true-positive rate for the top-5 ranked proteins is 43.8%.
  
  
  CONCLUSIONS
  Our approach shows good performance on a 2D-DIGE dataset comparing protein expression in uninfected and HIV-1 infected T-cells. We expect our method to be highly useful in (re-)mining other 2D-DIGE experiments in which especially the low-abundant protein spots remain to be identified.
authors: Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. u.k.nandal@amc.uva.nl.
authors: Umesh K
authors: UK
authors: Nandal
authors: Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. wytze.vlietstra@gmail.com.
authors: Wytze J
authors: WJ
authors: Vlietstra
authors: Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. carsten@byrman.demon.nl.
authors: Carsten
authors: C
authors: Byrman
authors: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. r.jeeninga@amc.uva.nl.
authors: Rienk E
authors: RE
authors: Jeeninga
authors: Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. J.H.Ringrose@uu.nl.
authors: Jeffrey H
authors: JH
authors: Ringrose
authors: Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. a.h.vankampen@amc.uva.nl.|Biosystems Data Analysis Group, University of Amsterdam, Science Park 9041098, XH Amsterdam, The Netherlands. a.h.vankampen@amc.uva.nl.
authors: Antoine H C
authors: AH
authors: van Kampen
authors: Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. d.speijer@amc.uva.nl.
authors: Dave
authors: D
authors: Speijer
authors: Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. p.d.moerland@amc.uva.nl.
authors: Perry D
authors: PD
authors: Moerland
mesh_terms: D002478:Cells, Cultured; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D015658:HIV Infections / Q000378:metabolism* / Q000821:virology; D015497:HIV-1 / Q000378:metabolism; D006801:Humans; D010446:Peptide Fragments / Q000032:analysis; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D013601:T-Lymphocytes / Q000378:metabolism* / Q000821:virology; D057825:Two-Dimensional Difference Gel Electrophoresis / Q000379:methods*
chemical_list: D010446:Peptide Fragments; D011506:Proteins
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