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Title: A Review on Quantitative Multiplexed Proteomics

Abstract

Over the last few decades, mass spectrometry-based proteomics has become an increasingly powerful tool that is now able to routinely detect and quantify thousands of proteins. A major advance for global protein quantification was the introduction of isobaric tags, which in a single experiment enable the global quantification of proteins across multiple samples. We refer to these methods as multiplexed proteomics. We discuss the principles, advantages, and drawbacks of various multiplexed proteomics techniques, and compare them to alternative approaches. We discuss how the emerging combination of multiplexing with targeted proteomics might enable the reliable and high-quality quantification of very low-abundance proteins across multiple conditions. We suggest that fusing multiplexed proteomics with data-independent acquisition approaches might enable the comparison of hundreds of different samples without missing values while maintaining the superb measurement precision and accuracy obtainable with isobaric tag quantification.

Authors:
 [1];  [1]; ORCiD logo [1]
+ Show Author Affiliations
  1. Princeton Univ., NJ (United States). Dept. of Molecular Biology. The Lewis-Sigler Inst. of Integrative Genomics
Publication Date:
Research Org.:
Princeton Univ., NJ (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Inst. of Health (NIH) (United States)
OSTI Identifier:
1489826
Alternate Identifier(s):
OSTI ID: 1507613
Grant/Contract Number:  
SC0018420; SC0018260; T32GM007388; 1R35GM128813
Resource Type:
Accepted Manuscript
Journal Name:
ChemBioChem: a European journal of chemical biology
Additional Journal Information:
Journal Volume: 20; Journal Issue: 10; Journal ID: ISSN 1439-4227
Publisher:
ChemPubSoc Europe
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; quantitative proteomics; isobaric tags; data-independent-acquisition; multiplexing

Citation Formats

Pappireddi, Nishant, Martin, Lance, and Wühr, Martin. A Review on Quantitative Multiplexed Proteomics. United States: N. p., 2019. Web. doi:10.1002/cbic.201800650.
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Pappireddi, Nishant, Martin, Lance, & Wühr, Martin. A Review on Quantitative Multiplexed Proteomics. United States. https://doi.org/10.1002/cbic.201800650
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Pappireddi, Nishant, Martin, Lance, and Wühr, Martin. Fri . "A Review on Quantitative Multiplexed Proteomics". United States. https://doi.org/10.1002/cbic.201800650. https://www.osti.gov/servlets/purl/1489826.
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@article{osti_1489826,
title = {A Review on Quantitative Multiplexed Proteomics},
author = {Pappireddi, Nishant and Martin, Lance and Wühr, Martin},
abstractNote = {Over the last few decades, mass spectrometry-based proteomics has become an increasingly powerful tool that is now able to routinely detect and quantify thousands of proteins. A major advance for global protein quantification was the introduction of isobaric tags, which in a single experiment enable the global quantification of proteins across multiple samples. We refer to these methods as multiplexed proteomics. We discuss the principles, advantages, and drawbacks of various multiplexed proteomics techniques, and compare them to alternative approaches. We discuss how the emerging combination of multiplexing with targeted proteomics might enable the reliable and high-quality quantification of very low-abundance proteins across multiple conditions. We suggest that fusing multiplexed proteomics with data-independent acquisition approaches might enable the comparison of hundreds of different samples without missing values while maintaining the superb measurement precision and accuracy obtainable with isobaric tag quantification.},
doi = {10.1002/cbic.201800650},
journal = {ChemBioChem: a European journal of chemical biology},
number = 10,
volume = 20,
place = {United States},
year = {Fri Jan 04 00:00:00 EST 2019},
month = {Fri Jan 04 00:00:00 EST 2019}
}
Copy to clipboard
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journal, July 2019

  • Peshkin, Leonid; Gupta, Meera; Ryazanova, Lillia
  • Molecular & Cellular Proteomics, Vol. 18, Issue 10
  • DOI: 10.1074/mcp.tir119.001317

Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags.
text, January 2018

  • O'Brien, Jonathon J.; O'Connell, Jeremy D.; Paulo, Joao A.
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.20319

Tandem Mass Tags:  A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS
journal, June 2006

  • Thompson, Andrew; Schaefer, Juergen; Kuhn, Karsten
  • Analytical Chemistry, Vol. 78, Issue 12
  • DOI: 10.1021/ac060310l

Selected reaction monitoring for quantitative proteomics: a tutorial
text, January 2008

Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases
text, January 2008

  • Pierce, A.; Unwin, R. D.; Evans, C. A.
  • American Society for Biochemistry and Molecular Biology
  • DOI: 10.5167/uzh-13774

Tandem Mass Tags:  A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS
journal, August 2003

  • Thompson, Andrew; Schäfer, Jürgen; Kuhn, Karsten
  • Analytical Chemistry, Vol. 75, Issue 18
  • DOI: 10.1021/ac030267r
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