title: Multidimensional protein fractionation using ProteomeLab PF 2D for profiling amyotrophic lateral sclerosis immunity: A preliminary report.
abstract: BACKGROUND
  The ProteomeLab PF 2D platform is a relatively new approach to global protein profiling. Herein, it was used for investigation of plasma proteome changes in amyotrophic lateral sclerosis (ALS) patients before and during immunization with glatiramer acetate (GA) in a clinical trial.
  
  
  RESULTS
  The experimental design included immunoaffinity depletion of 12 most abundant proteins from plasma samples with the ProteomeLab IgY-12 LC10 column kit as first dimension separation, also referred to as immuno-partitioning. Second and third dimension separations of the enriched proteome were performed on the PF 2D platform utilizing 2D isoelectric focusing and RP-HPLC with the resulting fractions collected for analysis. 1D gel electrophoresis was added as a fourth dimension when sufficient protein was available. Protein identification from collected fractions was performed using nano-LC-MS/MS approach. Analysis of differences in the resulting two-dimensional maps of fractions obtained from the PF 2D and the ability to identify proteins from these fractions allowed sensitivity threshold measurements. Masked proteins in the PF 2D fractions are discussed.
  
  
  CONCLUSIONS
  We offer some insight into the strengths and limitations of this emerging proteomic platform.
authors.affiliation: Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, USA. jschlautman@unmc.edu
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Schlautman
authors.forename: Wojciech
authors.initials: W
authors.lastname: Rozek
authors.forename: Robert
authors.initials: R
authors.lastname: Stetler
authors.forename: R Lee
authors.initials: RL
authors.lastname: Mosley
authors.forename: Howard E
authors.initials: HE
authors.lastname: Gendelman
authors.forename: Pawel
authors.initials: P
authors.lastname: Ciborowski
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