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Title: Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry

Abstract

Current proteomics approaches are comprised of both broad discovery measurements as well as more quantitative targeted measurements. These two different measurement types are used to initially identify potentially important proteins (e.g., candidate biomarkers) and then enable improved quantification for a limited number of selected proteins. However, both approaches suffer from limitations, particularly the lower sensitivity, accuracy, and quantitation precision for discovery approaches compared to targeted approaches, and the limited proteome coverage provided by targeted approaches. Herein, we describe a new proteomics approach that allows both discovery and targeted monitoring (DTM) in a single analysis using liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled peptides for target ions are spiked into tryptic digests and both the labeled and unlabeled peptides are broadly detected using LC-IMS-MS instrumentation, allowing the benefits of discovery and targeted approaches. To understand the possible improvement of the DTM approach, it was compared to LC-MS broad measurements using an accurate mass and time tag database and selected reaction monitoring (SRM) targeted measurements. The DTM results yielded greater peptide/protein coverage and a significant improvement in the detection of lower abundance species compared to LC-MS discovery measurements. DTM was also observed to have similar detectionmore » limits as SRM for the targeted measurements indicating its potential for combining the discovery and targeted approaches.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1340756
Report Number(s):
PNNL-SA-118308
Journal ID: ISSN 1535-9476; 48680; 48135; 453040220
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Molecular and Cellular Proteomics; Journal Volume: 15; Journal Issue: 12
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Burnum-Johnson, Kristin E., Nie, Song, Casey, Cameron P., Monroe, Matthew E., Orton, Daniel J., Ibrahim, Yehia M., Gritsenko, Marina A., Clauss, Therese R. W., Shukla, Anil K., Moore, Ronald J., Purvine, Samuel O., Shi, Tujin, Qian, Weijun, Liu, Tao, Baker, Erin S., and Smith, Richard D. Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry. United States: N. p., 2016. Web. doi:10.1074/mcp.M116.061143.
Burnum-Johnson, Kristin E., Nie, Song, Casey, Cameron P., Monroe, Matthew E., Orton, Daniel J., Ibrahim, Yehia M., Gritsenko, Marina A., Clauss, Therese R. W., Shukla, Anil K., Moore, Ronald J., Purvine, Samuel O., Shi, Tujin, Qian, Weijun, Liu, Tao, Baker, Erin S., & Smith, Richard D. Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry. United States. doi:10.1074/mcp.M116.061143.
Burnum-Johnson, Kristin E., Nie, Song, Casey, Cameron P., Monroe, Matthew E., Orton, Daniel J., Ibrahim, Yehia M., Gritsenko, Marina A., Clauss, Therese R. W., Shukla, Anil K., Moore, Ronald J., Purvine, Samuel O., Shi, Tujin, Qian, Weijun, Liu, Tao, Baker, Erin S., and Smith, Richard D. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry". United States. doi:10.1074/mcp.M116.061143.
@article{osti_1340756,
title = {Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry},
author = {Burnum-Johnson, Kristin E. and Nie, Song and Casey, Cameron P. and Monroe, Matthew E. and Orton, Daniel J. and Ibrahim, Yehia M. and Gritsenko, Marina A. and Clauss, Therese R. W. and Shukla, Anil K. and Moore, Ronald J. and Purvine, Samuel O. and Shi, Tujin and Qian, Weijun and Liu, Tao and Baker, Erin S. and Smith, Richard D.},
abstractNote = {Current proteomics approaches are comprised of both broad discovery measurements as well as more quantitative targeted measurements. These two different measurement types are used to initially identify potentially important proteins (e.g., candidate biomarkers) and then enable improved quantification for a limited number of selected proteins. However, both approaches suffer from limitations, particularly the lower sensitivity, accuracy, and quantitation precision for discovery approaches compared to targeted approaches, and the limited proteome coverage provided by targeted approaches. Herein, we describe a new proteomics approach that allows both discovery and targeted monitoring (DTM) in a single analysis using liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled peptides for target ions are spiked into tryptic digests and both the labeled and unlabeled peptides are broadly detected using LC-IMS-MS instrumentation, allowing the benefits of discovery and targeted approaches. To understand the possible improvement of the DTM approach, it was compared to LC-MS broad measurements using an accurate mass and time tag database and selected reaction monitoring (SRM) targeted measurements. The DTM results yielded greater peptide/protein coverage and a significant improvement in the detection of lower abundance species compared to LC-MS discovery measurements. DTM was also observed to have similar detection limits as SRM for the targeted measurements indicating its potential for combining the discovery and targeted approaches.},
doi = {10.1074/mcp.M116.061143},
journal = {Molecular and Cellular Proteomics},
number = 12,
volume = 15,
place = {United States},
year = 2016,
month = 9
}
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