Molecular & Cellular Proteomics

Article	Citations
CellEKT: A Robust Chemical Proteomics Workflow to Profile Cellular Target Engagement of Kinase Inhibitors	230
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing	188
Quantitative Proteomic Analysis Reveals Functional Alterations of the Peripheral Immune System in Colorectal Cancer	142
Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid	102
Employing Expression-Matched Controls Enables High-Confidence Proximity-Based Interactome Classification	93
Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model	82
Spatial Proteomics Reveals Distinct Protein Patterns in Cortical Migration Disorders Caused by LIN28A Overexpression and WNT Activation	79
Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression	74
Temporal Wheat Proteome Remodeling by Deoxynivalenol Reveals Novel Detoxification Signatures and Strategies Across Cultivars	71
LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections	64
Sequencing of Polyclonal Antibodies by Integrating Intact Mass, Middle-Down and De Novo Bottom-Up Mass Spectrometry	62
Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation	62
mTORC2 Regulates Non-homologous End Joining Through Modulating the Temporal Dynamics of 53BP1	59
A Methanolic Urea-Enhanced Protein Extraction Enabling the Largest Bacterial Phosphorylation Resource	57
Region- and Cell-type–Resolved Multiomic Atlas of the Heart	55
Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p	54
Proteomic portrait of degranulation program in human circulating neutrophils upon multi-inflammatory and infectious activation	54
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	51
PROTEOMIC CHANGES TO THE ANTERIOR CEREBRAL ARTERY IN ALZHEIMER’S DISEASE	50
Table of Contents	49
Easier, More Robust, and Faster Low-flow Quantitative Proteomics Approach	46
CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1	45
A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development	41
Prenylated PALM2 Promotes the Migration of Esophageal Squamous Cell Carcinoma Cells Through Activating Ezrin	40
Clinical Proteomics for Solid Organ Tissues	39

Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides	39
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	39
Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis	38
Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine	37
Proteome Profiling of Cerebrospinal Fluid and Machine Learning Reveal Protein Classifiers of Two Forms of Alzheimer’s Disease Characterized by Increased or Not Altered Levels of Tau	35
HEXB Drives Raised Paucimannosylation in Colorectal Cancer and Stratifies Patient Risk	34
Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development	34
Phosphoproteome Analysis Identifies a Synaptotagmin-1-Associated Complex Involved in Ischemic Neuron Injury	33
Bridging the Gap From Proteomics Technology to Clinical Application: Highlights From the 68th Benzon Foundation Symposium	33
Proximity Labeling and SILAC-Based Proteomic Approach Identifies Proteins at the Interface of Homotypic and Heterotypic Cancer Cell Interactions	33
Filter-Aided Extracellular Vesicle Enrichment (FAEVEr) for Proteomics	33
Phosphoproteome Profiling of the Receptor Tyrosine Kinase MuSK Identifies Tyrosine Phosphorylation of Rab GTPases	31
Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification	31
The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation	31
WITHDRAWN	31
A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell	31
Developing Cross-linking Mass Spectrometry to Define Protein Interaction Landscapes	30
Toward Comprehensive, Single-molecule Proteomics: Protein Identification by Shortepitope Mapping	29
PRM-LIVE Accelerates Target Class-based Selectivity Profiling of Small Molecule Inhibitors	29
The rise of molecular glues and bifunctional compounds	29
High-throughput subcellular proteomics reveals phospho-signaling dynamics	29
Development of a Fit-For-Purpose Multi-Marker Panel for Early Diagnosis of Pancreatic Ductal Adenocarcinoma	28
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	28
In Situ Cell-Surface Proteomics: Method Development and Applications in Neurobiology	28
DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis	27
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions	27
Proteomics, Transcriptomics, and Phosphoproteomics Reveal the Mechanism of Talaroconvolutin-A Suppressing Bladder Cancer via Blocking Cell Cycle and Triggering Ferroptosis	27
Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate	27
Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin	27
Integrative Proteomics and N-Glycoproteomics Analyses of Rheumatoid Arthritis Synovium Reveal Immune-Associated Glycopeptides	26
Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA	26
Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates	26
Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics	26
Recent Advances in Mass Spectrometry-Based Studies of Post-Translational Modifications in Alzheimer’s Disease	25
Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification	25
Improved Mass Spectrometry–Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles	25
The in vivo Interaction Landscape of Histones H3.1 and H3.3	25
Recent Advances in Mass Spectrometry-Based Protein Interactome Studies	25
Accurate MS-Based Diagnostic Amyloid Typing Using Endogenously Normalized Protein Intensities in Formalin-Fixed Paraffin-Embedded Tissue	24
Multi-Omics Analysis Unveils Nsun5-Mediated Molecular Alterations in the Somatosensory Cortex and Its Impact on Pain Sensation	24
From Discovery to Delivery: A Rapid and Targeted Proteomics Workflow for Monitoring Chinese Hamster Ovary Biomanufacturing	23
The One Hour Human Proteome	22
Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection	22
An Automated Workflow to Address Proteome Complexity and the Large Search Space Problem in Proteomics and HLA-I Immunopeptidomics	22
(Sialyl)Lewis Antigen Expression on Glycosphingolipids, N-, and O-Glycans in Colorectal Cancer Cell Lines is Linked to a Colon-Like Differentiation Program	22
Enhanced In Situ Spatial Proteomics by Effective Combination of MALDI Imaging and LC-MS/MS	22
In-Depth Analysis of miRNA Binding Sites Reveals the Complex Response of Uterine Epithelium to miR-26a-5p and miR-125b-5p During Early Pregnancy	22
Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays	21
Mapping diverse proteome responses with intelligent mass spectrometry	21
Highly multiplexed proteome-wide quantitation of functional residues enabled by a novel 11plex-AzidoTMT reagent	21

Proteomic Identification of Autophagy Cargo Using Novel Tools in Combination with Quantitative Proteomics.	21
Mass spectrometry and SomaScan technologies to detect a plasma copper proteome in two human populations	21
Multi-nanoparticle Workflow Enables Deep Plasma Proteomics at Scale, with Enhanced Precision, and Depths of Coverage	21
Prospective on Imaging Mass Spectrometry in Clinical Diagnostics	20
TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics	20
Automated workflows for DIA data using DIA-NN on the PaSER platform	20
The Role of Clinical Glyco(proteo)mics in Precision Medicine	20
Highly multiplexed label-free imaging of tissue proteoforms using individual ion mass spectrometry	20
Cover	19
Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification	19
Causal Inference and Annotation of Phosphoproteomics Data in Multiomics Cancer Studies	19
pXg: Comprehensive Identification of Noncanonical MHC-I–Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads	19
Whole blood proteome dynamics defines predictive diagnostic and prognostic signatures of cryptococcal infection	18
A Time Point Proteomic Analysis Reveals Protein Dynamics of Plasmodium Oocysts	18
MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets	18
Clinical Proteomics: A Promise Becoming Reality	18
Chemical Proteomics Reveals Nε-Fatty-Acylation of Septins by Rho Inactivation Domain (RID) of the Vibrio MARTX Toxin to Alter Septin Localization and Organization	18
Generation of a Deep Mouse Brain Spectral Library for Transmembrane Proteome Profiling in Mental Disease Models	18
Mapping Hydrogen Migration Thresholds for Site-Specific HDX-MS	18
Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses	18
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling	17
Computational challenges of identification and quantification algorithms in single-cell proteomic data.	17
Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes	17
11th Asia Oceania Human Proteome Organization Congress Report	17
Cover	17
Deciphering the highly complex cancer immunopeptidome	17
Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress	17
Mapping the Degradable Kinome: A Resource for Expedited Degrader Development	17
Three-dimensional feature matching improves the sensitivity of single-cell and spatial proteomics	17
Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation	17
Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer	17
Yellow Fever Blood Proteomics Study by Trapped Ion Mobility Mass Spectrometry	17
Back Cover	17
SIRT3 Functions as an Eraser of Histone H3K9 Lactylation to Modulate Transcription for Inhibiting the Progression of Esophageal Cancer	17
Elucidating Fibroblast Growth Factor–Induced Kinome Dynamics Using Targeted Mass Spectrometry and Dynamic Modeling	17
TEAD Proteins Associate With DNA Repair Proteins to Facilitate Cellular Recovery From DNA Damage	17
Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector	16
Localized K63 Ubiquitin Signaling Is Regulated by VCP/p97 During Oxidative Stress	16
Phosphorylation Dynamics in a flg22-Induced, G Protein–Dependent Network Reveals the AtRGS1 Phosphatase	16
Early Life Exposure to Deltamethrin Impairs Synaptic Function by Altering the Brain-Derived Extracellular Vesicle Proteome	16
Restrained Wnt Signaling Pathway by Enhanced EsGSK3β Activity Facilitates the Infection of Spiroplasma and Leads to Neuropathic Diseases in Crustaceans	16
Landscape of Steroid Dynamics in Pregnancy: Insights From the Maternal-Placental-Fetal Unit and Placental Models	16
Jolkinolide B Activates Mitophagy to Exhibit Antipancreatic Cancer Activity and Alleviate Cognitive Deficits in Alzheimer's Disease	16
Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades	16
Comparative N-Glycoproteomics Reveals Subtype-Specific N-Glycosylation Signatures and Immune Associations in Cholangiocarcinoma	16
MSstatsTMT Improves Accuracy of Thermal Proteome Profiling	15
AMPylation Regulates 5′-3′ Exonuclease PLD3 Processing	15
An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity	15
Phosphoproteomic Analysis of FLCN Inactivation Highlights Differential Kinase Pathways and Regulatory TFEB Phosphoserines	15
Multi-omics Characterization of Acquired Olaparib Resistance in BRCA1 and BRCA2 Mutant Breast Cancer Cell Lines	15
Proteogenomic Analysis of Breast Cancer Transcriptomic and Proteomic Data, Using De Novo Transcript Assembly: Genome-Wide Identification of Novel Peptides and Clinical Implications	15
Cover	15
WITHDRAWN	15
Quantification and Proteomic Characterization of β-Hydroxybutyrylation Modification in the Hearts of AMPKα2 Knockout Mice	15
Zscan4 as a candidate conveyor of early developmental defects in O-GlcNAc transferase intellectual disability	15
Large-Scale Plasma Proteome Epitome Profiling is an Efficient Tool for the Discovery of Cancer Biomarkers	15
A New Monoclonal Antibody Enables BAR Analysis of Subcellular Importin β1 Interactomes	15
msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level	15
Experience-Induced Remodeling of the Hippocampal Post-synaptic Proteome and Phosphoproteome	14
Complexome profiling of mitochondrial oxidative phosphorylation knockout models.	14
Galectin-4 Antimicrobial Activity Primarily Occurs Through its C-Terminal Domain	14
Integrated Proteomics to Understand the Role of Neuritin (NRN1) as a Mediator of Cognitive Resilience to Alzheimer’s Disease	14
Exploring the Spatial Landscape of the Estrogen Receptor Proximal Proteome With Antibody-Based Proximity Labeling	14
Tracking drug action at the cell surface and the secreted proteome	14
Sulconazole Induces PANoptosis by Triggering Oxidative Stress and Inhibiting Glycolysis to Increase Radiosensitivity in Esophageal Cancer	14
Application of stable isotope labelingbased quantitative PTM proteomics and interactomics in study of Arabidopsis cell signaling	14
Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence	14
Trypanosoma cruzi cardiomyocyte infection promotes innate immune response and metabolic rewiring	14
A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans	14
Predicting Protein Pathways Associated to Tumor Heterogeneity by Correlating Spatial Lipidomics and Proteomics: The Dry Proteomic Concept	14
WITHDRAWN	13
Antibody Profiling of Pan-Cancer Viral Proteome Reveals Biomarkers for Nasopharyngeal Carcinoma Diagnosis and Prognosis	13
GRable Version 1.0: A Software Tool for Site-Specific Glycoform Analysis With Improved MS1-Based Glycopeptide Detection With Parallel Clustering and Confidence Evaluation With MS2 Information	13
Mass Spectrometry–Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes	13
Antibody-based enrichment of phosphotyrosine peptides using magnetic beads simplifies and outperforms results obtained using Protein A agarose beads	13
Evaluating timsTOF Pro 2 for the analysis of histone PTMs measured in Global Chromatin Profiling using dia-PASEF and prm-PASEF	13
Robust and accurate redox metabolomics and proteomics of clinical samples by in situ derivatization of free thiols	13
Nucleolar Proteomics Revealed the Regulation of RNA Exosome Localization by MTR4	13
WITHDRAWN	13
Analyzing N-Glycosylation Biosynthetic Networks Using Mass Spectrometry	13

Challenges and Opportunities for Single-cell Computational Proteomics	13
Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains	13
Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice	12
Application of Liquid-Liquid Extraction for N-terminal Myristoylation Proteomics	12
Cover	12
The Proteome of Large or Small Extracellular Vesicles in Pig Seminal Plasma Differs, Defining Sources and Biological Functions	12
High-Throughput Proteomic and Phosphoproteomic Analysis of Formalin-Fixed Paraffin-Embedded Tissues	12
Integrated Multiomics Reveals Alterations in Paucimannose and Complex Type N-Glycans in Cardiac Tissue of Patients with COVID-19	12
Bioinertization of NanoLC/MS/MS Systems by Depleting Metal Ions From the Mobile Phases for Phosphoproteomics	12
Cover	12
Single-Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived From Human iPSCs and Adult Hearts	12
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes	12
inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction	12
Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies	12
Insight Into the Dynamics of the Ixodes ricinus Nymphal Midgut Proteome	12
Serum Exosomes From Epithelial Ovarian Cancer Patients Contain LRP1, Which Promotes the Migration of Epithelial Ovarian Cancer Cell	12
Early Proteomic Characteristics and Changes in the Optic Nerve Head, Optic Nerve, and Retina in a Rat Model of Ocular Hypertension	11
Editorial Board	11
Super Enhanced Purification of Denatured-Refolded Ubiquitinated Proteins by ThUBD Revealed Ubiquitinome Dysfunction in Liver Fibrosis	11
An Improved Method for Sampling and Quantitative Protein Analytics of Cerebrospinal Fluid of Individual Mice	11
Ciliopathy-Associated Missense Mutations in IFT140 are Tolerated by the Inherent Resilience of the IFT Machinery	11
WITHDRAWN	11
Post-translational Modifications and Their Effects on the Conformation and Function of Hsp90 in Embryonic Stem Cells	11
Cover	11
Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay	11
ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis	11
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell–Derived Cells	11
The Proteome and Phosphoproteome Uncovers Candidate Proteins Associated With Vacuolar Phosphate Signal Multipled by Vacuolar Phosphate Transporter 1 (VPT1) in Arabidopsis	11
Global Proteomics Reveals Distinct Muscle Adaptations to Menstrual Cycle Phase-Based Sprint Interval Training in Endurance-Trained Females	11
An AI-driven leap forward in peptide identification through deconvolution of chimeric spectra	11
Insights Into Glycobiology and the Protein-Glycan Interactome Using Glycan Microarray Technologies	11
Innovations Toward Immunopeptidomics	11
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics	11
Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics	11
Exploring Virus–Host Interactions Through Combined Proteomic Approaches Identifies BANF1 as a New Essential Factor for African Swine Fever Virus	11
Cover	11
Serum N-glycans as independent predictors of death: A prospective investigation in the AEGIS Cohort	11
An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics	11
LncRNA MALAT1 Facilitates HIV-1 Replication by Upregulation of CHCHD2 and Downregulation of IFN-I Expression	11
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals	11
Early Days in the Hunt Laboratory at UVA, 1969 to 1980	10
diaPASEF Analysis for HLA-I Peptides Enables Quantification of Common Cancer Neoantigens	10
Proteomics and β-hydroxybutyrylation Modification Characterization in the Hearts of Naturally Senescent Mice	10
Change in Publication Schedule	10
BAMS: A Robust Analytical Platform for Quantifying Histone Modifications and Various Proteoforms by IP MALDI MS	10
WITHDRAWN	10
Proteomic Profiling of Muscular Adaptations to Short-Term Concentric Versus Eccentric Exercise Training in Humans	10
iProPhos: A Web-Based Interactive Platform for Integrated Proteome and Phosphoproteome Analysis	10
Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities	10
Corrigendum for “Mass Spectrometry-Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease”	10
Correction: Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β	10
Proteome imaging of human pancreas with a novel microPOTS platform	10
Intelligent Data Acquisition Approaches for Single Cell Proteomics	10
Proteomic Analysis Reveals Trilaciclib-Induced Senescence	10
Cover	10
Impact of Bmal1 Rescue and Time-Restricted Feeding on Liver and Muscle Proteomes During the Active Phase in Mice	10
eEF2K Activity Determines Synergy to Cotreatment of Cancer Cells With PI3K and MEK Inhibitors	10
STK33 Phosphorylates Fibrous Sheath Protein AKAP3/4 to Regulate Sperm Flagella Assembly in Spermiogenesis	10
Proteogenomic analysis of multiple myeloma reveals therapeutic opportunities and predictive signatures	10
Proteomic Characterization of Renal Cell Carcinoma Using MALDI-MS Imaging	10
Inducible Protein Degradation as a Strategy to Identify Phosphoprotein Phosphatase 6 Substrates in RAS-Mutant Colorectal Cancer Cells	10
Soluble VCAM-1 May Serve as a Pharmacodynamic CSF Marker to Monitor BACE2 Activity in Non-Human Primates	10