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Title: Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells

Abstract

Comprehensive phosphoproteomic analysis of small populations of cells remains a daunting task due primarily to the insufficient MS signal intensity from low concentrations of enriched phosphopeptides. Isobaric labeling has a unique multiplexing feature where the “total” peptide signal from all channels (or samples) triggers MS/MS fragmentation for peptide identification while the reporter ions provide quantitative information. In light of this feature, we tested the concept of using a “boosting” sample (e.g., a biological sample mimicking the study samples but available in much larger quantity) in multiplexed analysis to enable sensitive and comprehensive quantitative phosphoproteomic measurements with <100,000 cells. This simple Boosting to Amplify Signal with Isobaric Labeling (BASIL) strategy increased the overall number of quantifiable phosphorylation sites more than 4-fold. Good reproducibility in quantification was demonstrated with a median CV of 15.3% and Pearson correlation coefficient of 0.95 from biological replicates. A proof-of-concept experiment demonstrated the ability of BASIL to distinguish acute myeloid leukemia cells based on the phosphoproteome data. Moreover, in a pilot application, this strategy enabled quantitative analysis of over 20,000 phosphorylation sites from human pancreatic islets treated with interleukin-1ß and interferon-gamma. Together, this signal boosting strategy provides an attractive solution to comprehensive and quantitative phosphoproteome profiling ofmore » relatively small populations of cells where traditional phosphoproteomic workflows provide insufficient sensitivity.« less

Authors:
 [1];  [1];  [2];  [1];  [3];  [1];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1];  [3];  [3];  [2]; ORCiD logo [1]; ORCiD logo [1]
  1. BATTELLE (PACIFIC NW LAB)
  2. Harvard Medical School
  3. University of Florida
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1530853
Report Number(s):
PNNL-SA-140381
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 91; Journal Issue: 9
Country of Publication:
United States
Language:
English
Subject:
phosphorylation, phosphoproteomics, pancreatic islets, small populations of cells

Citation Formats

Yi, Lian, Tsai, Chia-Feng, Dirice, Ercument, Swensen, Adam C., Chen, Jing, Shi, Tujin, Gritsenko, Marina A., Chu, Rosalie K., Piehowski, Paul D., Smith, Richard D., Rodland, Karin D., Atkinson, Mark A., Mathews, Clayton E., Kulkarni, Rohit N., Liu, Tao, and Qian, Weijun. Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells. United States: N. p., 2019. Web. doi:10.1021/acs.analchem.9b00024.
Yi, Lian, Tsai, Chia-Feng, Dirice, Ercument, Swensen, Adam C., Chen, Jing, Shi, Tujin, Gritsenko, Marina A., Chu, Rosalie K., Piehowski, Paul D., Smith, Richard D., Rodland, Karin D., Atkinson, Mark A., Mathews, Clayton E., Kulkarni, Rohit N., Liu, Tao, & Qian, Weijun. Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells. United States. doi:10.1021/acs.analchem.9b00024.
Yi, Lian, Tsai, Chia-Feng, Dirice, Ercument, Swensen, Adam C., Chen, Jing, Shi, Tujin, Gritsenko, Marina A., Chu, Rosalie K., Piehowski, Paul D., Smith, Richard D., Rodland, Karin D., Atkinson, Mark A., Mathews, Clayton E., Kulkarni, Rohit N., Liu, Tao, and Qian, Weijun. Tue . "Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells". United States. doi:10.1021/acs.analchem.9b00024.
@article{osti_1530853,
title = {Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells},
author = {Yi, Lian and Tsai, Chia-Feng and Dirice, Ercument and Swensen, Adam C. and Chen, Jing and Shi, Tujin and Gritsenko, Marina A. and Chu, Rosalie K. and Piehowski, Paul D. and Smith, Richard D. and Rodland, Karin D. and Atkinson, Mark A. and Mathews, Clayton E. and Kulkarni, Rohit N. and Liu, Tao and Qian, Weijun},
abstractNote = {Comprehensive phosphoproteomic analysis of small populations of cells remains a daunting task due primarily to the insufficient MS signal intensity from low concentrations of enriched phosphopeptides. Isobaric labeling has a unique multiplexing feature where the “total” peptide signal from all channels (or samples) triggers MS/MS fragmentation for peptide identification while the reporter ions provide quantitative information. In light of this feature, we tested the concept of using a “boosting” sample (e.g., a biological sample mimicking the study samples but available in much larger quantity) in multiplexed analysis to enable sensitive and comprehensive quantitative phosphoproteomic measurements with <100,000 cells. This simple Boosting to Amplify Signal with Isobaric Labeling (BASIL) strategy increased the overall number of quantifiable phosphorylation sites more than 4-fold. Good reproducibility in quantification was demonstrated with a median CV of 15.3% and Pearson correlation coefficient of 0.95 from biological replicates. A proof-of-concept experiment demonstrated the ability of BASIL to distinguish acute myeloid leukemia cells based on the phosphoproteome data. Moreover, in a pilot application, this strategy enabled quantitative analysis of over 20,000 phosphorylation sites from human pancreatic islets treated with interleukin-1ß and interferon-gamma. Together, this signal boosting strategy provides an attractive solution to comprehensive and quantitative phosphoproteome profiling of relatively small populations of cells where traditional phosphoproteomic workflows provide insufficient sensitivity.},
doi = {10.1021/acs.analchem.9b00024},
journal = {Analytical Chemistry},
number = 9,
volume = 91,
place = {United States},
year = {2019},
month = {5}
}