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 E. Gendelman; Pawel Ciborowski

doi:10.1186/1477-5956-6-26

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 E. Gendelman, Pawel Ciborowski

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

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 language	English (US)
Article number	26
Journal	Proteome Science
Volume	6
DOIs	https://doi.org/10.1186/1477-5956-6-26
State	Published - Sep 12 2008

ASJC Scopus subject areas

Biochemistry
Molecular Biology

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title = "Multidimensional protein fractionation using ProteomeLab PF 2D{\texttrademark} for profiling amyotrophic lateral sclerosis immunity: A preliminary report",

abstract = "Background: The ProteomeLab{\texttrademark} 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{\texttrademark} 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.",

author = "Schlautman, {Joshua D.} and Wojciech Rozek and Robert Stetler and Mosley, {R. Lee} and Gendelman, {Howard E.} and Pawel Ciborowski",

note = "Funding Information: The authors thank Ms. Robin Taylor for outstanding administrative and computer support and for her effort in helping put this manuscript together in a timely manner. This work was funded by NIH grants 1R21 MH075662-01 (P.C.), P01 NS43985, 5R37NS036126 (to H.E.G.).",

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doi = "10.1186/1477-5956-6-26",

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AU - Rozek, Wojciech

AU - Stetler, Robert

AU - Mosley, R. Lee

AU - Gendelman, Howard E.

AU - Ciborowski, Pawel

N1 - Funding Information: The authors thank Ms. Robin Taylor for outstanding administrative and computer support and for her effort in helping put this manuscript together in a timely manner. This work was funded by NIH grants 1R21 MH075662-01 (P.C.), P01 NS43985, 5R37NS036126 (to H.E.G.).

PY - 2008/9/12

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N2 - 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.

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

Abstract

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