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Title: Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples

Abstract

Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).

Authors:
 [1];  [2];  [3];  [1];  [4];  [4];  [3];  [4];  [3];  [3];  [4];  [1]; ORCiD logo [5]; ORCiD logo [6]
  1. Univ. of Western Australia, Perth, WA (Australia). ARC Centre of Excellence in Plant Energy Biology
  2. MRC Lab. of Molecular Biology, Cambridge (United Kingdom)
  3. Univ. of Cambridge (United Kingdom). Dept. of Biochemistry
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst.
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst.; Univ. of Melbourne (Australia). School of BioSciences
  6. Univ. of Cambridge (United Kingdom). Dept. of Biochemistry; Copenhagen Univ. (Denmark). Plant and Environmental Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Australian Research Council (ARC)
OSTI Identifier:
1432223
Grant/Contract Number:  
AC02-05CH11231; CE140100008; FT13010123
Resource Type:
Accepted Manuscript
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Volume: 92; Journal Issue: 6; Related Information: © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd; Journal ID: ISSN 0960-7412
Publisher:
Society for Experimental Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Arabidopsis; organelles; tissues; protein abundance; shotgun proteomics; selected reaction monitoring

Citation Formats

Hooper, Cornelia M., Stevens, Tim J., Saukkonen, Anna, Castleden, Ian R., Singh, Pragya, Mann, Gregory W., Fabre, Bertrand, Ito, Jun, Deery, Michael J., Lilley, Kathryn S., Petzold, Christopher J., Millar, A. Harvey, Heazlewood, Joshua L., and Parsons, Harriet T. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. United States: N. p., 2017. Web. doi:10.1111/tpj.13743.
Hooper, Cornelia M., Stevens, Tim J., Saukkonen, Anna, Castleden, Ian R., Singh, Pragya, Mann, Gregory W., Fabre, Bertrand, Ito, Jun, Deery, Michael J., Lilley, Kathryn S., Petzold, Christopher J., Millar, A. Harvey, Heazlewood, Joshua L., & Parsons, Harriet T. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. United States. doi:10.1111/tpj.13743.
Hooper, Cornelia M., Stevens, Tim J., Saukkonen, Anna, Castleden, Ian R., Singh, Pragya, Mann, Gregory W., Fabre, Bertrand, Ito, Jun, Deery, Michael J., Lilley, Kathryn S., Petzold, Christopher J., Millar, A. Harvey, Heazlewood, Joshua L., and Parsons, Harriet T. Thu . "Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples". United States. doi:10.1111/tpj.13743. https://www.osti.gov/servlets/purl/1432223.
@article{osti_1432223,
title = {Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples},
author = {Hooper, Cornelia M. and Stevens, Tim J. and Saukkonen, Anna and Castleden, Ian R. and Singh, Pragya and Mann, Gregory W. and Fabre, Bertrand and Ito, Jun and Deery, Michael J. and Lilley, Kathryn S. and Petzold, Christopher J. and Millar, A. Harvey and Heazlewood, Joshua L. and Parsons, Harriet T.},
abstractNote = {Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).},
doi = {10.1111/tpj.13743},
journal = {The Plant Journal},
number = 6,
volume = 92,
place = {United States},
year = {2017},
month = {10}
}

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Works referenced in this record:

Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling
journal, January 2012

  • Elmore, James Mitch; Liu, Jun; Smith, Barrett
  • Molecular & Cellular Proteomics, Vol. 11, Issue 4
  • DOI: 10.1074/mcp.M111.014555

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
journal, December 2006

  • Lu, Peng; Vogel, Christine; Wang, Rong
  • Nature Biotechnology, Vol. 25, Issue 1
  • DOI: 10.1038/nbt1270

Alternate partial root-zone irrigation reduces bundle-sheath cell leakage to CO2 and enhances photosynthetic capacity in maize leaves
journal, November 2011

  • Wang, Zhenchang; Kang, Shaozhong; Jensen, Christian R.
  • Journal of Experimental Botany, Vol. 63, Issue 3
  • DOI: 10.1093/jxb/err331

MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species
journal, January 2012


PPDB, the Plant Proteomics Database at Cornell
journal, October 2008

  • Sun, Qi; Zybailov, Boris; Majeran, Wojciech
  • Nucleic Acids Research, Vol. 37, Issue suppl_1
  • DOI: 10.1093/nar/gkn654

Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents
journal, September 2004

  • Ross, Philip L.; Huang, Yulin N.; Marchese, Jason N.
  • Molecular & Cellular Proteomics, Vol. 3, Issue 12
  • DOI: 10.1074/mcp.M400129-MCP200

Quantitative Proteomics in Plants: Choices in Abundance
journal, November 2007


Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes
journal, March 2009


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

  • Thompson, Andrew; Schäfer, Jürgen; Kuhn, Karsten
  • Analytical Chemistry, Vol. 75, Issue 8
  • DOI: 10.1021/ac0262560

Arabidopsis Plasmodesmal Proteome
journal, April 2011


Sorting Signals, N-Terminal Modifications and Abundance of the Chloroplast Proteome
journal, April 2008


SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis
journal, November 2012

  • Tanz, Sandra K.; Castleden, Ian; Hooper, Cornelia M.
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1151

A draft map of the mouse pluripotent stem cell spatial proteome
journal, January 2016

  • Christoforou, Andy; Mulvey, Claire M.; Breckels, Lisa M.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms9992

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life
journal, April 2012

  • Wang, M.; Weiss, M.; Simonovic, M.
  • Molecular & Cellular Proteomics, Vol. 11, Issue 8
  • DOI: 10.1074/mcp.O111.014704

Combining Experimental and Predicted Datasets for Determination of the Subcellular Location of Proteins in Arabidopsis
journal, October 2005

  • Heazlewood, Joshua L.; Tonti-Filippini, Julian; Verboom, Robert E.
  • Plant Physiology, Vol. 139, Issue 2
  • DOI: 10.1104/pp.105.065532

Analysis of the Arabidopsis Cytosolic Proteome Highlights Subcellular Partitioning of Central Plant Metabolism
journal, April 2011

  • Ito, Jun; Batth, Tanveer S.; Petzold, Christopher J.
  • Journal of Proteome Research, Vol. 10, Issue 4
  • DOI: 10.1021/pr1009433

An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets
journal, August 2007


Elevated CO2 induces physiological, biochemical and structural changes in leaves of Arabidopsis thaliana
journal, October 2006


If the antibody fails - a mass Western approach
journal, September 2008


Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search
journal, October 2002

  • Keller, Andrew; Nesvizhskii, Alexey I.; Kolker, Eugene
  • Analytical Chemistry, Vol. 74, Issue 20
  • DOI: 10.1021/ac025747h

On protein abundance distributions in complex mixtures
journal, January 2013


Correlations between RNA and protein expression profiles in 23 human cell lines
journal, January 2009


Legume proteomics: Progress, prospects, and challenges
journal, December 2015


Putative Glycosyltransferases and Other Plant Golgi Apparatus Proteins Are Revealed by LOPIT Proteomics
journal, August 2012

  • Nikolovski, Nino; Rubtsov, Denis; Segura, Marcelo P.
  • Plant Physiology, Vol. 160, Issue 2
  • DOI: 10.1104/pp.112.204263

Selected Reaction Monitoring to Determine Protein Abundance in Arabidopsis Using the Arabidopsis Proteotypic Predictor
journal, December 2013

  • Taylor, Nicolas L.; Fenske, Ricarda; Castleden, Ian
  • Plant Physiology, Vol. 164, Issue 2
  • DOI: 10.1104/pp.113.225524

Identification of Trans-Golgi Network Proteins in Arabidopsis thaliana Root Tissue
journal, December 2013

  • Groen, Arnoud J.; Sancho-Andrés, Gloria; Breckels, Lisa M.
  • Journal of Proteome Research, Vol. 13, Issue 2
  • DOI: 10.1021/pr4008464

SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome
journal, August 2014


The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
journal, December 2011

  • Lamesch, Philippe; Berardini, Tanya Z.; Li, Donghui
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1090

The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra
journal, May 2007

  • Shilov, Ignat V.; Seymour, Sean L.; Patel, Alpesh A.
  • Molecular & Cellular Proteomics, Vol. 6, Issue 9
  • DOI: 10.1074/mcp.T600050-MCP200

Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis
journal, January 2009

  • Piques, Maria; Schulze, Waltraud X.; Höhne, Melanie
  • Molecular Systems Biology, Vol. 5, Issue 1
  • DOI: 10.1038/msb.2009.68

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines
journal, March 2015

  • Wang, Mingcong; Herrmann, Christina J.; Simonovic, Milan
  • PROTEOMICS, Vol. 15, Issue 18
  • DOI: 10.1002/pmic.201400441

Beyond the Western front: targeted proteomics and organelle abundance profiling
journal, May 2015


Resource: Mapping the Triticum aestivum proteome
journal, February 2017

  • Duncan, Owen; Trösch, Josua; Fenske, Ricarda
  • The Plant Journal, Vol. 89, Issue 3
  • DOI: 10.1111/tpj.13402

Distribution of superoxide and hydrogen peroxide in Arabidopsis root and their influence on root development: possible interaction with peroxidases
journal, April 2007


AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope Proteins
journal, January 2010

  • Ferro, Myriam; Brugière, Sabine; Salvi, Daniel
  • Molecular & Cellular Proteomics, Vol. 9, Issue 6
  • DOI: 10.1074/mcp.M900325-MCP200

E3 ubiquitin ligase SP1 regulates peroxisome biogenesis in Arabidopsis
journal, October 2016

  • Pan, Ronghui; Satkovich, John; Hu, Jianping
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 46
  • DOI: 10.1073/pnas.1613530113

Heterogeneity of the Mitochondrial Proteome for Photosynthetic and Non-photosynthetic Arabidopsis Metabolism
journal, April 2008

  • Lee, Chun Pong; Eubel, Holger; O'Toole, Nicholas
  • Molecular & Cellular Proteomics, Vol. 7, Issue 7
  • DOI: 10.1074/mcp.M700535-MCP200

SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations
journal, November 2016

  • Hooper, Cornelia M.; Castleden, Ian R.; Tanz, Sandra K.
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1041

WallProtDB, a database resource for plant cell wall proteomics
journal, January 2015


The PEROXIN11 Protein Family Controls Peroxisome Proliferation in Arabidopsis
journal, January 2007


Mapping the Arabidopsis organelle proteome
journal, April 2006

  • Dunkley, T. P. J.; Hester, S.; Shadforth, I. P.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 17
  • DOI: 10.1073/pnas.0506958103

SUBA: the Arabidopsis Subcellular Database
journal, October 2006

  • Heazlewood, Joshua L.; Verboom, Robert E.; Tonti-Filippini, Julian
  • Nucleic Acids Research, Vol. 35, Issue suppl_1
  • DOI: 10.1093/nar/gkl863

Isolation and Proteomic Characterization of the Arabidopsis Golgi Defines Functional and Novel Components Involved in Plant Cell Wall Biosynthesis
journal, March 2012

  • Parsons, Harriet T.; Christiansen, Katy; Knierim, Bernhard
  • Plant Physiology, Vol. 159, Issue 1
  • DOI: 10.1104/pp.111.193151

The Design of a Quantitative Western Blot Experiment
journal, January 2014

  • Taylor, Sean C.; Posch, Anton
  • BioMed Research International, Vol. 2014
  • DOI: 10.1155/2014/361590

The different fates of mitochondria and chloroplasts during dark-induced senescence in Arabidopsis leaves
journal, December 2007


Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings
journal, February 2016

  • de Michele, Roberto; McFarlane, Heather E.; Parsons, Harriet T.
  • Journal of Proteome Research, Vol. 15, Issue 3
  • DOI: 10.1021/acs.jproteome.5b00876

Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL)
journal, November 2015

  • Hooper, Cornelia M.; Castleden, Ian R.; Aryamanesh, Nader
  • Plant and Cell Physiology, Vol. 57, Issue 1
  • DOI: 10.1093/pcp/pcv170

pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana
journal, January 2011

  • Baerenfaller, Katja; Hirsch-Hoffmann, Matthias; Svozil, Julia
  • Integrative Biology, Vol. 3, Issue 3
  • DOI: 10.1039/c0ib00078g