Molecular & Cellular Proteomics

Article	Citations
Cover	102
Isolation of proteins on chromatin (iPOC) reveals signaling pathway-dependent alterations in the DNA-bound proteome	92
Quantitative Proteomic Analysis Reveals Functional Alterations of the Peripheral Immune System in Colorectal Cancer	83
Multi-Omic Analysis of Esophageal Adenocarcinoma Uncovers Candidate Therapeutic Targets and Cancer-Selective Posttranscriptional Regulation	61
Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression	56
Global Proteomics Indicates Subcellular-Specific Anti-Ferroptotic Responses to Ionizing Radiation	47
Quantitative chromatin protein dynamics during replication origin firing in human cells	45
Cover	43
Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF	36
Personalized Drug Therapy: Innovative Concept Guided With Proteoformics	35
Molecular Signatures of Neurodegenerative Diseases Identified by Proteomic and Phosphoproteomic Analyses in Aging Mouse Brain	34
Cover	31
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes	30
Cover	29
The Urinary Proteomic Profile Implicates Key Regulators for Urologic Chronic Pelvic Pain Syndrome (UCPPS): A MAPP Research Network Study	28
Increasing the coverage, throughput and accessibility of single-cell proteomics	27
Identification of tumor antigens for cancer immunotherapy	27
Table of Contents	27
MS-based Detection of Pathogen Antigen Through Immunoprecipitation of Its Proteolytic Peptides	26
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	25
Proteomics of spatially identified tissues in whole organs	24
A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics	24
Increasing the Throughput of Activity-Based Proteome Profiling Studies with Real-Time Search and Sample Hyperplexing	23
Easier, More Robust, and Faster Low-flow Quantitative Proteomics Approach	22
Computational challenges of identification and quantification algorithms in single-cell proteomic data.	22

Discovery of GSTZ1 as a novel target by using fully functionalized fragment-like probes and chemical proteomics	22
PROTEOMIC CHANGES TO THE ANTERIOR CEREBRAL ARTERY IN ALZHEIMER’S DISEASE	22
Distribution analysis of small metabolites on lens using sand-rose-like ZnO for imaging mass spectrometry	21
Simultaneous quantification of GDF15 and IGFBP7 by LC-MS/MS for studies on hyperemesis gravidarum	21
Defining the molecular basis of immune heterogeneity between individuals using immunoproteomics	20
Chemoproteomic capture of RNA binding activity in living cells	20
ETV6-NTRK3 oncofusion variant interactomes	20
Post-Deconvolution MS/MS Spectra Extraction with Data-Independent Acquisition for Comprehensive Profiling of Urinary Conjugated Metabolome	20
An Atlas of the Knee Joint Proteins and Their Role in Osteoarthritis Defined by Literature Mining	19
The social architecture of an in-depth cellular protein interactome	19
Proteomics Profiling Reveals the Molecular Signatures and Potential Therapeutic Targets of Human Nasopharyngeal Carcinoma	18
Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry	18
New Global Insights on the Regulation of the Biphasic Life Cycle and Virulence Via ClpP-Dependent Proteolysis in Legionella pneumophila	18
Comprehensive Glycomic and Proteomic Analysis of Mouse Striatum and Lateral Hypothalamus Following Repeated Exposures to Cocaine or Methamphetamine	17
Cover	17
High-Throughput Human Complement C3 N-Glycoprofiling Identifies Markers of Early Onset Type 1 Diabetes Mellitus in Children	16
ProMetheusDB: An In-Depth Analysis of the High-Quality Human Methyl-proteome	16
MHC Class I Immunopeptidome: Past, Present, and Future	16
Deciphering Nucleic Acid Binding Proteome of Mouse Immune Organs Reveals Hub Proteins for Aging	16
Functional Impact of Protein–RNA Variation in Clinical Cancer Analyses	16
DIA-Based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia	15
FMRP Long-Range Transport and Degradation Are Mediated by Dynlrb1 in Sensory Neurons	15
EGFR-T790M Mutation–Derived Interactome Rerouted EGFR Translocation Contributing to Gefitinib Resistance in Non-Small Cell Lung Cancer	15
Analysis of the Healthy Platelet Proteome Identifies a New Form of Domain-Specific O-Fucosylation	15
Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression	15
High-Resolution Structural Proteomics of Mitochondria Using the ‘Build and Retrieve’ Methodology	15
Integrative Proteomic Analysis Reveals the Cytoskeleton Regulation and Mitophagy Difference Between Ischemic Cardiomyopathy and Dilated Cardiomyopathy	14
A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics	14
Insight Into the Dynamics of the Ixodes ricinus Nymphal Midgut Proteome	14
Tissue-Characteristic Expression of Mouse Proteome	14
inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction	13
Normics: Proteomic Normalization by Variance and Data-Inherent Correlation Structure	13
Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation	13
Targeted Dynamic Phospho-Proteogenomic Analysis of Gastric Cancer Cells Suggests Host Immunity Provides Survival Benefit	13
The Hyperproliferation Mechanism of Cholesteatoma Based on Proteomics: SNCA Promotes Autophagy-Mediated Cell Proliferation Through the PI3K/AKT/CyclinD1 Signaling Pathway	13
Biochemical Deconstruction and Reconstruction of Nuclear Matrix Reveals the Layers of Nuclear Organization	13
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	12
Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2) Is Upregulated in Breast Epithelial–Mesenchymal Transition and Responds to Oxidative Stress	12
Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p	12
Bioinertization of NanoLC/MS/MS Systems by Depleting Metal Ions From the Mobile Phases for Phosphoproteomics	12
Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model	12
Application of Liquid-Liquid Extraction for N-terminal Myristoylation Proteomics	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
An Integrated Approach to Protein Discovery and Detection From Complex Biofluids	11
Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies	11
CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1	11
Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis	11
Global Analysis of Post-Translational Side-Chain Arginylation Using Pan-Arginylation Antibodies	11
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	11
An Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics	10

Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	10
A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development	10
metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis	10
Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines	10
Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice	10
Cover	10
Proteomic Analysis Reveals the Composition of Glutamatergic Organelles of Auditory Inner Hair Cells	10
Integrated Liver and Plasma Proteomics in Obese Mice Reveals Complex Metabolic Regulation	9
Integrated Application of Multiomics Strategies Provides Insights Into the Environmental Hypoxia Response in Pelteobagrus vachelli Muscle	9
Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias	9
Clinical Proteomics for Solid Organ Tissues	9
The Proteome of Large or Small Extracellular Vesicles in Pig Seminal Plasma Differs, Defining Sources and Biological Functions	9
A Comparative Analysis of Data Analysis Tools for Data-Independent Acquisition Mass Spectrometry	9
CySP3-96 enables scalable, streamlined, and low-cost sample preparation for cysteine chemoproteomic applications	9
Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine	9
Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides	9
Prenylated PALM2 Promotes the Migration of Esophageal Squamous Cell Carcinoma Cells Through Activating Ezrin	9
MS-Based Proteomics of Body Fluids: The End of the Beginning	9
Secretome Analysis: Reading Cellular Sign Language to Understand Intercellular Communication	9
An Inflection Point in Cancer Protein Biomarkers: What was and What's Next	9
Facioscapulohumeral Muscular Dystrophy is Associated With Altered Myoblast Proteome Dynamics	9
Cover	8
Cover	8
Proteomics, Transcriptomics, and Phosphoproteomics Reveal the Mechanism of Talaroconvolutin-A Suppressing Bladder Cancer via Blocking Cell Cycle and Triggering Ferroptosis	8
Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid	8
LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections	8
Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients	8
DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis	8
Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay	8
Differential Analysis of Cereblon Neosubstrates in Rabbit Embryos Using Targeted Proteomics	8
Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors Into Peptide Identification	8
Dichotomous Responses to Chronic Fetal Hypoxia Lead to a Predetermined Aging Phenotype	8
Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts	8
The Plastidial Protein Acetyltransferase GNAT1 Forms a Complex With GNAT2, yet Their Interaction Is Dispensable for State Transitions	8
Serum Proteomics Identifies Biomarkers Associated With the Pathogenesis of Idiopathic Pulmonary Fibrosis	8
High-throughput and high-sensitivity biomarker monitoring in body fluid by FAIMS-enhanced fast LC SureQuant™ IS targeted quantitation	8
Ion Mobility–Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen	8
Interval-Based Secretomics Unravels Acute-Phase Response in Hepatocyte Model Systems	8
An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics	8
Cover	8
Mass Spectrometry–Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease	8
Detection of Pancreatic Ductal Adenocarcinoma-Associated Proteins in Serum	8
Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023	8
Multi–Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins	8
Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates	7
Epitope Mapping of Human Polyclonal Antibodies to the fHbp Antigen of a Neisseria Meningitidis Vaccine by Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS)	7
MCP’s New Editorial Posture Moving Forward	7
The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation	7
Early Proteomic Characteristics and Changes in the Optic Nerve Head, Optic Nerve, and Retina in a Rat Model of Ocular Hypertension	7
Identification and Analysis of Six Phosphorylation Sites Within the Xenopus laevis Linker Histone H1.0 C-Terminal Domain Indicate Distinct Effects on Nucleosome Structure	7
Universal Pretreatment Development for Low-input Proteomics Using Lauryl Maltose Neopentyl Glycol	7
Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP	7
Global Phosphoproteomics Unveils Kinase-Regulated Networks in Systemic Lupus Erythematosus	7
Characterization of p38α Signaling Networks in Cancer Cells Using Quantitative Proteomics and Phosphoproteomics	7
A Massive Proteogenomic Screen Identifies Thousands of Novel Peptides From the Human “Dark” Proteome	7
Into the Dark Serum Proteome: Personalized Features of IgG1 and IgA1 Repertoires in Severe COVID-19 Patients	7
A Novel Spectral Annotation Strategy Streamlines Reporting of Mono-ADP-ribosylated Peptides Derived from Mouse Liver and Spleen in Response to IFN-γ	7
Proteomic Dynamics of Breast Cancer Cell Lines Identifies Potential Therapeutic Protein Targets	7
Cover	7
Enhanced Proteomic Coverage in Tissue Microenvironment by Immune Cell Subtype Library-Assisted DIA-MS	7
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell–Derived Cells	7
Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification	7
Widespread Arginine Phosphorylation in Staphylococcus aureus	7
Integrative Proteomics and N-Glycoproteomics Analyses of Rheumatoid Arthritis Synovium Reveal Immune-Associated Glycopeptides	7
The Proteome and Phosphoproteome Uncovers Candidate Proteins Associated With Vacuolar Phosphate Signal Multipled by Vacuolar Phosphate Transporter 1 (VPT1) in Arabidopsis	7
Comparative Proteomic Analysis Identifies Key Metabolic Regulators of Gemcitabine Resistance in Pancreatic Cancer	7
The in vivo Interaction Landscape of Histones H3.1 and H3.3	7
The Second Asia-Oceania Human Proteome Organization (AOHUPO) Online Education Series on the Renaissance of Clinical Proteomics: Biomarkers, Imaging and Therapeutics	7
From AI-driven synthetic biology to prediction of molecular phenotypes	6
Histone Chaperone Deficiency in Arabidopsis Plants Triggers Adaptive Epigenetic Changes in Histone Variants and Modifications	6
Filter-aided extracellular vesicle enrichment (FAEVEr) for proteomics	6
Improved Mass Spectrometry–Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles	6
Integrative Structural Biology to Understand Biological Complexity	6
An AI-driven leap forward in peptide identification through deconvolution of chimeric spectra	6
Validation of Predicted Neoantigens in Patient Derived Material by Targeted Mass Spectrometry	6
Activity-based proteomic profiling reveals reduction of lipid hydrolase activity levels in non-small cell lung cancer tumors	6
In-Depth Mass Spectrometry Analysis Reveals the Plasma Proteomic and N-Glycoproteomic Impact of an Amish-Enriched Cardioprotective Variant in B4GALT1	6
Developing Cross-linking Mass Spectrometry to Define Protein Interaction Landscapes	6
Assessing Target Specificity of the Small Molecule Inhibitor MARIMASTAT to Snake Venom Toxins: A Novel Application of Thermal Proteome Profiling	6
WITHDRAWN	6

High-throughput subcellular proteomics reveals phospho-signaling dynamics	6
Direct DIA database search with PEAKS Online XPro increases HLA-I peptide identification and bypasses the requirement for large spectral libraries	6
Post-translational Modifications and Their Effects on the Conformation and Function of Hsp90 in Embryonic Stem Cells	6
The rise of molecular glues and bifunctional compounds	6
Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol	6
Identifying Patients With Rapid Progression From Hormone-Sensitive to Castration-Resistant Prostate Cancer: A Retrospective Study	6
Larval Exposure to Parasitic Varroa destructor Mites Triggers Specific Immune Responses in Different Honey Bee Castes and Species	6
Proteome, Lysine Acetylome, and Succinylome Identify Posttranslational Modification of STAT1 as a Novel Drug Target in Silicosis	6
Identification of novel viral class I-restricted peptides in Merkel cell carcinoma	6
Toward Comprehensive, Single-molecule Proteomics: Protein Identification by Shortepitope Mapping	6
WITHDRAWN	6
WITHDRAWN	6
Functional Diversity and Evolution of the Drosophila Sperm Proteome	5
Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry	5
Cover	5
Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development	5
WITHDRAWN	5
Proteome Dynamics in iPSC-Derived Human Dopaminergic Neurons	5
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	5
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions	5
In Situ Cell-Surface Proteomics: Method Development and Applications in Neurobiology	5
Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry–Based Proteomics	5
Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer	5
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals	5
A BioID-derived proximity interactome for Protein Phosphatase PP2A	5
Profiling the cellular signalling state by targeted phoshoproteomics	5
Proteome Remodeling of the Eye Lens at 50 Years Identified With Data-Independent Acquisition	5
Replisome Proximal Protein Associations and Dynamic Proteomic Changes at Stalled Replication Forks	5
WITHDRAWN	5
Phosphoproteome Profiling of the Receptor Tyrosine Kinase MuSK Identifies Tyrosine Phosphorylation of Rab GTPases	5
Discovery of shared cancer neoantigen epitopes through mass spectrometry analysis of engineered monoallelic cell lines	5
The Lysine Acetylation Modification in the Porin Aha1 of Aeromonas hydrophila Regulates the Uptake of Multidrug Antibiotics	5
Proteomics-Derived Biomarker Panel Facilitates Distinguishing Primary Lung Adenocarcinomas With Intestinal or Mucinous Differentiation From Lung Metastatic Colorectal Cancer	5
The Cancer Cell Mapping Initiative	5
Editorial Board	5
Fast and Accurate Disulfide Bridge Detection	5
A Carrier-Based Quantitative Proteomics Method Applied to Biomarker Discovery in Pericardial Fluid	5
PRM-LIVE Accelerates Target Class-based Selectivity Profiling of Small Molecule Inhibitors	5