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Title: A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy

Abstract

Characterization of the human blood plasma proteome is critical to the discovery of routinely useful clinical biomarkers. We used an Accurate Mass and Time (AMT) tag strategy with high-resolution mass accuracy capillary liquid chromatography Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (cLC-FTICR MS) to perform a global proteomic analysis of pilot study samples as part of the HUPO Plasma Proteome Project. HUPO reference serum and citrated plasma samples from African Americans, Asian Americans, and Caucasian Americans were analyzed, in addition to a Pacific Northwest National Laboratory reference serum and plasma. The AMT tag strategy allowed us to leverage two previously published “shotgun” proteomics experiments to perform global analyses on these samples in triplicate in less than 4 days total analysis time. A total of 722 (22% with multiple peptide identifications) International Protein Index (IPI) redundant proteins, or 377 protein families by ProteinProphet, were identified over the 6 individual HUPO serum and plasma samples. The samples yielded a similar number of identified redundant proteins in the plasma samples (average 446 +/-23) as found in the serum samples (average 440+/-20). These proteins were identified by an average of 956+/-35 unique peptides in plasma and 930+/-11 unique peptides in serum. In addition to thismore » high-throughput analysis, the AMT tag approach was used with a Z-score normalization to compare relative protein abundances. This analysis highlighted both known differences in serum and citrated plasma such as fibrinogens, and reproducible differences in peptide abundances from proteins such as soluble activin receptor-like kinase 7b and glycoprotein m6b. The AMT tag strategy not only improved our sample throughput, and provided a basis for estimated quantitation.« less

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
859425
Report Number(s):
PNWD-SA-6982
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Proteomics, 5(13):3454-3466
Country of Publication:
United States
Language:
English

Citation Formats

Adkins, Joshua N., Monroe, Matthew E., Auberry, Kenneth J., Shen, Yufeng, Jacobs, Jon M., Camp, David G., Vitzthum, Frank, Rodland, Karin D., Zangar, Richard C., Smith, Richard D., and Pounds, Joel G.. A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy. United States: N. p., 2005. Web. doi:10.1002/pmic.200401333.
Adkins, Joshua N., Monroe, Matthew E., Auberry, Kenneth J., Shen, Yufeng, Jacobs, Jon M., Camp, David G., Vitzthum, Frank, Rodland, Karin D., Zangar, Richard C., Smith, Richard D., & Pounds, Joel G.. A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy. United States. doi:10.1002/pmic.200401333.
Adkins, Joshua N., Monroe, Matthew E., Auberry, Kenneth J., Shen, Yufeng, Jacobs, Jon M., Camp, David G., Vitzthum, Frank, Rodland, Karin D., Zangar, Richard C., Smith, Richard D., and Pounds, Joel G.. 2005. "A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy". United States. doi:10.1002/pmic.200401333.
@article{osti_859425,
title = {A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy},
author = {Adkins, Joshua N. and Monroe, Matthew E. and Auberry, Kenneth J. and Shen, Yufeng and Jacobs, Jon M. and Camp, David G. and Vitzthum, Frank and Rodland, Karin D. and Zangar, Richard C. and Smith, Richard D. and Pounds, Joel G.},
abstractNote = {Characterization of the human blood plasma proteome is critical to the discovery of routinely useful clinical biomarkers. We used an Accurate Mass and Time (AMT) tag strategy with high-resolution mass accuracy capillary liquid chromatography Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (cLC-FTICR MS) to perform a global proteomic analysis of pilot study samples as part of the HUPO Plasma Proteome Project. HUPO reference serum and citrated plasma samples from African Americans, Asian Americans, and Caucasian Americans were analyzed, in addition to a Pacific Northwest National Laboratory reference serum and plasma. The AMT tag strategy allowed us to leverage two previously published “shotgun” proteomics experiments to perform global analyses on these samples in triplicate in less than 4 days total analysis time. A total of 722 (22% with multiple peptide identifications) International Protein Index (IPI) redundant proteins, or 377 protein families by ProteinProphet, were identified over the 6 individual HUPO serum and plasma samples. The samples yielded a similar number of identified redundant proteins in the plasma samples (average 446 +/-23) as found in the serum samples (average 440+/-20). These proteins were identified by an average of 956+/-35 unique peptides in plasma and 930+/-11 unique peptides in serum. In addition to this high-throughput analysis, the AMT tag approach was used with a Z-score normalization to compare relative protein abundances. This analysis highlighted both known differences in serum and citrated plasma such as fibrinogens, and reproducible differences in peptide abundances from proteins such as soluble activin receptor-like kinase 7b and glycoprotein m6b. The AMT tag strategy not only improved our sample throughput, and provided a basis for estimated quantitation.},
doi = {10.1002/pmic.200401333},
journal = {Proteomics, 5(13):3454-3466},
number = ,
volume = ,
place = {United States},
year = 2005,
month = 8
}
  • Proteome comparison of cell lines derived from breast cancer and normal breast epithelium provide opportunities to identify differentially expressed proteins and pathways associated with specific phenotypes. We employed trypsin-catalyzed 16O/18O peptide labeling, FTI-CR mass spectrometry, and the accurate mass and time (AMT) tag strategy to calculate compare the relative protein abundances of hundreds of proteins simultaneously in non-cancer and cancer cell lines derived from breast tissue. A reference panel of cell lines was created to facilitate comparisons of relative protein abundance amongst multiple cell lines and across multiple experiments. A peptide database generated from multidimensional LC separations and MS/MS analysismore » was used to facilitate subsequent AMT tag-based peptide identifications. This peptide database represented a total of 2,299 proteins, including 514 that were quantified using the AMT tag and 16O/18O strategies. Eighty-six proteins showed at least a 3-fold protein abundance change between cancer and non-cancer cell lines. A comparison of protein expression profiles with previously published gene expression data revealed that 21 of these proteins also had >3-fold differences between the non-cancer and cancer cell lines at the transcriptional level. Clustering of protein abundance ratios revealed that several groups of proteins were differentially expressed between the cancer cell lines« less
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