Multidimensional protein fractionation using ProteomeLab PF 2D™ for profiling amyotrophic lateral sclerosis immunity: A preliminary report

Joshua D. Schlautman, Wojciech Rozek, Robert Stetler, R Lee Mosley, Howard Eliot Gendelman, Pawel S Ciborowski

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21 Citations (Scopus)

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. Conclusion: We offer some insight into the strengths and limitations of this emerging proteomic platform.

Original languageEnglish (US)
Article number26
JournalProteome Science
Volume6
DOIs
StatePublished - Sep 12 2008

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Amyotrophic Lateral Sclerosis
Fractionation
Immunity
Proteome
Proteins
Immunization
Isoelectric Focusing
Electrophoresis
Proteomics
Design of experiments
Blood Proteins
Research Design
Gels
High Pressure Liquid Chromatography
Clinical Trials
Plasmas

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

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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. Conclusion: We offer some insight into the strengths and limitations of this emerging proteomic platform.",
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AU - Rozek, Wojciech

AU - Stetler, Robert

AU - Mosley, R Lee

AU - Gendelman, Howard Eliot

AU - Ciborowski, Pawel S

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