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Title: Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples

Authors:
 [1];  [1];  [2];  [2];  [3];  [3];  [1];  [2];  [2];  [1]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division
  3. California Inst. of Technology (CalTech), Pasadena, CA (United States). Division of Geological and Planetary Sciences
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
OSTI Identifier:
1395289
Alternate Identifier(s):
OSTI ID: 1379954; OSTI ID: 1413502
Report Number(s):
PNNL-SA-125645
Journal ID: ISSN 1387-3806; PII: S1387380617302130
Grant/Contract Number:  
AC02-05CH11231; AC05-76RL01830; P41 GM103493; R21 EB020976-01A1; 1R21EB020976-01A1
Resource Type:
Accepted Manuscript
Journal Name:
International Journal of Mass Spectrometry
Additional Journal Information:
Journal Volume: 427; Journal ID: ISSN 1387-3806
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Ultrasensitive; NanoLC; Orbitrap Fusion Lumos; Match between runs; Subnanogram proteomics; Small cell populations; 97 MATHEMATICS AND COMPUTING; ultrasensitive; nanoLC; match between runs; subnanogram proteomics; small cell populations

Citation Formats

Zhu, Ying, Zhao, Rui, Piehowski, Paul D., Moore, Ronald J., Lim, Sujung, Orphan, Victoria J., Paša-Tolić, Ljiljana, Qian, Wei-Jun, Smith, Richard D., and Kelly, Ryan T. Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples. United States: N. p., 2017. Web. doi:10.1016/J.IJMS.2017.08.016.
Zhu, Ying, Zhao, Rui, Piehowski, Paul D., Moore, Ronald J., Lim, Sujung, Orphan, Victoria J., Paša-Tolić, Ljiljana, Qian, Wei-Jun, Smith, Richard D., & Kelly, Ryan T. Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples. United States. doi:https://doi.org/10.1016/J.IJMS.2017.08.016
Zhu, Ying, Zhao, Rui, Piehowski, Paul D., Moore, Ronald J., Lim, Sujung, Orphan, Victoria J., Paša-Tolić, Ljiljana, Qian, Wei-Jun, Smith, Richard D., and Kelly, Ryan T. Fri . "Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples". United States. doi:https://doi.org/10.1016/J.IJMS.2017.08.016. https://www.osti.gov/servlets/purl/1395289.
@article{osti_1395289,
title = {Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples},
author = {Zhu, Ying and Zhao, Rui and Piehowski, Paul D. and Moore, Ronald J. and Lim, Sujung and Orphan, Victoria J. and Paša-Tolić, Ljiljana and Qian, Wei-Jun and Smith, Richard D. and Kelly, Ryan T.},
abstractNote = {},
doi = {10.1016/J.IJMS.2017.08.016},
journal = {International Journal of Mass Spectrometry},
number = ,
volume = 427,
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 11 works
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Figures / Tables:

Fig. 1 Fig. 1: Comparison of LC column size on the performance of proteomic analysis. (a1–a2) Base peak chromatograms of 10-ng tryptic digest of Shewanella oneidensis with (a1)75-μm and (a2) 30-μm i.d. LC columns and a LTQ-Orbitrap MS. Y axis was fixed at 8E6 to show the signal gain for the 30-μmmore » LC. (b) Peptide intensity ratio between 30-μm and 75-μm i.d. LC. Each point in the chart corresponds to a peptide identified from both LC columns. (c) The number of unique peptides and protein groups identified with 75-μm and 30-μm LC columns. In each condition, two replicates were analyzed and averaged to generate results. LC conditions: 30-μm i.d. column operated at 60 nL/min;75-μm i.d. column operated at 350 nL/min; a 150-min gradient from 5% to 28% Buffer B was used.« less

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Works referencing / citing this record:

Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS
journal, June 2018

  • Zhu, Ying; Clair, Geremy; Chrisler, William B.
  • Angewandte Chemie, Vol. 130, Issue 38
  • DOI: 10.1002/ange.201802843

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journal, June 2018

  • Zhu, Ying; Clair, Geremy; Chrisler, William B.
  • Angewandte Chemie International Edition, Vol. 57, Issue 38
  • DOI: 10.1002/anie.201802843

Nanowell-mediated multidimensional separations combining nanoLC with SLIM IM-MS for rapid, high-peak-capacity proteomic analyses
journal, November 2018

  • Dou, Maowei; Chouinard, Christopher D.; Zhu, Ying
  • Analytical and Bioanalytical Chemistry, Vol. 411, Issue 21
  • DOI: 10.1007/s00216-018-1452-5

Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution
journal, January 2020


New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells
journal, January 2019

  • Couvillion, Sneha P.; Zhu, Ying; Nagy, Gabe
  • The Analyst, Vol. 144, Issue 3
  • DOI: 10.1039/c8an01574k

Nanowell-mediated two-dimensional liquid chromatography enables deep proteome profiling of <1000 mammalian cells
journal, January 2018

  • Dou, Maowei; Zhu, Ying; Liyu, Andrey
  • Chemical Science, Vol. 9, Issue 34
  • DOI: 10.1039/c8sc02680g

Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry
journal, April 2019

  • Amon, Sabine; Meier-Abt, Fabienne; Gillet, Ludovic C.
  • Molecular & Cellular Proteomics, Vol. 18, Issue 7
  • DOI: 10.1074/mcp.tir119.001431

Nanoproteomics comes of age
journal, October 2018


Optimization of Data-Independent Acquisition Mass Spectrometry for Deep and Highly Sensitive Proteomic Analysis
journal, November 2019

  • Kawashima, Yusuke; Watanabe, Eiichiro; Umeyama, Taichi
  • International Journal of Molecular Sciences, Vol. 20, Issue 23
  • DOI: 10.3390/ijms20235932

Single-cell proteomics reveals changes in expression during hair-cell development
journal, November 2019

  • Zhu, Ying; Scheibinger, Mirko; Ellwanger, Daniel Christian
  • eLife, Vol. 8
  • DOI: 10.7554/elife.50777

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