Technologies and challenges in large-scale phosphoproteomics

Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis

(2012) Jacek R. Wiśniewski et al.   ANALYTICAL CHEMISTRY

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

(2012) Chad R. Weisbrod et al.   JOURNAL OF PROTEOME RESEARCH

Time-Resolved Quantitative Phosphoproteomics: New Insights into Angiotensin-(1–7) Signaling Networks in Human Endothelial Cells

(2012) Thiago Verano-Braga et al.   JOURNAL OF PROTEOME RESEARCH

Improve the Coverage for the Analysis of Phosphoproteome of HeLa Cells by a Tandem Digestion Approach

(2012) Yangyang Bian et al.   JOURNAL OF PROTEOME RESEARCH

TiSH — a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC

(2012) Kasper Engholm-Keller et al.   Journal of Proteomics

A Novel Method for the Simultaneous Enrichment, Identification, and Quantification of Phosphopeptides and Sialylated Glycopeptides Applied to a Temporal Profile of Mouse Brain Development

(2012) Giuseppe Palmisano et al.   MOLECULAR & CELLULAR PROTEOMICS

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

(2012) Amelia C. Peterson et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis

(2012) A. K. W. Elsholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Increasing phosphoproteomic coverage through sequential digestion by complementary proteases

(2011) Jason M. Gilmore et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Zwitterionic Hydrophilic Interaction Liquid Chromatography (ZIC-HILIC and ZIC-cHILIC) Provide High Resolution Separation and Increase Sensitivity in Proteome Analysis

(2011) Serena Di Palma et al.   ANALYTICAL CHEMISTRY

Microscale Phosphoproteome Analysis of 10 000 Cells from Human Cancer Cell Lines

(2011) Takeshi Masuda et al.   ANALYTICAL CHEMISTRY

Intact proteome fractionation strategies compatible with mass spectrometry

(2011) Alan A Doucette et al.   Expert Review of Proteomics

Selected reaction monitoring applied to proteomics

(2011) Sebastien Gallien et al.   JOURNAL OF MASS SPECTROMETRY

Protein Phosphorylation Is a Key Event of Flagellar Disassembly Revealed by Analysis of Flagellar Phosphoproteins during Flagellar Shortening inChlamydomonas

(2011) Junmin Pan et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Phosphoproteomics Studies Using Stable Isotope Dimethyl Labeling Coupled with IMAC-HILIC-nanoLC−MS/MS for Estrogen-Induced Transcriptional Regulation

(2011) Chin-Jen Wu et al.   JOURNAL OF PROTEOME RESEARCH

Multidimensional Strategy for Sensitive Phosphoproteomics Incorporating Protein Prefractionation Combined with SIMAC, HILIC, and TiO2Chromatography Applied to Proximal EGF Signaling

(2011) Kasper Engholm-Keller et al.   JOURNAL OF PROTEOME RESEARCH

The Problem with Peptide Presumption and Low Mascot Scoring

(2011) Bret Cooper   JOURNAL OF PROTEOME RESEARCH

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

Improved Peptide Identification by Targeted Fragmentation Using CID, HCD and ETD on an LTQ-Orbitrap Velos

(2011) Christian K. Frese et al.   JOURNAL OF PROTEOME RESEARCH

Online Nanoflow Multidimensional Fractionation for High Efficiency Phosphopeptide Analysis

(2011) Scott B. Ficarro et al.   MOLECULAR & CELLULAR PROTEOMICS

Evaluation of HCD- and CID-type Fragmentation Within Their Respective Detection Platforms For Murine Phosphoproteomics

(2011) Mark P. Jedrychowski et al.   MOLECULAR & CELLULAR PROTEOMICS

Mapping intact protein isoforms in discovery mode using top-down proteomics

(2011) John C. Tran et al.   NATURE

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

Effective Representation and Storage of Mass Spectrometry-Based Proteomic Data Sets for the Scientific Community

(2011) J. V. Olsen et al.   Science Signaling

The Potential Cost of High-Throughput Proteomics

(2011) F. M. White   Science Signaling

Effect of High-Accuracy Precursor Masses on Phosphopeptide Identification from MS3Spectra

(2010) Wiebke Timm et al.   ANALYTICAL CHEMISTRY

Exploring the Human Leukocyte Phosphoproteome Using a Microfluidic Reversed-Phase−TiO2−Reversed-Phase High-Performance Liquid Chromatography Phosphochip Coupled to a Quadrupole Time-of-Flight Mass Spectrometer

(2010) Reinout Raijmakers et al.   ANALYTICAL CHEMISTRY

Analyzing marginal cases in differential shotgun proteomics

(2010) Paulo C. Carvalho et al.   BIOINFORMATICS

Peptide fractionation in proteomics approaches

(2010) Bruno Manadas et al.   Expert Review of Proteomics

Strategies for quantitation of phosphoproteomic data

(2010) Giuseppe Palmisano et al.   Expert Review of Proteomics

Differential Phosphorylation of Dynamin I Isoforms in Subcellular Compartments Demonstrates the Hidden Complexity of Phosphoproteomes

(2010) Ling-Shan Chan et al.   JOURNAL OF PROTEOME RESEARCH

Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

Brain Phosphoproteome Obtained by a FASP-Based Method Reveals Plasma Membrane Protein Topology

(2010) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation

(2010) Nagarjuna Nagaraj et al.   JOURNAL OF PROTEOME RESEARCH

Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides

(2010) Bao Quoc Tran et al.   JOURNAL OF PROTEOME RESEARCH

Mass Spectrometry Detection of Histidine Phosphorylation on NM23-H1

(2010) John D. Lapek et al.   JOURNAL OF PROTEOME RESEARCH

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor–dependent signaling pathways in renal collecting duct cells

(2010) Markus M. Rinschen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From proteome lists to biological impact- tools and strategies for the analysis of large MS data sets

(2010) Rainer Malik et al.   PROTEOMICS

Achievements and perspectives of top-down proteomics

(2010) Andrea Armirotti et al.   PROTEOMICS

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Lys-N and Trypsin Cover Complementary Parts of the Phosphoproteome in a Refined SCX-Based Approach

(2009) Sharon Gauci et al.   ANALYTICAL CHEMISTRY

Reversed-Phase-Reversed-Phase Liquid Chromatography Approach with High Orthogonality for Multidimensional Separation of Phosphopeptides

(2009) Chunxia Song et al.   ANALYTICAL CHEMISTRY

The Chemical Biology of Protein Phosphorylation

(2009) Mary Katherine Tarrant et al.   Annual Review of Biochemistry

Phosphopeptide fragmentation and analysis by mass spectrometry

(2009) Paul J. Boersema et al.   JOURNAL OF MASS SPECTROMETRY

Normalization and Statistical Analysis of Quantitative Proteomics Data Generated by Metabolic Labeling

(2009) Lily Ting et al.   MOLECULAR & CELLULAR PROTEOMICS

Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics

(2009) Cuiping Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling

(2009) Paul J. Boersema et al.   MOLECULAR & CELLULAR PROTEOMICS

A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed

(2009) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Mislocalized Activation of Oncogenic RTKs Switches Downstream Signaling Outcomes

(2009) Chunaram Choudhary et al.   MOLECULAR CELL

Quantitative Proteomics Reveals a Dynamic Interactome and Phase-Specific Phosphorylation in the Neurospora Circadian Clock

(2009) Christopher L. Baker et al.   MOLECULAR CELL

The IntAct molecular interaction database in 2010

(2009) B. Aranda et al.   NUCLEIC ACIDS RESEARCH

Empirical Bayes Analysis of Quantitative Proteomics Experiments

(2009) Adam A. Margolin et al.   PLoS One

Evidence for phosphorylation of serine 753 in CFTR using a novel metal-ion affinity resin and matrix-assisted laser desorption mass spectrometry

(2009) David C. A. Neville et al.   PROTEIN SCIENCE

Phosphoproteomic analysis of the human pathogenTrypanosoma cruziat the epimastigote stage

(2009) Ernesto S. Nakayasu et al.   PROTEOMICS

High-accuracy identification and bioinformatic analysis ofin vivoprotein phosphorylation sites in yeast

(2009) Florian Gnad et al.   PROTEOMICS

The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS

(2009) Scott J. Geromanos et al.   PROTEOMICS

Positive Selection of Tyrosine Loss in Metazoan Evolution

(2009) C. S. H. Tan et al.   SCIENCE

McsB Is a Protein Arginine Kinase That Phosphorylates and Inhibits the Heat-Shock Regulator CtsR

(2009) J. Fuhrmann et al.   SCIENCE

Proteome-Wide Identification of Proteins and Their Modifications with Decreased Ambiguities and Improved False Discovery Rates Using Unique Sequence Tags

(2008) Yufeng Shen et al.   ANALYTICAL CHEMISTRY

Online Automatedin VivoZebrafish Phosphoproteomics: From Large-Scale Analysis Down to a Single Embryo

(2008) Simone Lemeer et al.   JOURNAL OF PROTEOME RESEARCH

TiO2-Based Phosphoproteomic Analysis of the Plasma Membrane and the Effects of Phosphatase Inhibitor Treatment

(2008) Tine E. Thingholm et al.   JOURNAL OF PROTEOME RESEARCH

Phosphoproteome Analysis of Fission Yeast

(2008) Joshua T. Wilson-Grady et al.   JOURNAL OF PROTEOME RESEARCH

Comparison of MS2-Only, MSA, and MS2/MS3Methodologies for Phosphopeptide Identification

(2008) Peter J. Ulintz et al.   JOURNAL OF PROTEOME RESEARCH

Hydrophilic Interaction Chromatography Reduces the Complexity of the Phosphoproteome and Improves Global Phosphopeptide Isolation and Detection

(2008) Dean E. McNulty et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions

(2008) Cuiping Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

Comparative Phosphoproteomics of Zebrafish Fyn/Yes Morpholino Knockdown Embryos

(2008) Simone Lemeer et al.   MOLECULAR & CELLULAR PROTEOMICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

A quantitative atlas of mitotic phosphorylation

(2008) N. Dephoure et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis

(2008) Judit Villén et al.   PROTEOMICS

Electrostatic Repulsion Hydrophilic Interaction Chromatography for Isocratic Separation of Charged Solutes and Selective Isolation of Phosphopeptides

(2007) Andrew J. Alpert   ANALYTICAL CHEMISTRY