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Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling

https://doi.org/10.1021/acs.analchem.5b04123

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Electron capture dissociation of singly and multiply phosphorylated peptides

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Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single‐Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry

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Phosphoproteomics—More than meets the eye

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Macroporous reversed‐phase separation of proteins combined with reversed‐phase separation of phosphopeptides and tandem mass spectrometry for profiling the phosphoproteome of MDA‐MB‐231 cells

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Recent advances in enrichment and separation strategies for mass spectrometry‐based phosphoproteomics

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Tissue phosphoproteomics with PolyMAC identifies potential therapeutic targets in a transgenic mouse model of HER2 positive breast cancer

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Phosphopeptide fragmentation and analysis by mass spectrometry

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Enrichment specificity of micro and nano‐sized titanium and zirconium dioxides particles in phosphopeptide mapping

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Combining UV photodissociation with electron transfer for peptide structure analysis

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Site‐specific separation and detection of phosphopeptide isomers with p H ‐mediated stacking capillary electrophoresis‐electrospray ionization‐tandem mass spectrometry

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Evolution and functional cross‐talk of protein post‐translational modifications

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Less label, more free: Approaches in label‐free quantitative mass spectrometry

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193‐nm photodissociation of singly and multiply charged peptide anions for acidic proteome characterization

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Electron transfer dissociation mass spectrometry in proteomics

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D ‐score: A search engine independent MD ‐score

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Technologies and challenges in large‐scale phosphoproteomics

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The next level of complexity: Crosstalk of posttranslational modifications

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In‐depth protein profiling of the postsynaptic density from mouse hippocampus using data‐independent acquisition proteomics

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Integrated approach using multistep enzyme digestion, TiO2 enrichment, and database search for in‐depth phosphoproteomic profiling

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Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10‐plex quantitative proteomics and phosphoproteomics

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Quantitative phosphoproteomics of Alzheimer's disease reveals cross‐talk between kinases and small heat shock proteins

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Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O‐GlcNAc in the DNA damage response pathway

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Role of phosphoproteomics in the development of personalized cancer therapies

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Dissociation of peptide ions by fast atom bombardment in a quadrupole ion trap

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Complementary Fe 3+ ‐ and Ti 4+ ‐immobilized metal ion affinity chromatography for purification of acidic and basic phosphopeptides

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Femtosecond laser‐induced ionization/dissociation tandem mass spectrometry (fsLID‐MS/MS) of deprotonated phosphopeptide anions

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Increasing phosphoproteomic coverage through sequential digestion by complementary proteases

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Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

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Advances in phosphopeptide enrichment techniques for phosphoproteomics

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Recent developments and applications of electron transfer dissociation mass spectrometry in proteomics

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Effects of Electron-Transfer Coupled with Collision-Induced Dissociation (ET/CID) on Doubly Charged Peptides and Phosphopeptides

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Systematic Comparison of Ultraviolet Photodissociation and Electron Transfer Dissociation for Peptide Anion Characterization

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Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer

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Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

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Neutron-Encoded Protein Quantification by Peptide Carbamylation

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Unblocking the Sink: Improved CID-Based Analysis of Phosphorylated Peptides by Enzymatic Removal of the Basic C -Terminal Residue

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Direct Identification of Tyrosine Sulfation by using Ultraviolet Photodissociation Mass Spectrometry

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Large-Scale Examination of Factors Influencing Phosphopeptide Neutral Loss during Collision Induced Dissociation

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21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: A National Resource for Ultrahigh Resolution Mass Analysis

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Sample Preparation for Phosphoproteomic Analysis of Circadian Time Series in Arabidopsis thaliana

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Evaluation of quantitative performance of sequential immobilized metal affinity chromatographic enrichment for phosphopeptides

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Multidimensional electrostatic repulsion–hydrophilic interaction chromatography (ERLIC) for quantitative analysis of the proteome and phosphoproteome in clinical and biomedical research

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Quantifying proteomes and their post-translational modifications by stable isotope label-based mass spectrometry

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Is phosphoproteomics ready for clinical research?

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A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

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A Single Kinase Generates the Majority of the Secreted Phosphoproteome

inferredcites →https://doi.org/10.1016/j.cell.2015.05.046openalex-snapshot

Monoclonal 1- and 3-Phosphohistidine Antibodies: New Tools to Study Histidine Phosphorylation

inferredcites →https://doi.org/10.1016/j.celrep.2013.01.003openalex-snapshot

In Vivo SILAC-Based Proteomics Reveals Phosphoproteome Changes during Mouse Skin Carcinogenesis

inferredcites →https://doi.org/10.1016/j.celrep.2014.07.036openalex-snapshot

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

inferredcites →https://doi.org/10.1016/j.celrep.2015.01.052openalex-snapshot

A Cell-Signaling Network Temporally Resolves Specific versus Promiscuous Phosphorylation

inferredcites →https://doi.org/10.1016/j.celrep.2015.05.029openalex-snapshot

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas

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A Quantitative Map of the Liver Mitochondrial Phosphoproteome Reveals Posttranslational Control of Ketogenesis

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Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

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Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation

inferredcites →https://doi.org/10.1016/j.cmet.2015.09.001openalex-snapshot

Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates

inferredcites →https://doi.org/10.1016/j.cmet.2015.10.004openalex-snapshot

Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates

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Evaluation of phosphopeptide enrichment strategies for quantitative TMT analysis of complex network dynamics in cancer-associated cell signalling

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Potential regulatory phosphorylation sites in a Medicago truncatula plasma membrane proton pump implicated during early symbiotic signaling in roots

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Fragmentation of phosphorylated and singly charged peptide ions via interaction with metastable atoms

inferredcites →https://doi.org/10.1016/j.ijms.2014.04.015openalex-snapshot

Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer

inferredcites →https://doi.org/10.1016/j.ijms.2014.08.032openalex-snapshot

In-depth analyses of B cell signaling through tandem mass spectrometry of phosphopeptides enriched by PolyMAC

inferredcites →https://doi.org/10.1016/j.ijms.2015.05.009openalex-snapshot

Near-UV photodissociation of phosphopeptide cation-radicals

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Infrared multiphoton dissociation (IRMPD) and collisionally activated dissociationof peptides in a quadrupole ion trapwith selective IRMPD of phosphopeptides

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Time-resolved observation of product ions generated by 157 nm photodissociation of singly protonated phosphopeptides

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Enhanced characterization of singly protonated phosphopeptide ions by femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fs-LID-MS/MS)

inferredcites →https://doi.org/10.1016/j.jprot.2012.08.007openalex-snapshot

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

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Quantitative phosphoproteomic profiling of human non-small cell lung cancer tumors

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Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography

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An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome

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Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation

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SPECHT — Single-stage phosphopeptide enrichment and stable-isotope chemical tagging: Quantitative phosphoproteomics of insulin action in muscle

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Proteomics reveals evidence of cross-talk between protein modifications in bacteria: focus on acetylation and phosphorylation

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Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis

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Protein Polyphosphorylation of Lysine Residues by Inorganic Polyphosphate

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Identifying post-translational modifications of NEMO by tandem mass spectrometry after high affinity purification

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Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

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Platforms for enrichment of phosphorylated proteins and peptides in proteomics

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Quantitative comparison of the fasted and re-fed mouse liver phosphoproteomes using lower pH reductive dimethylation

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The regulation of protein function by multisite phosphorylation – a 25 year update

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Evolution of protein kinase signaling from yeast to man

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Selective, Sensitive, and Rapid Phosphopeptide Identification in Enzymatic Digests Using ESI-FTICR-MS with Infrared Multiphoton Dissociation

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Phosphopeptide Anion Characterization via Sequential Charge Inversion and Electron-Transfer Dissociation

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Supplemental Activation Method for High-Efficiency Electron-Transfer Dissociation of Doubly Protonated Peptide Precursors

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Rapid and Reproducible Single-Stage Phosphopeptide Enrichment of Complex Peptide Mixtures: Application to General and Phosphotyrosine-Specific Phosphoproteomics Experiments

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Advances in Quantitative Phosphoproteomics

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Ultra Acidic Strong Cation Exchange Enabling the Efficient Enrichment of Basic Phosphopeptides

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

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High-Resolution Enabled TMT 8-plexing

inferredcites →https://doi.org/10.1021/ac301572topenalex-snapshot

Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses

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Toward Full Peptide Sequence Coverage by Dual Fragmentation Combining Electron-Transfer and Higher-Energy Collision Dissociation Tandem Mass Spectrometry

inferredcites →https://doi.org/10.1021/ac400476wopenalex-snapshot

Neutron Encoded Labeling for Peptide Identification

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Enhanced Detection of Multiply Phosphorylated Peptides and Identification of Their Sites of Modification

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Front-End Electron Transfer Dissociation: A New Ionization Source

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Novel Parallelized Quadrupole/Linear Ion Trap/Orbitrap Tribrid Mass Spectrometer Improving Proteome Coverage and Peptide Identification Rates

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Sequential Phosphoproteomic Enrichment through Complementary Metal-Directed Immobilized Metal Ion Affinity Chromatography

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Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics

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Specific Visualization and Identification of Phosphoproteome in Gels

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Characterization of Biases in Phosphopeptide Enrichment by Ti 4+ -Immobilized Metal Affinity Chromatography and TiO 2 Using a Massive Synthetic Library and Human Cell Digests

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MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

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Reproducible Automated Phosphopeptide Enrichment Using Magnetic TiO2 and Ti-IMAC

inferredcites →https://doi.org/10.1021/ac502708mopenalex-snapshot

Highly Sensitive Phosphoproteomics by Tailoring Solid-Phase Extraction to Electrostatic Repulsion-Hydrophilic Interaction Chromatography

inferredcites →https://doi.org/10.1021/ac503593dopenalex-snapshot

Multiplexed Quantification for Data-Independent Acquisition

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Hybridizing Ultraviolet Photodissociation with Electron Transfer Dissociation for Intact Protein Characterization

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Evaluating Multiplexed Quantitative Phosphopeptide Analysis on a Hybrid Quadrupole Mass Filter/Linear Ion Trap/Orbitrap Mass Spectrometer

inferredcites →https://doi.org/10.1021/ac504420copenalex-snapshot

Anion-Exchange Chromatography of Phosphopeptides: Weak Anion Exchange versus Strong Anion Exchange and Anion-Exchange Chromatography versus Electrostatic Repulsion–Hydrophilic Interaction Chromatography

inferredcites →https://doi.org/10.1021/ac504740popenalex-snapshot

Improving Label-Free Quantitative Proteomics Strategies by Distributing Shared Peptides and Stabilizing Variance

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Collisions or Electrons? Protein Sequence Analysis in the 21st Century

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Negative Electron Transfer Dissociation of Deprotonated Phosphopeptide Anions: Choice of Radical Cation Reagent and Competition between Electron and Proton Transfer

inferredcites →https://doi.org/10.1021/acs.analchem.5b00162openalex-snapshot

Benchmarking Multiple Fragmentation Methods on an Orbitrap Fusion for Top-down Phospho-Proteoform Characterization

inferredcites →https://doi.org/10.1021/acs.analchem.5b00881openalex-snapshot

Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins

inferredcites →https://doi.org/10.1021/acs.analchem.5b01389openalex-snapshot

Gas-Phase Rearrangement in Lysine Phosphorylated Peptides During Electron-Transfer Dissociation Tandem Mass Spectrometry

inferredcites →https://doi.org/10.1021/acs.analchem.5b01833openalex-snapshot

Comparing Multistep Immobilized Metal Affinity Chromatography and Multistep TiO2 Methods for Phosphopeptide Enrichment

inferredcites →https://doi.org/10.1021/acs.analchem.5b02457openalex-snapshot

Over 2300 Phosphorylated Peptide Identifications with Single-Shot Capillary Zone Electrophoresis-Tandem Mass Spectrometry in a 100 min Separation

inferredcites →https://doi.org/10.1021/acs.analchem.5b03040openalex-snapshot

Triomics Analysis of Imatinib-Treated Myeloma Cells Connects Kinase Inhibition to RNA Processing and Decreased Lipid Biosynthesis

inferredcites →https://doi.org/10.1021/acs.jproteome.5b00050openalex-snapshot

Confident Site Localization Using a Simulated Phosphopeptide Spectral Library

inferredcites →https://doi.org/10.1021/acs.jproteome.5b00236openalex-snapshot

Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence

inferredcites →https://doi.org/10.1021/acs.jproteome.5b00249openalex-snapshot

Construction and Deciphering of Human Phosphorylation-Mediated Signaling Transduction Networks

inferredcites →https://doi.org/10.1021/acs.jproteome.5b00404openalex-snapshot

Sample Collection Method Bias Effects in Quantitative Phosphoproteomics

inferredcites →https://doi.org/10.1021/acs.jproteome.5b00529openalex-snapshot

PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal Molecular Networks

inferredcites →https://doi.org/10.1021/acs.jproteome.5b00599openalex-snapshot

Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search

inferredcites →https://doi.org/10.1021/acsami.5b01254openalex-snapshot

Development of the Affinity Materials for Phosphorylated Proteins/Peptides Enrichment in Phosphoproteomics Analysis

inferredcites →https://doi.org/10.1021/cb200445wopenalex-snapshot

Chasing Phosphohistidine, an Elusive Sibling in the Phosphoamino Acid Family

inferredcites →https://doi.org/10.1021/cb500904bopenalex-snapshot

Mass Spectrometry-Based Detection and Assignment of Protein Posttranslational Modifications

inferredcites →https://doi.org/10.1021/cr3003533openalex-snapshot

Protein Analysis by Shotgun/Bottom-up Proteomics

inferredcites →https://doi.org/10.1021/ja207736yopenalex-snapshot

Negative-Ion Electron Capture Dissociation: Radical-Driven Fragmentation of Charge-Increased Gaseous Peptide Anions

inferredcites →https://doi.org/10.1021/ja4029654openalex-snapshot

Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation

inferredcites →https://doi.org/10.1021/ja507614fopenalex-snapshot

A Phosphohistidine Proteomics Strategy Based on Elucidation of a Unique Gas-Phase Phosphopeptide Fragmentation Mechanism

inferredcites →https://doi.org/10.1021/ja507886sopenalex-snapshot

Site-Specifically Phosphorylated Lysine Peptides

inferredcites →https://doi.org/10.1021/ja511833yopenalex-snapshot

Specific Enrichment of Phosphoproteins Using Functionalized Multivalent Nanoparticles

inferredcites →https://doi.org/10.1021/ja8023719openalex-snapshot

Site-Specific Radical Directed Dissociation of Peptides at Phosphorylated Residues

inferredcites →https://doi.org/10.1021/ja8089119openalex-snapshot

Femtosecond Laser-Induced Ionization/Dissociation of Protonated Peptides

inferredcites →https://doi.org/10.1021/ol503320popenalex-snapshot

A Second-Generation Phosphohistidine Analog for Production of Phosphohistidine Antibodies

inferredcites →https://doi.org/10.1021/pr0499794openalex-snapshot

Novel Linear Quadrupole Ion Trap/FT Mass Spectrometer: Performance Characterization and Use in the Comparative Analysis of Histone H3 Post-translational Modifications

inferredcites →https://doi.org/10.1021/pr100637qopenalex-snapshot

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

inferredcites →https://doi.org/10.1021/pr100951topenalex-snapshot

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

inferredcites →https://doi.org/10.1021/pr200611nopenalex-snapshot

Universal and Confident Phosphorylation Site Localization Using phosphoRS

inferredcites →https://doi.org/10.1021/pr2008175openalex-snapshot

Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

inferredcites →https://doi.org/10.1021/pr300242wopenalex-snapshot

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

inferredcites →https://doi.org/10.1021/pr300273gopenalex-snapshot

Large-Scale Quantitative Assessment of Different In-Solution Protein Digestion Protocols Reveals Superior Cleavage Efficiency of Tandem Lys-C/Trypsin Proteolysis over Trypsin Digestion

inferredcites →https://doi.org/10.1021/pr300375dopenalex-snapshot

Combinatorial Use of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) and Strong Cation Exchange (SCX) Chromatography for In-Depth Phosphoproteome Analysis

inferredcites →https://doi.org/10.1021/pr3004166openalex-snapshot

Fully Automated Multifunctional Ultrahigh Pressure Liquid Chromatography System for Advanced Proteome Analyses

inferredcites →https://doi.org/10.1021/pr300503zopenalex-snapshot

Depletion of Acidic Phosphopeptides by SAX To Improve the Coverage for the Detection of Basophilic Kinase Substrates

inferredcites →https://doi.org/10.1021/pr3005474openalex-snapshot

A Strategy for Large-Scale Phosphoproteomics and SRM-Based Validation of Human Breast Cancer Tissue Samples

inferredcites →https://doi.org/10.1021/pr300630kopenalex-snapshot

Toward a Comprehensive Characterization of a Human Cancer Cell Phosphoproteome

inferredcites →https://doi.org/10.1021/pr301061qopenalex-snapshot

Citric Acid-Assisted Two-Step Enrichment with TiO2 Enhances the Separation of Multi- and Monophosphorylated Peptides and Increases Phosphoprotein Profiling

inferredcites →https://doi.org/10.1021/pr301130kopenalex-snapshot

Unambiguous Phosphosite Localization using Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)

inferredcites →https://doi.org/10.1021/pr400198eopenalex-snapshot

Displacement of N/Q-rich Peptides on TiO2Beads Enhances the Depth and Coverage of Yeast Phosphoproteome Analyses

inferredcites →https://doi.org/10.1021/pr400402sopenalex-snapshot

Comparison of Alternative MS/MS and Bioinformatics Approaches for Confident Phosphorylation Site Localization

inferredcites →https://doi.org/10.1021/pr400417gopenalex-snapshot

Comparison of SILAC and mTRAQ Quantification for Phosphoproteomics on a Quadrupole Orbitrap Mass Spectrometer

inferredcites →https://doi.org/10.1021/pr4005234openalex-snapshot

Combination of Multistep IMAC Enrichment with High-pH Reverse Phase Separation for In-Depth Phosphoproteomic Profiling

inferredcites →https://doi.org/10.1021/pr400546uopenalex-snapshot

Optimization of Enrichment Conditions on TiO2Chromatography Using Glycerol As an Additive Reagent for Effective Phosphoproteomic Analysis

inferredcites →https://doi.org/10.1021/pr4007443openalex-snapshot

Expanding Tandem Mass Spectral Libraries of Phosphorylated Peptides: Advances and Applications

inferredcites →https://doi.org/10.1021/pr4007969openalex-snapshot

Rapid Combinatorial ERLIC–SCX Solid-Phase Extraction for In-Depth Phosphoproteome Analysis

inferredcites →https://doi.org/10.1021/pr401122mopenalex-snapshot

Deep Proteome Mapping of Mouse Kidney Based on OFFGel Prefractionation Reveals Remarkable Protein Post- Translational Modifications

inferredcites →https://doi.org/10.1021/pr401181yopenalex-snapshot

Impact of Digestion Conditions on Phosphoproteomics

inferredcites →https://doi.org/10.1021/pr4011926openalex-snapshot

Lifelong Exercise Training Modulates Cardiac Mitochondrial Phosphoproteome in Rats

inferredcites →https://doi.org/10.1021/pr401268vopenalex-snapshot

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

inferredcites →https://doi.org/10.1021/pr401278jopenalex-snapshot

Intelligent Data Acquisition Blends Targeted and Discovery Methods

inferredcites →https://doi.org/10.1021/pr5003017openalex-snapshot

Hybrid Data Acquisition and Processing Strategies with Increased Throughput and Selectivity: pSMART Analysis for Global Qualitative and Quantitative Analysis

inferredcites →https://doi.org/10.1021/pr500860copenalex-snapshot

Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites

inferredcites →https://doi.org/10.1021/pr500880bopenalex-snapshot

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

inferredcites →https://doi.org/10.1021/pr500889vopenalex-snapshot

Phospho-iTRAQ: Assessing Isobaric Labels for the Large-Scale Study Of Phosphopeptide Stoichiometry

inferredcites →https://doi.org/10.1021/pr500893mopenalex-snapshot

Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

inferredcites →https://doi.org/10.1021/pr500985wopenalex-snapshot

Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

inferredcites →https://doi.org/10.1021/pr501138hopenalex-snapshot

Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics

inferredcites →https://doi.org/10.1021/pr800834eopenalex-snapshot

Electron Transfer Dissociation in Conjunction with Collision Activation To Investigate the Drosophila melanogaster Phosphoproteome

inferredcites →https://doi.org/10.1038/nature13079openalex-snapshot

Cell-cycle-regulated activation of Akt kinase by phosphorylation at its carboxyl terminus

inferredcites →https://doi.org/10.1038/nature13736openalex-snapshot

Tyrosine phosphorylation of histone H2A by CK2 regulates transcriptional elongation

inferredcites →https://doi.org/10.1038/nbt.1511openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nbt.2585openalex-snapshot

A large synthetic peptide and phosphopeptide reference library for mass spectrometry–based proteomics

inferredcites →https://doi.org/10.1038/nbt.2841openalex-snapshot

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

inferredcites →https://doi.org/10.1038/nbt.3267openalex-snapshot

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

inferredcites →https://doi.org/10.1038/nbt.3327openalex-snapshot

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

inferredcites →https://doi.org/10.1038/nbt1240openalex-snapshot

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

inferredcites →https://doi.org/10.1038/ncb2860openalex-snapshot

Sin1 phosphorylation impairs mTORC2 complex integrity and inhibits downstream Akt signalling to suppress tumorigenesis

inferredcites →https://doi.org/10.1038/nchembio.1259openalex-snapshot

A pan-specific antibody for direct detection of protein histidine phosphorylation

inferredcites →https://doi.org/10.1038/ncomms1871openalex-snapshot

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues

inferredcites →https://doi.org/10.1038/ncomms6277openalex-snapshot

MS-GF+ makes progress towards a universal database search tool for proteomics

inferredcites →https://doi.org/10.1038/ncomms6924openalex-snapshot

MARQUIS: A multiplex method for absolute quantification of peptides and posttranslational modifications

inferredcites →https://doi.org/10.1038/ncomms7622openalex-snapshot

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics

inferredcites →https://doi.org/10.1038/ncomms9033openalex-snapshot

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data

inferredcites →https://doi.org/10.1038/ncomms9364openalex-snapshot

Bub1 autophosphorylation feeds back to regulate kinetochore docking and promote localized substrate phosphorylation

inferredcites →https://doi.org/10.1038/nmeth.1647openalex-snapshot

Large-scale phosphosite quantification in tissues by a spike-in SILAC method

inferredcites →https://doi.org/10.1038/nmeth.1714openalex-snapshot

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

inferredcites →https://doi.org/10.1038/nmeth.1716openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nmeth.2378openalex-snapshot

Neutron-encoded mass signatures for multiplexed proteome quantification

inferredcites →https://doi.org/10.1038/nmeth.2518openalex-snapshot

Integrated proteomic analysis of post-translational modifications by serial enrichment

inferredcites →https://doi.org/10.1038/nmeth.2519openalex-snapshot

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation

inferredcites →https://doi.org/10.1038/nmeth.2528openalex-snapshot

Multiplexed MS/MS for improved data-independent acquisition

inferredcites →https://doi.org/10.1038/nmeth.2703openalex-snapshot

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

inferredcites →https://doi.org/10.1038/nmeth.2767openalex-snapshot

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

inferredcites →https://doi.org/10.1038/nmeth.3255openalex-snapshot

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

inferredcites →https://doi.org/10.1038/nprot.2013.010openalex-snapshot

Robust phosphoproteome enrichment using monodisperse microsphere–based immobilized titanium (IV) ion affinity chromatography

inferredcites →https://doi.org/10.1038/nprot.2013.013openalex-snapshot

Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments

inferredcites →https://doi.org/10.1038/nprot.2015.015openalex-snapshot

Building high-quality assay libraries for targeted analysis of SWATH MS data

inferredcites →https://doi.org/10.1038/nprot.2015.040openalex-snapshot

One-hour proteome analysis in yeast

inferredcites →https://doi.org/10.1038/nprot.2015.086openalex-snapshot

Complementary IMAC enrichment methods for HLA-associated phosphopeptide identification by mass spectrometry

showing the first 200 of 285 · page through all 285

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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In-Situ Digestion Assisted Multi-Template Imprinted Nanoparticles for Efficient Analysis of Protein Phosphorylation

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Monodisperse Chemical Oligophosphorylation of Peptides via Protected Oligophosphorimidazolide Reagents

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Monodisperse Chemical Oligophosphorylation of Peptides via Protected Oligophosphorimidazolide Reagents

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Metal Oxides Catalyze Formation of Dehydroamino Acids by Phosphate β‐Elimination Under Physiological Conditions

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Mechanistic insights into intramolecular phosphate group transfer during collision induced dissociation of phosphopeptides

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Facile synthesis of titanium(IV) ion‐immobilized poly‐glycidyl methacrylate microparticles functionalized with polyethylenimine and adenosine triphosphate for highly specific enrichment of intact phosphoproteins

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Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non‐small cell lung cancer

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Time, space, and disorder in the expanding proteome universe

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Quantitative phosphoproteome analysis of cisplatin‐induced apoptosis in Jurkat T cells

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Global Lysine Crotonylation Profiling of Mouse Liver

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Advances in quantitative high‐throughput phosphoproteomics with sample multiplexing

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Computational systems approach towards phosphoproteomics and their downstream regulation

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Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification

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Integrated Transcriptomic, Proteomic, and Pharmacologic Profiling of 2D and 3D Patient‐Derived GCTB Cell Lines Reveals Culture‐Dependent Drug Response Determinants

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Proteomic discovery of host kinase signaling in bacterial infections

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Enrichment of intact phosphoproteins using immobilized titanium(IV) affinity chromatography microspheres

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Multiple Site-Specific Phosphorylation of IDPs Monitored by NMR

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Mass Spectrometry-Based Proteomics for Analysis of Hydrophilic Phosphopeptides

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Label-Based Mass Spectrometry Approaches for Robust Quantification of the Phosphoproteome and Total Proteome in Toxoplasma gondii

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The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein–Protein Interactions (PPIs)

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Electron transfer in protein modifications: from detection to imaging

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Unblocking the Sink: Improved CID-Based Analysis of Phosphorylated Peptides by Enzymatic Removal of the Basic C -Terminal Residue

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Hyphenations of one-dimensional capillary liquid chromatography with mass spectrometry

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Phosphoprotein dynamics of interacting T cells and tumor cells by HySic

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Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

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Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity

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Chemoproteomics reveals immunogenic and tumor-associated cell surface substrates of ectokinase CK2α

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Retention time prediction for post-translationally modified peptides: Ser, Thr, Tyr-phosphorylation

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Electrostatic Repulsion Hydrophilic Interaction Liquid Chromatography (ERLIC) for the Quantitative Analysis of Polyamines

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Characterization of intact sialylated glycopeptides and phosphorylated glycopeptides from IMAC enriched samples by EThcD fragmentation: Toward combining phosphoproteomics and glycoproteomics

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Probing arginine-phosphopeptide interactions in non-covalent peptide-peptide ion complexes using gas-phase cross-linking and Born-Oppenheimer molecular dynamics calculations

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Ion/ion charge inversion/attachment in conjunction with dipolar DC collisional activation as a selective screen for sulfo- and phosphopeptides

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D/E-rich peptides are less suitable than D/E-deficient peptides for identification by negative-ion HCD due to scarce production of sequencing ions from multiply charged precursors

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Covalent inhibition of Plasmodium falciparum Ubc13 impairs global protein synthesis

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Sialoglycans on human T cells attenuate death programs executed through the Fas pathway

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Ferulic acid in Chaihu Shugan San modulates depression-like behavior, endothelial and gastrointestinal dysfunction in rats via the Ghrl-Edn1/Mecp2/P-mTOR/VEGFA pathway: A multi-omics study

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PhoPepMass: A database and search tool assisting human phosphorylation peptide identification from mass spectrometry data

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Parallel reaction monitoring on a Q Exactive mass spectrometer increases reproducibility of phosphopeptide detection in bacterial phosphoproteomics measurements

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Integrating phosphoproteomics into kinase-targeted cancer therapies in precision medicine

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Pathological implication of protein post-translational modifications in cancer

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Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry–Based Proteomics

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Extracting Informative Glycan-Specific Ions From Glycopeptide MS/MS Spectra With GlyCounter

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Proteomics approaches to decipher new signaling pathways

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New Ti-IMAC magnetic polymeric nanoparticles for phosphopeptide enrichment from complex real samples

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Bioinformatics approaches for improving seminal plasma proteome analysis

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Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety

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The benefits of hybrid fragmentation methods for glycoproteomics

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Advances and applications of stable isotope labeling-based methods for proteome relative quantitation

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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review

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Recent advances in metal oxide affinity chromatography materials for phosphoproteomics

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Targeting protein phosphorylation with molecularly imprinted polymer receptors

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Protocol to quantify protein phosphorylation in mouse extended pluripotent stem cell-derived blastoids

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Molecularly Imprinted and Cladded Nanoparticles Provide Better Phosphorylation Recognition

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Phosphoproteome Profiling Using an Isobaric Carrier without the Need for Phosphoenrichment

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Instrumentation at the Leading Edge of Proteomics

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Ion Activation Methods for Peptides and Proteins

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Profiling Glycoproteins Enriched by Multinanoparticle Protein Corona

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Preparation of Polypropylene Spin Tips Filled with Immobilized Titanium(IV) Ion Monolithic Adsorbent for Robust Phosphoproteome Analysis

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Modulation of Phosphopeptide Fragmentation via Dual Spray Ion/Ion Reactions Using a Sulfonate-Incorporating Reagent

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Phosphoproteomics with Activated Ion Electron Transfer Dissociation

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Implementation of Activated Ion Electron Transfer Dissociation on a Quadrupole-Orbitrap-Linear Ion Trap Hybrid Mass Spectrometer

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The Role of Electron Transfer Dissociation in Modern Proteomics

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Impact of Phosphorylation on the Mass Spectrometry Quantification of Intact Phosphoproteins

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Improved LC/MS Methods for the Analysis of Metal-Sensitive Analytes Using Medronic Acid as a Mobile Phase Additive

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Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update

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Gaining Confidence in the Elusive Histidine Phosphoproteome

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Ion Activation Methods for Peptides and Proteins

inferred← citeshttps://doi.org/10.1021/acs.chemrev.0c00884openalex-snapshot

Analytical and Biochemical Perspectives of Protein O-GlcNAcylation

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00119openalex-snapshot

Crystal-C: A Computational Tool for Refinement of Open Search Results

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00218openalex-snapshot

Optimal Dissociation Methods Differ for N - and O -Glycopeptides

inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00508openalex-snapshot

Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment

inferred← citeshttps://doi.org/10.1021/acs.jproteome.1c00150openalex-snapshot

Using Multilayer Heterogeneous Networks to Infer Functions of Phosphorylated Sites

inferred← citeshttps://doi.org/10.1021/acs.jproteome.1c00865openalex-snapshot

Interrogating Kinase–Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment

inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00172openalex-snapshot

Improving Phosphoproteomics Profiling Using Data-Independent Mass Spectrometry

inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00823openalex-snapshot

Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets

inferred← citeshttps://doi.org/10.1021/acs.jproteome.2c00838openalex-snapshot

An Introduction to Mass Spectrometry-Based Proteomics

inferred← citeshttps://doi.org/10.1021/acs.jproteome.3c00186openalex-snapshot

Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data

inferred← citeshttps://doi.org/10.1021/acs.jproteome.3c00425openalex-snapshot

Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides

inferred← citeshttps://doi.org/10.1021/acs.jproteome.4c00010openalex-snapshot

High-Throughput Proteomics and Phosphoproteomics of Rat Tissues Using Microflow Zeno SWATH

inferred← citeshttps://doi.org/10.1021/acs.jproteome.5c00185openalex-snapshot

Integrated Single-Tip IMAC-HILIC Enables Simultaneous Analysis of Plant Phosphoproteomics and N-Glycoproteomics

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00289openalex-snapshot

193 nm Ultraviolet Photodissociation Mass Spectrometry for Phosphopeptide Characterization in the Positive and Negative Ion Modes

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00728openalex-snapshot

Contribution of Mass Spectrometry-Based Proteomics to the Understanding of TNF-α Signaling

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00732openalex-snapshot

Study of O ‑Phosphorylation Sites in Proteins Involved in Photosynthesis-Related Processes in Synechocystis sp. Strain PCC 6803: Application of the SRM Approach

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00753openalex-snapshot

Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00825openalex-snapshot

Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)n and (X)nK/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics

inferred← citeshttps://doi.org/10.1021/acs.jproteome.6b00868openalex-snapshot

Differential Phosphoproteomic Analysis of Recombinant Chinese Hamster Ovary Cells Following Temperature Shift

inferred← citeshttps://doi.org/10.1021/acs.jproteome.7b00520openalex-snapshot

TiO2 with Tandem Fractionation (TAFT): An Approach for Rapid, Deep, Reproducible, and High-Throughput Phosphoproteome Analysis

inferred← citeshttps://doi.org/10.1021/acs.jproteome.8b00927openalex-snapshot

A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis

inferred← citeshttps://doi.org/10.1021/acs.jproteome.9b00615openalex-snapshot

Comprehensive Spectral Library from the Pathogenic Bacterium Streptococcus pneumoniae with Focus on Phosphoproteins

inferred← citeshttps://doi.org/10.1021/acs.langmuir.7b02488openalex-snapshot

Altering the Peptide Binding Selectivity of Polymeric Reverse Micelle Assemblies via Metal Ion Loading

inferred← citeshttps://doi.org/10.1021/acsami.6b10948openalex-snapshot

Synthesis of Polyethylenimine Functionalized Mesoporous Silica for In-Pipet-Tip Phosphopeptide Enrichment

inferred← citeshttps://doi.org/10.1021/acschembio.0c00024openalex-snapshot

Engineering Orthogonal, Plasma Membrane-Specific SLIPT Systems for Multiplexed Chemical Control of Signaling Pathways in Living Single Cells

inferred← citeshttps://doi.org/10.1021/acschembio.6b00729openalex-snapshot

Mapping the Phosphorylation Pattern of Drosophila melanogaster RNA Polymerase II Carboxyl-Terminal Domain Using Ultraviolet Photodissociation Mass Spectrometry

inferred← citeshttps://doi.org/10.1021/acsmeasuresciau.6c00077openalex-snapshot

GlycoDiveR: A Modular R Framework to Analyze and Visualize Highly Dimensional Glycoproteomics Data

inferred← citeshttps://doi.org/10.1021/acsomega.0c04030openalex-snapshot

Benchmarking Quantitative Performance in Label-Free Proteomics

inferred← citeshttps://doi.org/10.1021/acsomega.2c05616openalex-snapshot

Evaluation of the Potential Risk of Analyzing Phosphopeptides with Easy-nLC 1200-Coupled Mass Spectrometers

inferred← citeshttps://doi.org/10.1021/jasms.4c00147openalex-snapshot

Sequencing of Phosphopeptides Using a Sequential Charge Inversion Ion/Ion Reaction and Electron Capture Dissociation Workflow

inferred← citeshttps://doi.org/10.1038/nature26140openalex-snapshot

The protein histidine phosphatase LHPP is a tumour suppressor

inferred← citeshttps://doi.org/10.1038/s41386-018-0155-0openalex-snapshot

Phosphoproteomic approach for agonist-specific signaling in mouse brains: mTOR pathway is involved in κ opioid aversion

inferred← citeshttps://doi.org/10.1038/s41467-018-05742-zopenalex-snapshot

In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer

inferred← citeshttps://doi.org/10.1038/s41467-019-09222-wopenalex-snapshot

Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis

inferred← citeshttps://doi.org/10.1038/s41467-021-22759-zopenalex-snapshot

A data-independent acquisition-based global phosphoproteomics system enables deep profiling

inferred← citeshttps://doi.org/10.1038/s41467-024-46794-8openalex-snapshot

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions

inferred← citeshttps://doi.org/10.1038/s41467-024-51274-0openalex-snapshot

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

inferred← citeshttps://doi.org/10.1038/s41467-024-54643-xopenalex-snapshot

Robust collection and processing for label-free single voxel proteomics

inferred← citeshttps://doi.org/10.1038/s41467-025-59404-yopenalex-snapshot

Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells

inferred← citeshttps://doi.org/10.1038/s41585-018-0014-0openalex-snapshot

Personalization of prostate cancer therapy through phosphoproteomics

inferred← citeshttps://doi.org/10.1038/s41586-022-05575-3openalex-snapshot

An atlas of substrate specificities for the human serine/threonine kinome

inferred← citeshttps://doi.org/10.1038/s41586-025-08584-0openalex-snapshot

Mass-spectrometry-based proteomics: from single cells to clinical applications

inferred← citeshttps://doi.org/10.1038/s41589-026-02274-2openalex-snapshot

Proteoform-specific enrichment of phosphopeptide isomers by polymer-based synthetic receptors

inferred← citeshttps://doi.org/10.1038/s41592-021-01177-5openalex-snapshot

Impact of phosphorylation on thermal stability of proteins

inferred← citeshttps://doi.org/10.1038/s41596-018-0014-9openalex-snapshot

High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform

inferred← citeshttps://doi.org/10.1038/s41598-017-04798-zopenalex-snapshot

Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome

inferred← citeshttps://doi.org/10.1038/s42255-025-01349-zopenalex-snapshot

The insulin signalling network

inferred← citeshttps://doi.org/10.1038/s43587-021-00071-1openalex-snapshot

Quantitative phosphoproteomics uncovers dysregulated kinase networks in Alzheimer’s disease

inferred← citeshttps://doi.org/10.1038/s44320-024-00050-9openalex-snapshot

µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics

inferred← citeshttps://doi.org/10.1039/c6sc05435hopenalex-snapshot

Coupling functionalized cobalt ferrite nanoparticle enrichment with online LC/MS/MS for top-down phosphoproteomics

inferred← citeshttps://doi.org/10.1039/c7an00570aopenalex-snapshot

Insights into chemoselectivity principles in metal oxide affinity chromatography using tailored nanocast metal oxide microspheres and mass spectrometry-based phosphoproteomics

inferred← citeshttps://doi.org/10.1039/c7an00985bopenalex-snapshot

Recent advances in phosphoproteomics and application to neurological diseases

inferred← citeshttps://doi.org/10.1039/c7ra00385dopenalex-snapshot

Hierarchically templated beads with tailored pore structure for phosphopeptide capture and phosphoproteomics

inferred← citeshttps://doi.org/10.1039/c7ra08870aopenalex-snapshot

Plasmonic nanodisc arrays on calcinated titania for multimodal analysis of phosphorylated peptides

inferred← citeshttps://doi.org/10.1039/d0cb00180eopenalex-snapshot

Development and biological applications of sulfur–triazole exchange (SuTEx) chemistry

inferred← citeshttps://doi.org/10.1039/d1mo00104copenalex-snapshot

Analysis of pancreatic extracellular matrix protein post-translational modifications via electrostatic repulsion-hydrophilic interaction chromatography coupled with mass spectrometry

inferred← citeshttps://doi.org/10.1042/bcj20220220openalex-snapshot

Principles of phosphoproteomics and applications in cancer research

inferred← citeshttps://doi.org/10.1042/ebc20190055openalex-snapshot

The challenge of detecting modifications on proteins

inferred← citeshttps://doi.org/10.1073/pnas.2012408118openalex-snapshot

Modulation of immune cell reactivity with cis -binding Siglec agonists

inferred← citeshttps://doi.org/10.1074/jbc.ra118.004867openalex-snapshot

Polo-like kinase 4 maintains centriolar satellite integrity by phosphorylation of centrosomal protein 131 (CEP131)

inferred← citeshttps://doi.org/10.1074/mcp.m117.067462openalex-snapshot

Phosphoproteome Analysis Reveals Differential Mode of Action of Sorafenib in Wildtype and Mutated FLT3 Acute Myeloid Leukemia (AML) Cells

inferred← citeshttps://doi.org/10.1074/mcp.p120.001997openalex-snapshot

High-speed Analysis of Large Sample Sets – How Can This Key Aspect of the Omics Be Achieved?

inferred← citeshttps://doi.org/10.1074/mcp.r119.001790openalex-snapshot

Profiling Cell Signaling Networks at Single-cell Resolution

inferred← citeshttps://doi.org/10.1074/mcp.r120.002277openalex-snapshot

A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics

inferred← citeshttps://doi.org/10.1074/mcp.ra120.002232openalex-snapshot

In-Depth Characterization of the Staphylococcus aureus Phosphoproteome Reveals New Targets of Stk1

inferred← citeshttps://doi.org/10.1074/mcp.tir117.000518openalex-snapshot

Defeating Major Contaminants in Fe3+- Immobilized Metal Ion Affinity Chromatography (IMAC) Phosphopeptide Enrichment

inferred← citeshttps://doi.org/10.1080/14789450.2018.1483340openalex-snapshot

Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry

inferred← citeshttps://doi.org/10.1080/14789450.2019.1575206openalex-snapshot

Origins and clinical relevance of proteoforms in pediatric malignancies

inferred← citeshttps://doi.org/10.1080/14789450.2025.2601523openalex-snapshot

Mass spectrometry (MS)-based proteomics and the sulfome: clinical potential

inferred← citeshttps://doi.org/10.1080/21655979.2021.2024957openalex-snapshot

Novel protein kinase C phosphorylated kinase inhibitor-matrine suppresses replication of hepatitis B virus via modulating the mitogen-activated protein kinase signal

inferred← citeshttps://doi.org/10.1093/bib/bbac074openalex-snapshot

MutateX: an automated pipeline for in silico saturation mutagenesis of protein structures and structural ensembles

inferred← citeshttps://doi.org/10.1093/bib/bbx031openalex-snapshot

Identification of differentially expressed peptides in high-throughput proteomics data

inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa916openalex-snapshot

Phosphomatics: interactive interrogation of substrate–kinase networks in global phosphoproteomics datasets

inferred← citeshttps://doi.org/10.1093/bioinformatics/btad488openalex-snapshot

SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets

inferred← citeshttps://doi.org/10.1093/intbio/zyz025openalex-snapshot

Substrate-based kinase activity inference identifies MK2 as driver of colitis

inferred← citeshttps://doi.org/10.1093/molecular-omics/aaiag009openalex-snapshot

Exploring infection biology with mass spectrometry-based proteomics

inferred← citeshttps://doi.org/10.1096/fj.202201344ropenalex-snapshot

CDK6 activity in a recurring convergent kinase network motif

inferred← citeshttps://doi.org/10.1097/hep.0000000000001250openalex-snapshot

Phosphoproteomics delineates hepatocellular carcinoma subtypes and pinpoints therapeutic targets

inferred← citeshttps://doi.org/10.1101/2020.04.13.038810openalex-snapshot

Zirconium(IV)-IMAC for phosphopeptide enrichment in phosphoproteomics

inferred← citeshttps://doi.org/10.1101/2020.06.12.148908openalex-snapshot

Identification of the Molecular Basis of Anti-fibrotic Effects of Soluble Guanylate Cyclase Activator Using the Human Lung Fibroblast Phosphoproteome

inferred← citeshttps://doi.org/10.1101/2022.03.13.484137openalex-snapshot

Systematic dissection of phosphorylation-dependent YAP1 complex formation elucidates a key role for PTPN14 in Hippo signal integration

inferred← citeshttps://doi.org/10.1101/2022.12.21.521419openalex-snapshot

Molecular anatomy of eosinophil activation by IL5 and IL33

inferred← citeshttps://doi.org/10.1101/2023.04.04.535617openalex-snapshot

µPhos: a scalable and sensitive platform for functional phosphoproteomics

inferred← citeshttps://doi.org/10.1101/2023.06.05.541905openalex-snapshot

Phosphoprotein dynamics of interacting tumor and T cells by HySic

inferred← citeshttps://doi.org/10.1101/2023.07.15.549150openalex-snapshot

A bespoke analytical workflow for the confident identification of sulfopeptides and their discrimination from phosphopeptides

inferred← citeshttps://doi.org/10.1101/2023.08.01.551433openalex-snapshot

Pathogenic mutations of human phosphorylation sites affect protein-protein interactions

inferred← citeshttps://doi.org/10.1101/2025.09.18.677062openalex-snapshot

The functional maturation of mouse spermatozoa is underpinned by global remodeling of the cellular phosphoproteome

inferred← citeshttps://doi.org/10.1101/211680openalex-snapshot

Multi-omics profiling establishes the polypharmacology of FDA Approved CDK4/6 inhibitors and the potential for differential clinical activity

inferred← citeshttps://doi.org/10.1111/febs.14491openalex-snapshot

Crosstalk between phosphorylation and O‐Glc NA cylation: friend or foe

inferred← citeshttps://doi.org/10.1113/jp273904openalex-snapshot

A map of the phosphoproteomic alterations that occur after a bout of maximal‐intensity contractions

inferred← citeshttps://doi.org/10.1124/molpharm.120.000170openalex-snapshot

Phosphoproteomics-Based Characterization of Prostaglandin E2 Signaling in T Cells

inferred← citeshttps://doi.org/10.1124/pharmrev.120.000056openalex-snapshot

Psychedelics in Psychiatry: Neuroplastic, Immunomodulatory, and Neurotransmitter Mechanisms

inferred← citeshttps://doi.org/10.1126/sciadv.aeg5294openalex-snapshot

AMPK phosphorylation proceeds through hierarchical proteoform cascades revealed by integrated mass spectrometry

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