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Title: Nanoproteomics Comes of Age

Abstract

Substantial technological advances have been made towards making enabling a nanoproteomics capability, i.e., quantitative proteome profiling of small cell populations (<5000 cells). These advances include new technologies or approaches from all areas of the overall proteomics workflow ranging from sample isolation, sample processing, high resolution separations, MS detection, to informatics. Herein we present a brief review of the recent technological advances, the current state of nanoproteomics, and future perspectives on both the technological direction and potential enabling applications.

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. BATTELLE (PACIFIC NW LAB)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1582608
Report Number(s):
PNNL-SA-136396
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Expert Review of Proteomics
Additional Journal Information:
Journal Volume: 15; Journal Issue: 11
Country of Publication:
United States
Language:
English
Subject:
Nanoproteomics, small cell populations, single cell proteomics, spatially resolved, nanoPOTS, Laser capture microdissection

Citation Formats

Zhu, Ying, Piehowski, Paul D., Kelly, Ryan T., and Qian, Weijun. Nanoproteomics Comes of Age. United States: N. p., 2018. Web. doi:10.1080/14789450.2018.1537787.
Zhu, Ying, Piehowski, Paul D., Kelly, Ryan T., & Qian, Weijun. Nanoproteomics Comes of Age. United States. doi:10.1080/14789450.2018.1537787.
Zhu, Ying, Piehowski, Paul D., Kelly, Ryan T., and Qian, Weijun. Thu . "Nanoproteomics Comes of Age". United States. doi:10.1080/14789450.2018.1537787.
@article{osti_1582608,
title = {Nanoproteomics Comes of Age},
author = {Zhu, Ying and Piehowski, Paul D. and Kelly, Ryan T. and Qian, Weijun},
abstractNote = {Substantial technological advances have been made towards making enabling a nanoproteomics capability, i.e., quantitative proteome profiling of small cell populations (<5000 cells). These advances include new technologies or approaches from all areas of the overall proteomics workflow ranging from sample isolation, sample processing, high resolution separations, MS detection, to informatics. Herein we present a brief review of the recent technological advances, the current state of nanoproteomics, and future perspectives on both the technological direction and potential enabling applications.},
doi = {10.1080/14789450.2018.1537787},
journal = {Expert Review of Proteomics},
number = 11,
volume = 15,
place = {United States},
year = {2018},
month = {11}
}

Works referenced in this record:

Mass-spectrometric exploration of proteome structure and function
journal, September 2016


The Coming Age of Complete, Accurate, and Ubiquitous Proteomes
journal, February 2013


Advances in microscale separations towards nanoproteomics applications
journal, November 2017


Development of Mass Spectrometry-Based Shotgun Method for Proteome Analysis of 500 to 5000 Cancer Cells
journal, March 2010

  • Wang, Nan; Xu, Mingguo; Wang, Peng
  • Analytical Chemistry, Vol. 82, Issue 6
  • DOI: 10.1021/ac9023022

Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method
journal, December 2005

  • Wang, Haixing; Qian, Wei-Jun; Mottaz, Heather M.
  • Journal of Proteome Research, Vol. 4, Issue 6
  • DOI: 10.1021/pr050160f

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells
journal, February 2018


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 International Edition, Vol. 57, Issue 38
  • DOI: 10.1002/anie.201802843

Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI?
journal, May 2003

  • Schmidt, Andrea; Karas, Michael; Dülcks, Thomas
  • Journal of the American Society for Mass Spectrometry, Vol. 14, Issue 5
  • DOI: 10.1016/S1044-0305(03)00128-4

Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last?
journal, September 1994

  • Wilm, Matthias S.; Mann, Matthias
  • International Journal of Mass Spectrometry and Ion Processes, Vol. 136, Issue 2-3
  • DOI: 10.1016/0168-1176(94)04024-9

Analytical Properties of the Nanoelectrospray Ion Source
journal, January 1996

  • Wilm, Matthias; Mann, Matthias
  • Analytical Chemistry, Vol. 68, Issue 1
  • DOI: 10.1021/ac9509519

Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS
journal, January 2004

  • Shen, Yufeng; Tolić, Nikola; Masselon, Christophe
  • Analytical Chemistry, Vol. 76, Issue 1, p. 144-154
  • DOI: 10.1021/ac030096q

Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples
journal, April 2018


An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood
journal, March 2015

  • Li, Siyang; Plouffe, Brian D.; Belov, Arseniy M.
  • Molecular & Cellular Proteomics, Vol. 14, Issue 6
  • DOI: 10.1074/mcp.M114.045724

Ultrasensitive and Fast Bottom-up Analysis of Femtogram Amounts of Complex Proteome Digests
journal, October 2013

  • Sun, Liangliang; Zhu, Guijie; Zhao, Yimeng
  • Angewandte Chemie International Edition, Vol. 52, Issue 51
  • DOI: 10.1002/anie.201308139

Orbitrap Mass Spectrometry
journal, May 2013

  • Zubarev, Roman A.; Makarov, Alexander
  • Analytical Chemistry, Vol. 85, Issue 11
  • DOI: 10.1021/ac4001223

Dynamics of ions of intact proteins in the Orbitrap mass analyzer
journal, August 2009

  • Makarov, Alexander; Denisov, Eduard
  • Journal of the American Society for Mass Spectrometry, Vol. 20, Issue 8
  • DOI: 10.1016/j.jasms.2009.03.024

High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies
journal, October 2012

  • Rose, Rebecca J.; Damoc, Eugen; Denisov, Eduard
  • Nature Methods, Vol. 9, Issue 11
  • DOI: 10.1038/nmeth.2208

An Ion Funnel Interface for Improved Ion Focusing and Sensitivity Using Electrospray Ionization Mass Spectrometry
journal, October 1998

  • Shaffer, Scott A.; Prior, David C.; Anderson, Gordon A.
  • Analytical Chemistry, Vol. 70, Issue 19, p. 4111-4119
  • DOI: 10.1021/ac9802170

Subambient Pressure Ionization with Nanoelectrospray Source and Interface for Improved Sensitivity in Mass Spectrometry
journal, March 2008

  • Page, Jason S.; Tang, Keqi; Kelly, Ryan T.
  • Analytical Chemistry, Vol. 80, Issue 5
  • DOI: 10.1021/ac702354b

Achieving 50% Ionization Efficiency in Subambient Pressure Ionization with Nanoelectrospray
journal, November 2010

  • Marginean, Ioan; Page, Jason S.; Tolmachev, Aleksey V.
  • Analytical Chemistry, Vol. 82, Issue 22
  • DOI: 10.1021/ac1019123

Proteomic analyses using an accurate mass and time tag strategy
journal, October 2004

  • Paša-Tolić, Ljiljana; Masselon, Christophe; Barry, Richard C.
  • BioTechniques, Vol. 37, Issue 4
  • DOI: 10.2144/04374RV01

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
journal, October 2016


IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts
journal, May 2018

  • Shen, Xiaomeng; Shen, Shichen; Li, Jun
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 21
  • DOI: 10.1073/pnas.1800541115

Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling
journal, April 2016


SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities
journal, March 2016

  • Huang, Eric L.; Piehowski, Paul D.; Orton, Daniel J.
  • Endocrinology, Vol. 157, Issue 3
  • DOI: 10.1210/en.2015-1821

Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples
journal, December 2016

  • Clair, Geremy; Piehowski, Paul D.; Nicola, Teodora
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep39223

Quantitative proteomic analysis of single pancreatic islets
journal, October 2009

  • Waanders, Leonie F.; Chwalek, Karolina; Monetti, Mara
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 45
  • DOI: 10.1073/pnas.0908351106

Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis
journal, June 2015


Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to Nanodroplets
journal, June 2018

  • Zhu, Ying; Dou, Maowei; Piehowski, Paul D.
  • Molecular & Cellular Proteomics, Vol. 17, Issue 9
  • DOI: 10.1074/mcp.TIR118.000686

Ultrasensitive proteome analysis using paramagnetic bead technology
journal, October 2014

  • Hughes, Christopher S.; Foehr, Sophia; Garfield, David A.
  • Molecular Systems Biology, Vol. 10, Issue 10
  • DOI: 10.15252/msb.20145625

Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes
journal, May 2016

  • Virant-Klun, Irma; Leicht, Stefan; Hughes, Christopher
  • Molecular & Cellular Proteomics, Vol. 15, Issue 8
  • DOI: 10.1074/mcp.M115.056887

Laser-capture microdissection
journal, June 2006

  • Espina, Virginia; Wulfkuhle, Julia D.; Calvert, Valerie S.
  • Nature Protocols, Vol. 1, Issue 2
  • DOI: 10.1038/nprot.2006.85

Set of Novel Automated Quantitative Microproteomics Protocols for Small Sample Amounts and Its Application to Kidney Tissue Substructures
journal, November 2016

  • de Graaf, Erik Leonardus; Pellegrini, Davide; McDonnell, Liam A.
  • Journal of Proteome Research, Vol. 15, Issue 12
  • DOI: 10.1021/acs.jproteome.6b00889

NanoLC-MS coupling of liquid microjunction microextraction for on-tissue proteomic analysis
journal, July 2017

  • Quanico, Jusal; Franck, Julien; Cardon, Tristan
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1865, Issue 7
  • DOI: 10.1016/j.bbapap.2016.11.002

Enhanced Spatially Resolved Proteomics Using On-Tissue Hydrogel-Mediated Protein Digestion
journal, February 2017


Top Down proteomics: Facts and perspectives
journal, March 2014

  • Catherman, Adam D.; Skinner, Owen S.; Kelleher, Neil L.
  • Biochemical and Biophysical Research Communications, Vol. 445, Issue 4
  • DOI: 10.1016/j.bbrc.2014.02.041

Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway
journal, March 2018