Molecular & Cellular Proteomics

Article	Citations
Cover	144
Quantitative Proteomic Analysis Reveals Functional Alterations of the Peripheral Immune System in Colorectal Cancer	123
Cover	106
Region and cell-type resolved multi-omic altas of the heart	73
Isolation of Proteins on Chromatin Reveals Signaling Pathway–Dependent Alterations in the DNA-Bound Proteome	67
Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts	60
Quantitative Chromatin Protein Dynamics During Replication Origin Firing in Human Cells	52
Personalized Drug Therapy: Innovative Concept Guided With Proteoformics	51
Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation	50
Cover	50
Cover	48
Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression	46
Identification of tumor antigens for cancer immunotherapy	42
Increasing the coverage, throughput and accessibility of single-cell proteomics	41
Table of Contents	39
MS-based Detection of Pathogen Antigen Through Immunoprecipitation of Its Proteolytic Peptides	36
A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics	34
Targeted LC/MRM-MS analysis of 60 biomarkers on the Health Surveillance Panel (HSP) and DIA analysis of matched venous whole blood, plasma and capillary whole blood collected on remote sampling device	34
Proteomics of spatially identified tissues in whole organs	33
Increasing the Throughput of Activity-Based Proteome Profiling Studies with Real-Time Search and Sample Hyperplexing	33
PROTEOMIC CHANGES TO THE ANTERIOR CEREBRAL ARTERY IN ALZHEIMER’S DISEASE	32
Computational challenges of identification and quantification algorithms in single-cell proteomic data.	31
Easier, More Robust, and Faster Low-flow Quantitative Proteomics Approach	30
Distribution analysis of small metabolites on lens using sand-rose-like ZnO for imaging mass spectrometry	29
Simultaneous quantification of GDF15 and IGFBP7 by LC-MS/MS for studies on hyperemesis gravidarum	29

Discovery of GSTZ1 as a novel target by using fully functionalized fragment-like probes and chemical proteomics	29
Chemoproteomic capture of RNA binding activity in living cells	27
Post-Deconvolution MS/MS Spectra Extraction with Data-Independent Acquisition for Comprehensive Profiling of Urinary Conjugated Metabolome	26
Defining the molecular basis of immune heterogeneity between individuals using immunoproteomics	26
ETV6-NTRK3 oncofusion variant interactomes	26
An Atlas of the Knee Joint Proteins and Their Role in Osteoarthritis Defined by Literature Mining	25
The social architecture of an in-depth cellular protein interactome	25
An Integrated Approach to Protein Discovery and Detection From Complex Biofluids	25
New Global Insights on the Regulation of the Biphasic Life Cycle and Virulence Via ClpP-Dependent Proteolysis in Legionella pneumophila	25
Global Analysis of Post-Translational Side-Chain Arginylation Using Pan-Arginylation Antibodies	25
Cover	24
Functional Impact of Protein–RNA Variation in Clinical Cancer Analyses	24
ProMetheusDB: An In-Depth Analysis of the High-Quality Human Methyl-proteome	24
Normics: Proteomic Normalization by Variance and Data-Inherent Correlation Structure	23
Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression	22
FMRP Long-Range Transport and Degradation Are Mediated by Dynlrb1 in Sensory Neurons	22
Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid	21
DIA-Based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia	21
Integrated Liver and Plasma Proteomics in Obese Mice Reveals Complex Metabolic Regulation	20
High-Throughput Human Complement C3 N-Glycoprofiling Identifies Markers of Early Onset Type 1 Diabetes Mellitus in Children	20
EGFR-T790M Mutation–Derived Interactome Rerouted EGFR Translocation Contributing to Gefitinib Resistance in Non-Small Cell Lung Cancer	20
CySP3-96 enables scalable, streamlined, and low-cost sample preparation for cysteine chemoproteomic applications	19
High-Resolution Structural Proteomics of Mitochondria Using the ‘Build and Retrieve’ Methodology	19
An Inflection Point in Cancer Protein Biomarkers: What was and What's Next	19
Identifying Receptor Kinase Substrates Using an 8000 Peptide Kinase Client Library Enriched for Conserved Phosphorylation Sites	19
Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p	18
Application of Liquid-Liquid Extraction for N-terminal Myristoylation Proteomics	18
Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2) Is Upregulated in Breast Epithelial–Mesenchymal Transition and Responds to Oxidative Stress	18
Targeted Dynamic Phospho-Proteogenomic Analysis of Gastric Cancer Cells Suggests Host Immunity Provides Survival Benefit	18
Deciphering Nucleic Acid Binding Proteome of Mouse Immune Organs Reveals Hub Proteins for Aging	18
Proteomic Analysis Reveals the Composition of Glutamatergic Organelles of Auditory Inner Hair Cells	17
A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development	17
Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model	17
Cover	17
PEPSeek-mediated identification of novel epitopes from viral and bacterial pathogens and the impact on host cell immunopeptidomes	17
metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis	17
The Quantitative Biotinylproteomics Studies Reveal a WInd-Related Kinase 1 (Raf-Like Kinase 36) Functioning as an Early Signaling Component in Wind-Induced Thigmomorphogenesis and Gravitropism	16
Insight Into the Dynamics of the Ixodes ricinus Nymphal Midgut Proteome	16
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	16
CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1	16
Mass Spectrometry–Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease	16
The Urinary Proteomic Profile Implicates Key Regulators for Urologic Chronic Pelvic Pain Syndrome (UCPPS): A MAPP Research Network Study	16
Bioinertization of NanoLC/MS/MS Systems by Depleting Metal Ions From the Mobile Phases for Phosphoproteomics	16
Prenylated PALM2 Promotes the Migration of Esophageal Squamous Cell Carcinoma Cells Through Activating Ezrin	15
Proteomics Profiling Reveals the Molecular Signatures and Potential Therapeutic Targets of Human Nasopharyngeal Carcinoma	15
Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry	15
The Hyperproliferation Mechanism of Cholesteatoma Based on Proteomics: SNCA Promotes Autophagy-Mediated Cell Proliferation Through the PI3K/AKT/CyclinD1 Signaling Pathway	15
Clinical Proteomics for Solid Organ Tissues	15
Serum Proteomics Identifies Biomarkers Associated With the Pathogenesis of Idiopathic Pulmonary Fibrosis	15
LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections	14

In-Cell Chemical Crosslinking Identifies Hotspots for SQSTM-1/p62-IκBα Interaction That Underscore a Critical Role of p62 in Limiting NF-κB Activation Through IκBα Stabilization	14
The Plastidial Protein Acetyltransferase GNAT1 Forms a Complex With GNAT2, yet Their Interaction Is Dispensable for State Transitions	14
Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients	14
The Proteome of Large or Small Extracellular Vesicles in Pig Seminal Plasma Differs, Defining Sources and Biological Functions	14
Global Proteomics Indicates Subcellular-Specific Anti-Ferroptotic Responses to Ionizing Radiation	14
Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies	14
Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine	14
Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines	13
Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice	13
Integrated Application of Multiomics Strategies Provides Insights Into the Environmental Hypoxia Response in Pelteobagrus vachelli Muscle	13
Biochemical Deconstruction and Reconstruction of Nuclear Matrix Reveals the Layers of Nuclear Organization	13
Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias	13
Comprehensive Glycomic and Proteomic Analysis of Mouse Striatum and Lateral Hypothalamus Following Repeated Exposures to Cocaine or Methamphetamine	12
Molecular Signatures of Neurodegenerative Diseases Identified by Proteomic and Phosphoproteomic Analyses in Aging Mouse Brain	12
High-throughput and high-sensitivity biomarker monitoring in body fluid by FAIMS-enhanced fast LC SureQuant™ IS targeted quantitation	12
Integrated Multiomics Reveals Alterations in Paucimannose and Complex Type N-Glycans in Cardiac Tissue of Patients with COVID-19	12
Facioscapulohumeral Muscular Dystrophy is Associated With Altered Myoblast Proteome Dynamics	12
Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication	12
inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction	12
Tissue-Characteristic Expression of Mouse Proteome	12
Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis	12
Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides	12
A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics	11
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes	11
Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023	11
Analysis of the Healthy Platelet Proteome Identifies a New Form of Domain-Specific O-Fucosylation	11
An Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics	11
MHC Class I Immunopeptidome: Past, Present, and Future	11
The Role of Serine/Threonine-Specific Protein Kinases in Cyanobacteria - SpkB Is Involved in Acclimation to Fluctuating Conditions in Synechocystis sp. PCC 6803	11
Integrative Proteomic Analysis Reveals the Cytoskeleton Regulation and Mitophagy Difference Between Ischemic Cardiomyopathy and Dilated Cardiomyopathy	11
A Comparative Analysis of Data Analysis Tools for Data-Independent Acquisition Mass Spectrometry	11
MS-Based Proteomics of Body Fluids: The End of the Beginning	10
Dichotomous Responses to Chronic Fetal Hypoxia Lead to a Predetermined Aging Phenotype	10
Detection of Pancreatic Ductal Adenocarcinoma-Associated Proteins in Serum	10
Phosphoproteome Profiling of the Receptor Tyrosine Kinase MuSK Identifies Tyrosine Phosphorylation of Rab GTPases	10
Addressing NHS chemistry: Efficient quenching of excess TMT reagent and reversing TMT-over labelling in proteomic samples by methylamine	10
Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF	10
Cover	10
Screening of Cancer-Specific Biomarkers for Hepatitis B-Related Hepatocellular Carcinoma Based on a Proteome Microarray	10
Cover	10
Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification	10
Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate	10
Multi-Omic Analysis of Esophageal Adenocarcinoma Uncovers Candidate Therapeutic Targets and Cancer-Selective Posttranscriptional Regulation	10
Cover	10
Ion Mobility–Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen	10
Larval Exposure to Parasitic Varroa destructor Mites Triggers Specific Immune Responses in Different Honey Bee Castes and Species	10
The Cancer Cell Mapping Initiative	9
Cover	9
HEXB Drives Raised Paucimannosylation in Colorectal Cancer and Stratifies Patient Risk	9
Filter-Aided Extracellular Vesicle Enrichment (FAEVEr) for Proteomics	9
WITHDRAWN	9
Direct DIA database search with PEAKS Online XPro increases HLA-I peptide identification and bypasses the requirement for large spectral libraries	9
WITHDRAWN	9
Toward Comprehensive, Single-molecule Proteomics: Protein Identification by Shortepitope Mapping	9
Proteogenomic analyses of CRISPR inhibited expression of a panel genes associated with Alzheimer's disease and related dementias in iPSC-derived neurons using a fully automated workflow	9
Multitiered Proteome Analysis Displays the Hyperpermeability of the Rheumatoid Synovial Compartment for Plasma Proteins	9
Recent Advances in Mass Spectrometry-Based Protein Interactome Studies	9
Editorial Board	9
Profiling the cellular signalling state by targeted phoshoproteomics	9
Identification of novel viral class I-restricted peptides in Merkel cell carcinoma	9
A BioID-derived proximity interactome for Protein Phosphatase PP2A	9
MCP’s New Editorial Posture Moving Forward	9
Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer	9
Alzheimer's Disease Biomarker Analysis Using Targeted Mass Spectrometry	9
PRM-LIVE Accelerates Target Class-based Selectivity Profiling of Small Molecule Inhibitors	9
Validation of Predicted Neoantigens in Patient Derived Material by Targeted Mass Spectrometry	9
An AI-driven leap forward in peptide identification through deconvolution of chimeric spectra	9
The rise of molecular glues and bifunctional compounds	8
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell–Derived Cells	8
Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices With Zeno SWATH Data-Independent Acquisition	8
Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters	8
PhosphoDisco: A Toolkit for Co-regulated Phosphorylation Module Discovery in Phosphoproteomic Data	8
From AI-driven synthetic biology to prediction of molecular phenotypes	8
WITHDRAWN	8
Post-translational Modifications and Their Effects on the Conformation and Function of Hsp90 in Embryonic Stem Cells	8
High-throughput subcellular proteomics reveals phospho-signaling dynamics	8
Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP	8
Into the Dark Serum Proteome: Personalized Features of IgG1 and IgA1 Repertoires in Severe COVID-19 Patients	8
An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics	8
WITHDRAWN	8

In Situ Cell-Surface Proteomics: Method Development and Applications in Neurobiology	8
Activity-based proteomic profiling reveals reduction of lipid hydrolase activity levels in non-small cell lung cancer tumors	8
WITHDRAWN	8
Cover	8
The Proteome and Phosphoproteome Uncovers Candidate Proteins Associated With Vacuolar Phosphate Signal Multipled by Vacuolar Phosphate Transporter 1 (VPT1) in Arabidopsis	8
Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification	8
SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines	8
Developing Cross-linking Mass Spectrometry to Define Protein Interaction Landscapes	8
Discovery of shared cancer neoantigen epitopes through mass spectrometry analysis of engineered monoallelic cell lines	8
Integrative Structural Biology to Understand Biological Complexity	8
Histone Chaperone Deficiency in Arabidopsis Plants Triggers Adaptive Epigenetic Changes in Histone Variants and Modifications	7
Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development	7
Characterization of p38α Signaling Networks in Cancer Cells Using Quantitative Proteomics and Phosphoproteomics	7
Proteome, Lysine Acetylome, and Succinylome Identify Posttranslational Modification of STAT1 as a Novel Drug Target in Silicosis	7
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions	7
Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry	7
Identifying Patients With Rapid Progression From Hormone-Sensitive to Castration-Resistant Prostate Cancer: A Retrospective Study	7
A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell	7
Proteomic Dynamics of Breast Cancer Cell Lines Identifies Potential Therapeutic Protein Targets	7
Pupylation-Based Proximity-Tagging of FERONIA-Interacting Proteins in Arabidopsis	7
Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay	7
Differential Analysis of Cereblon Neosubstrates in Rabbit Embryos Using Targeted Proteomics	7
Replisome Proximal Protein Associations and Dynamic Proteomic Changes at Stalled Replication Forks	7
Insights Into Glycobiology and the Protein-Glycan Interactome Using Glycan Microarray Technologies	7
Super Enhanced Purification of Denatured-Refolded Ubiquitinated Proteins by ThUBD Revealed Ubiquitinome Dysfunction in Liver Fibrosis	7
Assessing Target Specificity of the Small Molecule Inhibitor MARIMASTAT to Snake Venom Toxins: A Novel Application of Thermal Proteome Profiling	7
The Second Asia-Oceania Human Proteome Organization (AOHUPO) Online Education Series on the Renaissance of Clinical Proteomics: Biomarkers, Imaging and Therapeutics	7
A Massive Proteogenomic Screen Identifies Thousands of Novel Peptides From the Human “Dark” Proteome	7