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Title: Phosphoproteomics in photosynthetic organisms: Proteomics and 2DE

 [1];  [1];  [1];  [1]
  1. Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill NC USA
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Center for Advanced Biofuel Systems (CABS)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
DOE Contract Number:  
Resource Type:
Journal Article
Journal Name:
Additional Journal Information:
Journal Volume: 35; Journal Issue: 24; Related Information: CABS partners with the Donald Danforth Plant Science Center (lead); Michigan State University; New Mexico Consortium; University of Nebraska; University of Missouri – St. Louis; Washington State University; Journal ID: ISSN 0173-0835
Country of Publication:
United States

Citation Formats

Slade, William O., Werth, Emily G., Chao, Alex, and Hicks, Leslie M. Phosphoproteomics in photosynthetic organisms: Proteomics and 2DE. United States: N. p., 2014. Web. doi:10.1002/elps.201400154.
Slade, William O., Werth, Emily G., Chao, Alex, & Hicks, Leslie M. Phosphoproteomics in photosynthetic organisms: Proteomics and 2DE. United States. doi:10.1002/elps.201400154.
Slade, William O., Werth, Emily G., Chao, Alex, and Hicks, Leslie M. Thu . "Phosphoproteomics in photosynthetic organisms: Proteomics and 2DE". United States. doi:10.1002/elps.201400154.
title = {Phosphoproteomics in photosynthetic organisms: Proteomics and 2DE},
author = {Slade, William O. and Werth, Emily G. and Chao, Alex and Hicks, Leslie M.},
abstractNote = {},
doi = {10.1002/elps.201400154},
journal = {Electrophoresis},
issn = {0173-0835},
number = 24,
volume = 35,
place = {United States},
year = {2014},
month = {7}

Works referenced in this record:

Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
journal, July 2003

Quantitative plant phosphoproteomics
journal, October 2011

  • Kline-Jonakin, Kelli G.; Barrett-Wilt, Gregory A.; Sussman, Michael R.
  • Current Opinion in Plant Biology, Vol. 14, Issue 5
  • DOI: 10.1016/j.pbi.2011.06.008

Targeted proteome investigation via selected reaction monitoring mass spectrometry
journal, June 2012

Progress and challenges for abiotic stress proteomics of crop plants
journal, June 2013

  • Barkla, Bronwyn J.; Vera-Estrella, Rosario; Pantoja, Omar
  • PROTEOMICS, Vol. 13, Issue 12-13
  • DOI: 10.1002/pmic.201200401

Comprehensive Comparison of iTRAQ and Label-free LC-Based Quantitative Proteomics Approaches Using Two Chlamydomonas reinhardtii Strains of Interest for Biofuels Engineering
journal, December 2011

  • Wang, Hongxia; Alvarez, Sophie; Hicks, Leslie M.
  • Journal of Proteome Research, Vol. 11, Issue 1
  • DOI: 10.1021/pr2008225

Identification of Novel PAMP-Triggered Phosphorylation and Dephosphorylation Events in Arabidopsis thaliana by Quantitative Phosphoproteomic Analysis
journal, March 2014

  • Rayapuram, Naganand; Bonhomme, Ludovic; Bigeard, Jean
  • Journal of Proteome Research, Vol. 13, Issue 4
  • DOI: 10.1021/pr401268v

Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns
journal, April 2005

  • Larsen, Martin R.; Thingholm, Tine E.; Jensen, Ole N.
  • Molecular & Cellular Proteomics, Vol. 4, Issue 7
  • DOI: 10.1074/mcp.T500007-MCP200

Interrogating the human genome using uninterpreted mass spectrometry data
journal, April 2001

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

Histidine Kinase Activity of the Ethylene Receptor ETR1 Facilitates the Ethylene Response in Arabidopsis
journal, March 2012

  • Hall, Brenda P.; Shakeel, Samina N.; Amir, Madiha
  • Plant Physiology, Vol. 159, Issue 2
  • DOI: 10.1104/pp.112.196790

Extending SILAC to Proteomics of Plant Cell Lines
journal, May 2011

  • Schütz, Wolfgang; Hausmann, Niklas; Krug, Karsten
  • The Plant Cell, Vol. 23, Issue 5
  • DOI: 10.1105/tpc.110.082016

Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation
journal, May 2011

A Peptide Hormone and Its Receptor Protein Kinase Regulate Plant Cell Expansion
journal, January 2014

Hydrophilic Interaction Chromatography Reduces the Complexity of the Phosphoproteome and Improves Global Phosphopeptide Isolation and Detection
journal, January 2008

Precision, Proteome Coverage, and Dynamic Range of Arabidopsis Proteome Profiling Using 15 N Metabolic Labeling and Label-free Approaches
journal, May 2012

  • Arsova, Borjana; Zauber, Henrik; Schulze, Waltraud X.
  • Molecular & Cellular Proteomics, Vol. 11, Issue 9
  • DOI: 10.1074/mcp.M112.017178

Statistical Inference from Multiple iTRAQ Experiments without Using Common Reference Standards
journal, January 2013

  • Herbrich, Shelley M.; Cole, Robert N.; West, Keith P.
  • Journal of Proteome Research, Vol. 12, Issue 2
  • DOI: 10.1021/pr300624g

Plant phosphoproteomics: A long road ahead
journal, October 2006

  • Kersten, Birgit; Agrawal, Ganesh Kumar; Iwahashi, Hitoshi
  • PROTEOMICS, Vol. 6, Issue 20
  • DOI: 10.1002/pmic.200600232

Digestion and depletion of abundant proteins improves proteomic coverage
journal, November 2012

  • Fonslow, Bryan R.; Stein, Benjamin D.; Webb, Kristofor J.
  • Nature Methods, Vol. 10, Issue 1
  • DOI: 10.1038/nmeth.2250

A call for transparent reporting to optimize the predictive value of preclinical research
journal, October 2012

  • Landis, Story C.; Amara, Susan G.; Asadullah, Khusru
  • Nature, Vol. 490, Issue 7419
  • DOI: 10.1038/nature11556

Proteome Turnover in the Green Alga Ostreococcus tauri by Time Course 15 N Metabolic Labeling Mass Spectrometry
journal, December 2011

  • Martin, Sarah F.; Munagapati, Vijaya S.; Salvo-Chirnside, Eliane
  • Journal of Proteome Research, Vol. 11, Issue 1
  • DOI: 10.1021/pr2009302

Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses
journal, August 2012

  • McAlister, Graeme C.; Huttlin, Edward L.; Haas, Wilhelm
  • Analytical Chemistry, Vol. 84, Issue 17
  • DOI: 10.1021/ac301572t

Proteomics of wine additives: Mining for the invisible via combinatorial peptide ligand libraries
journal, August 2010

Phosphoproteomic Analysis of Rhodopseudomonas palustris Reveals the Role of Pyruvate Phosphate Dikinase Phosphorylation in Lipid Production
journal, October 2012

  • Hu, Chia-Wei; Lin, Miao-Hsia; Huang, Hsuan-Cheng
  • Journal of Proteome Research, Vol. 11, Issue 11
  • DOI: 10.1021/pr300582p

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics
journal, October 2011

  • Ting, Lily; Rad, Ramin; Gygi, Steven P.
  • Nature Methods, Vol. 8, Issue 11
  • DOI: 10.1038/nmeth.1714

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging
journal, October 2011

  • Wenger, Craig D.; Lee, M. Violet; Hebert, Alexander S.
  • Nature Methods, Vol. 8, Issue 11
  • DOI: 10.1038/nmeth.1716

Phosphopeptide enrichment using metal oxide affinity chromatography
journal, February 2010

Increased Selectivity, Analytical Precision, and Throughput in Targeted Proteomics
journal, July 2010

  • Kiyonami, Reiko; Schoen, Alan; Prakash, Amol
  • Molecular & Cellular Proteomics, Vol. 10, Issue 2
  • DOI: 10.1074/mcp.M110.002931

Panning for phosphohistidine
journal, May 2013

  • Piggott, Matthew J.; Attwood, Paul V.
  • Nature Chemical Biology, Vol. 9, Issue 7
  • DOI: 10.1038/nchembio.1273

Tackling the plant proteome: practical approaches, hurdles and experimental tools
journal, September 2004

Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance
journal, August 2012

  • Sun, F.; Ding, Y.; Ji, Q.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 38
  • DOI: 10.1073/pnas.1205952109

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions
journal, May 2012

  • Picotti, Paola; Aebersold, Ruedi
  • Nature Methods, Vol. 9, Issue 6
  • DOI: 10.1038/nmeth.2015

Addressing Accuracy and Precision Issues in iTRAQ Quantitation
journal, April 2010

  • Karp, Natasha A.; Huber, Wolfgang; Sadowski, Pawel G.
  • Molecular & Cellular Proteomics, Vol. 9, Issue 9
  • DOI: 10.1074/mcp.M900628-MCP200

Robust and Sensitive iTRAQ Quantification on an LTQ Orbitrap Mass Spectrometer
journal, May 2008

  • Bantscheff, Marcus; Boesche, Markus; Eberhard, Dirk
  • Molecular & Cellular Proteomics, Vol. 7, Issue 9
  • DOI: 10.1074/mcp.M800029-MCP200

Using phosphoproteomics to reveal signalling dynamics in plants
journal, September 2007

Protein phosphorylation and protein phosphatasesDe Panne, Belgium, September 19–24, 1999
journal, February 2000

A critical evaluation of sample extraction techniques for enhanced proteomic analysis of recalcitrant plant tissues
journal, September 2004

Quantitative Phosphoproteomics after Auxin-stimulated Lateral Root Induction Identifies an SNX1 Protein Phosphorylation Site Required for Growth
journal, January 2013

  • Zhang, Hongtao; Zhou, Houjiang; Berke, Lidija
  • Molecular & Cellular Proteomics, Vol. 12, Issue 5
  • DOI: 10.1074/mcp.M112.021220

Protein extraction from plant tissues for 2DE and its application in proteomic analysis
journal, February 2014

Cross species applicability of abundant protein depletion columns for ribulose-1,5-bisphosphate carboxylase/oxygenase
journal, January 2008

  • Cellar, Nicholas A.; Kuppannan, Krishnamoorthy; Langhorst, Marsha L.
  • Journal of Chromatography B, Vol. 861, Issue 1
  • DOI: 10.1016/j.jchromb.2007.11.024

The ProteoMiner in the proteomic arena: A non-depleting tool for discovering low-abundance species
journal, August 2008

Quantitative mass spectrometry in proteomics: a critical review
journal, August 2007

  • Bantscheff, Marcus; Schirle, Markus; Sweetman, Gavain
  • Analytical and Bioanalytical Chemistry, Vol. 389, Issue 4
  • DOI: 10.1007/s00216-007-1486-6

Accurate Label-Free Protein Quantitation with High- and Low-Resolution Mass Spectrometers
journal, December 2013

  • Krey, Jocelyn F.; Wilmarth, Phillip A.; Shin, Jung-Bum
  • Journal of Proteome Research, Vol. 13, Issue 2
  • DOI: 10.1021/pr401017h

Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action
journal, June 2013

  • Wang, P.; Xue, L.; Batelli, G.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 27
  • DOI: 10.1073/pnas.1308974110

Quantitative Measurement of Phosphoproteome Response to Osmotic Stress in Arabidopsis Based on Library-Assisted eXtracted Ion Chromatogram (LAXIC)
journal, May 2013

  • Xue, Liang; Wang, Pengcheng; Wang, Lianshui
  • Molecular & Cellular Proteomics, Vol. 12, Issue 8
  • DOI: 10.1074/mcp.O113.027284

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry
journal, September 2008

Depletion of abundant plant RuBisCO protein using the protamine sulfate precipitation method
journal, June 2013

Options and considerations when selecting a quantitative proteomics strategy
journal, July 2010

  • Domon, Bruno; Aebersold, Ruedi
  • Nature Biotechnology, Vol. 28, Issue 7
  • DOI: 10.1038/nbt.1661

High Precision Quantitative Proteomics Using iTRAQ on an LTQ Orbitrap: A New Mass Spectrometric Method Combining the Benefits of All
journal, October 2009

  • Köcher, Thomas; Pichler, Peter; Schutzbier, Michael
  • Journal of Proteome Research, Vol. 8, Issue 10
  • DOI: 10.1021/pr900451u

journal, January 2014

Quantitative Analysis of the Mitochondrial and Plastid Proteomes of the Moss Physcomitrella patens Reveals Protein Macrocompartmentation and Microcompartmentation
journal, February 2014

  • Mueller, Stefanie J.; Lang, Daniel; Hoernstein, Sebastian N. W.
  • Plant Physiology, Vol. 164, Issue 4
  • DOI: 10.1104/pp.114.235754

In-depth exploration of Hevea brasiliensis latex proteome and “hidden allergens” via combinatorial peptide ligand libraries
journal, May 2010

Noah's nectar: The proteome content of a glass of red wine
journal, November 2010

Proteomics: the first decade and beyond
journal, March 2003

  • Patterson, Scott D.; Aebersold, Ruedi H.
  • Nature Genetics, Vol. 33, Issue S3
  • DOI: 10.1038/ng1106

The Coming of Age of Phosphoproteomics—from Large Data Sets to Inference of Protein Functions
journal, September 2013

  • Roux, Philippe P.; Thibault, Pierre
  • Molecular & Cellular Proteomics, Vol. 12, Issue 12
  • DOI: 10.1074/mcp.R113.032862

Post‐translational modification of host proteins in pathogen‐triggered defence signalling in plants
journal, June 2008

journal, November 2011

Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome
journal, April 2001

  • Oda, Yoshiya; Nagasu, Takeshi; Chait, Brian T.
  • Nature Biotechnology, Vol. 19, Issue 4
  • DOI: 10.1038/86783

Quantitative Phosphoproteomic Analysis of T Cell Receptor Signaling Reveals System-Wide Modulation of Protein-Protein Interactions
journal, August 2009

Phosphoproteome analysis of the human mitotic spindle
journal, March 2006

  • Nousiainen, M.; Sillje, H. H. W.; Sauer, G.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 14
  • DOI: 10.1073/pnas.0507066103

Searching for allergens in maize kernels via proteomic tools
journal, April 2009

Solubilization of Plant Membrane Proteins for Analysis by Two-Dimensional Gel Electrophoresis
journal, July 1986

  • Hurkman, William J.; Tanaka, Charlene K.
  • Plant Physiology, Vol. 81, Issue 3
  • DOI: 10.1104/pp.81.3.802

Ti4+-phosphate functionalized cellulose for phosphopeptides enrichment and its application in rice phosphoproteome analysis
journal, August 2012

Parallel Proteomic and Phosphoproteomic Analyses of Successive Stages of Maize Leaf Development
journal, August 2013

  • Facette, Michelle R.; Shen, Zhouxin; Björnsdóttir, Fjola R.
  • The Plant Cell, Vol. 25, Issue 8
  • DOI: 10.1105/tpc.113.112227

Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis
journal, June 2012

  • Rose, Christopher M.; Venkateshwaran, Muthusubramanian; Volkening, Jeremy D.
  • Molecular & Cellular Proteomics, Vol. 11, Issue 9
  • DOI: 10.1074/mcp.M112.019208

Successive and Selective Release of Phosphorylated Peptides Captured by Hydroxy Acid-Modified Metal Oxide Chromatography
journal, October 2008

  • Kyono, Yutaka; Sugiyama, Naoyuki; Imami, Koshi
  • Journal of Proteome Research, Vol. 7, Issue 10
  • DOI: 10.1021/pr800305y

The Human Plasma Proteome: History, Character, and Diagnostic Prospects
journal, October 2002

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
journal, May 2003

  • Gerber, S. A.; Rush, J.; Stemman, O.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 12
  • DOI: 10.1073/pnas.0832254100

Comparison of IMAC and MOAC for phosphopeptide enrichment by column chromatography
journal, April 2012

Plant proteome changes under abiotic stress — Contribution of proteomics studies to understanding plant stress response
journal, August 2011

Shotguns in the Front Line: Phosphoproteomics in Plants
journal, October 2011

  • Nakagami, H.; Sugiyama, N.; Ishihama, Y.
  • Plant and Cell Physiology, Vol. 53, Issue 1
  • DOI: 10.1093/pcp/pcr148

Histidine kinases in plants: Cross talk between hormone and stress responses
journal, October 2012

  • Nongpiur, Ramsong; Soni, Praveen; Karan, Ratna
  • Plant Signaling & Behavior, Vol. 7, Issue 10
  • DOI: 10.4161/psb.21516

N-terminal Processing of Lhca3 Is a Key Step in Remodeling of the Photosystem I-Light-harvesting Complex Under Iron Deficiency in Chlamydomonas reinhardtii
journal, March 2005

  • Naumann, Bianca; Stauber, Einar J.; Busch, Andreas
  • Journal of Biological Chemistry, Vol. 280, Issue 21
  • DOI: 10.1074/jbc.M414486200

A comparative proteomic analysis of tomato leaves in response to waterlogging stress
journal, December 2007

Amine-reactive Neutron-encoded Labels for Highly Plexed Proteomic Quantitation
journal, July 2013

  • Hebert, Alexander S.; Merrill, Anna E.; Stefely, Jonathan A.
  • Molecular & Cellular Proteomics, Vol. 12, Issue 11
  • DOI: 10.1074/mcp.M113.032011

PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
journal, December 2007

  • Heazlewood, J. L.; Durek, P.; Hummel, J.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm812

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
journal, August 2005

Relative, label-free protein quantitation: Spectral counting error statistics from nine replicate MudPIT samples
journal, September 2010

  • Cooper, Bret; Feng, Jian; Garrett, Wesley M.
  • Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 9
  • DOI: 10.1016/j.jasms.2010.05.001

Implications of15N-metabolic labeling for automated peptide identification inArabidopsis thaliana
journal, April 2007

  • Nelson, Clark J.; Huttlin, Edward L.; Hegeman, Adrian D.
  • PROTEOMICS, Vol. 7, Issue 8
  • DOI: 10.1002/pmic.200600832

Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies
journal, January 2010

Proteomics quality and standard: From a regulatory perspective
journal, January 2014

Abiotic stress response in plants: When post-transcriptional and post-translational regulations control transcription
journal, April 2008

Quantitative Phosphoproteomics Reveals Extensive Cellular Reprogramming during HIV-1 Entry
journal, May 2013

  • Wojcechowskyj, Jason A.; Didigu, Chuka A.; Lee, Jessica Y.
  • Cell Host & Microbe, Vol. 13, Issue 5
  • DOI: 10.1016/j.chom.2013.04.011

Data processing methods and quality control strategies for label-free LC–MS protein quantification
journal, January 2014

  • Sandin, Marianne; Teleman, Johan; Malmström, Johan
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1844, Issue 1
  • DOI: 10.1016/j.bbapap.2013.03.026

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
journal, January 2003

Popeye strikes again: The deep proteome of spinach leaves
journal, January 2011

Deciphering the plant phosphoproteome: tools and strategies for a challenging task
journal, December 2004

  • Laugesen, Sabrina; Bergoin, Alexis; Rossignol, Michel
  • Plant Physiology and Biochemistry, Vol. 42, Issue 12
  • DOI: 10.1016/j.plaphy.2004.09.007

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles
journal, January 2011

  • Aryal, Uma K.; Stöckel, Jana; Krovvidi, Ravi K.
  • BMC Systems Biology, Vol. 5, Issue 1
  • DOI: 10.1186/1752-0509-5-194

Quantitative Proteomics Reveals a Dynamic Association of Proteins to Detergent-resistant Membranes upon Elicitor Signaling in Tobacco
journal, June 2009

  • Stanislas, Thomas; Bouyssie, David; Rossignol, Michel
  • Molecular & Cellular Proteomics, Vol. 8, Issue 9
  • DOI: 10.1074/mcp.M900090-MCP200

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
journal, December 2008

  • Huang, Da Wei; Sherman, Brad T.; Lempicki, Richard A.
  • Nature Protocols, Vol. 4, Issue 1
  • DOI: 10.1038/nprot.2008.211

Promiscuous Stimulation of ParF Protein Polymerization by Heterogeneous Centromere Binding Factors
journal, November 2007

  • Machón, Cristina; Fothergill, Timothy J. G.; Barillà, Daniela
  • Journal of Molecular Biology, Vol. 374, Issue 1
  • DOI: 10.1016/j.jmb.2007.09.025

Reconstruction of protein networks from an atlas of maize seed proteotypes
journal, November 2013

  • Walley, J. W.; Shen, Z.; Sartor, R.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 49
  • DOI: 10.1073/pnas.1319113110

Looking Deep Inside: Detection of Low-Abundance Proteins in Leaf Extracts of Arabidopsis and Phloem Exudates of Pumpkin
journal, May 2012

  • Fröhlich, Andreas; Gaupels, Frank; Sarioglu, Hakan
  • Plant Physiology, Vol. 159, Issue 3
  • DOI: 10.1104/pp.112.198077

In-depth Analyses of Kinase-dependent Tyrosine Phosphoproteomes Based on Metal Ion-functionalized Soluble Nanopolymers
journal, June 2010

  • Iliuk, Anton B.; Martin, Victoria A.; Alicie, Bethany M.
  • Molecular & Cellular Proteomics, Vol. 9, Issue 10
  • DOI: 10.1074/mcp.M110.000091

Phosphoproteome Dynamics Upon Changes in Plant Water Status Reveal Early Events Associated With Rapid Growth Adjustment in Maize Leaves
journal, July 2012

  • Bonhomme, Ludovic; Valot, Benoît; Tardieu, François
  • Molecular & Cellular Proteomics, Vol. 11, Issue 10
  • DOI: 10.1074/mcp.M111.015867

Comparison of Full Versus Partial Metabolic Labeling for Quantitative Proteomics Analysis in Arabidopsis thaliana
journal, February 2007

  • Huttlin, Edward L.; Hegeman, Adrian D.; Harms, Amy C.
  • Molecular & Cellular Proteomics, Vol. 6, Issue 5
  • DOI: 10.1074/mcp.M600347-MCP200

P 3 DB 3.0: From plant phosphorylation sites to protein networks
journal, November 2013

  • Yao, Qiuming; Ge, Huangyi; Wu, Shangquan
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1135

Orthogonality of Separation in Two-Dimensional Liquid Chromatography
journal, October 2005

  • Gilar, Martin; Olivova, Petra; Daly, Amy E.
  • Analytical Chemistry, Vol. 77, Issue 19
  • DOI: 10.1021/ac050923i

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics
journal, March 2009

  • Boersema, Paul J.; Raijmakers, Reinout; Lemeer, Simone
  • Nature Protocols, Vol. 4, Issue 4
  • DOI: 10.1038/nprot.2009.21

Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach
journal, January 2014

  • Carr, Steven A.; Abbatiello, Susan E.; Ackermann, Bradley L.
  • Molecular & Cellular Proteomics, Vol. 13, Issue 3
  • DOI: 10.1074/mcp.M113.036095

Quality control in LC-MS/MS
journal, February 2011

Advances in Quantitative Phosphoproteomics
journal, November 2011

Stable Isotope Labeling of Arabidopsis thaliana Cells and Quantitative Proteomics by Mass Spectrometry
journal, August 2005

  • Gruhler, Albrecht; Schulze, Waltraud X.; Matthiesen, Rune
  • Molecular & Cellular Proteomics, Vol. 4, Issue 11
  • DOI: 10.1074/mcp.M500190-MCP200

Quantitative Phosphoproteomics Reveals the Role of Protein Arginine Phosphorylation in the Bacterial Stress Response
journal, November 2013

  • Schmidt, Andreas; Trentini, Débora Broch; Spiess, Silvia
  • Molecular & Cellular Proteomics, Vol. 13, Issue 2
  • DOI: 10.1074/mcp.M113.032292

Attempting to rewrite History: challenges with the analysis of histidine-phosphorylated peptides
journal, July 2013

  • Gonzalez-Sanchez, Maria-Belen; Lanucara, Francesco; Helm, Matthew
  • Biochemical Society Transactions, Vol. 41, Issue 4
  • DOI: 10.1042/BST20130072

Optimization of Enrichment Conditions on TiO 2 Chromatography Using Glycerol As an Additive Reagent for Effective Phosphoproteomic Analysis
journal, November 2013

  • Fukuda, Isao; Hirabayashi-Ishioka, Yoshino; Sakikawa, Ikue
  • Journal of Proteome Research, Vol. 12, Issue 12
  • DOI: 10.1021/pr400546u

Prospects for stable analogues of phosphohistidine
journal, July 2013

  • McAllister, Tom E.; Hollins, Jeffrey J.; Webb, Michael E.
  • Biochemical Society Transactions, Vol. 41, Issue 4
  • DOI: 10.1042/BST20130071

Ionic Liquids and Their Interaction with Cellulose
journal, December 2009

  • Pinkert, André; Marsh, Kenneth N.; Pang, Shusheng
  • Chemical Reviews, Vol. 109, Issue 12
  • DOI: 10.1021/cr9001947

A Comparison of Labeling and Label-Free Mass Spectrometry-Based Proteomics Approaches
journal, July 2009

  • Patel, Vibhuti J.; Thalassinos, Konstantinos; Slade, Susan E.
  • Journal of Proteome Research, Vol. 8, Issue 7
  • DOI: 10.1021/pr900080y

A universal and rapid protocol for protein extraction from recalcitrant plant tissues for proteomic analysis
journal, July 2006

Implementation of Statistical Process Control for Proteomic Experiments Via LC MS/MS
journal, February 2014

  • Bereman, Michael S.; Johnson, Richard; Bollinger, James
  • Journal of The American Society for Mass Spectrometry, Vol. 25, Issue 4
  • DOI: 10.1007/s13361-013-0824-5

Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics
journal, January 2006

  • Hendrickson, Erik L.; Xia, Qiangwei; Wang, Tiansong
  • The Analyst, Vol. 131, Issue 12
  • DOI: 10.1039/b610957h

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

Targeted Quantitative Phosphoproteomics Approach for the Detection of Phospho-tyrosine Signaling in Plants
journal, December 2011

  • Mithoe, Sharon C.; Boersema, Paul J.; Berke, Lidija
  • Journal of Proteome Research, Vol. 11, Issue 1
  • DOI: 10.1021/pr200893k

Selected reaction monitoring for quantitative proteomics: a tutorial
journal, January 2008

  • Lange, Vinzenz; Picotti, Paola; Domon, Bruno
  • Molecular Systems Biology, Vol. 4, Issue 1
  • DOI: 10.1038/msb.2008.61

Simple and universal tool to remove on-line impurities in mono- or two-dimensional liquid chromatography–mass spectrometry analysis
journal, May 2008

Application of an Improved Proteomics Method for Abundant Protein Cleanup: Molecular and Genomic Mechanisms Study in Plant Defense
journal, August 2013

  • Zhang, Yixiang; Gao, Peng; Xing, Zhuo
  • Molecular & Cellular Proteomics, Vol. 12, Issue 11
  • DOI: 10.1074/mcp.M112.025213

Battle through Signaling between Wheat and the Fungal Pathogen Septoria tritici Revealed by Proteomics and Phosphoproteomics
journal, May 2013

  • Yang, Fen; Melo-Braga, Marcella N.; Larsen, Martin R.
  • Molecular & Cellular Proteomics, Vol. 12, Issue 9
  • DOI: 10.1074/mcp.M113.027532

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

Phosphorylation of basic amino acid residues in proteins: important but easily missed.
journal, May 2011

  • Cieśla, Joanna; Frączyk, Tomasz; Rode, Wojciech
  • Acta Biochimica Polonica, Vol. 58, Issue 2
  • DOI: 10.18388/abp.2011_2258