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Title: Advances in targeted proteomics and applications to biomedical research

Abstract

Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074–1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectivesmore » on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA USA
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1340855
Report Number(s):
PNNL-SA-120776
Journal ID: ISSN 1615-9853; 48666; 48505; 453040220
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Proteomics; Journal Volume: 16; Journal Issue: 15-16
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Shi, Tujin, Song, Ehwang, Nie, Song, Rodland, Karin D., Liu, Tao, Qian, Wei-Jun, and Smith, Richard D.. Advances in targeted proteomics and applications to biomedical research. United States: N. p., 2016. Web. doi:10.1002/pmic.201500449.
Shi, Tujin, Song, Ehwang, Nie, Song, Rodland, Karin D., Liu, Tao, Qian, Wei-Jun, & Smith, Richard D.. Advances in targeted proteomics and applications to biomedical research. United States. doi:10.1002/pmic.201500449.
Shi, Tujin, Song, Ehwang, Nie, Song, Rodland, Karin D., Liu, Tao, Qian, Wei-Jun, and Smith, Richard D.. Mon . "Advances in targeted proteomics and applications to biomedical research". United States. doi:10.1002/pmic.201500449.
@article{osti_1340855,
title = {Advances in targeted proteomics and applications to biomedical research},
author = {Shi, Tujin and Song, Ehwang and Nie, Song and Rodland, Karin D. and Liu, Tao and Qian, Wei-Jun and Smith, Richard D.},
abstractNote = {Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074–1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.},
doi = {10.1002/pmic.201500449},
journal = {Proteomics},
number = 15-16,
volume = 16,
place = {United States},
year = {Mon Aug 01 00:00:00 EDT 2016},
month = {Mon Aug 01 00:00:00 EDT 2016}
}