Molecular & Cellular Proteomics

Article	Citations
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	167
Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine	142
LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections	114
CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1	81
Clinical Proteomics for Solid Organ Tissues	74
Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model	70
Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid	60
Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis	57
Quantitative Proteomic Analysis Reveals Functional Alterations of the Peripheral Immune System in Colorectal Cancer	54
Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression	53
Table of Contents	51
PROTEOMIC CHANGES TO THE ANTERIOR CEREBRAL ARTERY IN ALZHEIMER’S DISEASE	50
Easier, More Robust, and Faster Low-flow Quantitative Proteomics Approach	48
Prenylated PALM2 Promotes the Migration of Esophageal Squamous Cell Carcinoma Cells Through Activating Ezrin	46
Region- and Cell-type–Resolved Multiomic Atlas of the Heart	44
Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p	43
CellEKT: a robust chemical proteomics workflow to profile cellular target engagement of kinase inhibitors	40
Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation	40
Temporal wheat proteome remodeling by deoxynivalenol reveals novel detoxification signatures and strategies across cultivars	39
Employing Expression-Matched Controls Enables High Confidence Proximity-Based Interactome Classification	37
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	36
Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides	33
A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development	33
Developing Cross-linking Mass Spectrometry to Define Protein Interaction Landscapes	32
The rise of molecular glues and bifunctional compounds	32

WITHDRAWN	31
High-throughput subcellular proteomics reveals phospho-signaling dynamics	30
PRM-LIVE Accelerates Target Class-based Selectivity Profiling of Small Molecule Inhibitors	30
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	29
Toward Comprehensive, Single-molecule Proteomics: Protein Identification by Shortepitope Mapping	29
DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis	28
In Situ Cell-Surface Proteomics: Method Development and Applications in Neurobiology	28
HEXB Drives Raised Paucimannosylation in Colorectal Cancer and Stratifies Patient Risk	28
Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development	28
Bridging the Gap From Proteomics Technology to Clinical Application: Highlights From the 68th Benzon Foundation Symposium	28
The in vivo Interaction Landscape of Histones H3.1 and H3.3	26
Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification	26
Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates	26
Development of a Fit-For-Purpose Multi-Marker Panel for Early Diagnosis of Pancreatic Ductal Adenocarcinoma	26
The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation	25
Phosphoproteome Profiling of the Receptor Tyrosine Kinase MuSK Identifies Tyrosine Phosphorylation of Rab GTPases	25
Integrative Proteomics and N-Glycoproteomics Analyses of Rheumatoid Arthritis Synovium Reveal Immune-Associated Glycopeptides	25
Phosphoproteome Analysis Identifies a Synaptotagmin-1-Associated Complex Involved in Ischemic Neuron Injury	25
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions	24
Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics	24
Proteomics, Transcriptomics, and Phosphoproteomics Reveal the Mechanism of Talaroconvolutin-A Suppressing Bladder Cancer via Blocking Cell Cycle and Triggering Ferroptosis	24
Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification	24
Recent Advances in Mass Spectrometry-Based Protein Interactome Studies	23
Filter-Aided Extracellular Vesicle Enrichment (FAEVEr) for Proteomics	23
Improved Mass Spectrometry–Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles	22
Proximity labeling and SILAC based proteomic approach identifies proteins at the interface of homotypic and heterotypic cancer cell interactions	22
Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin	21
Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA	21
Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate	21
A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell	21
Enhanced In Situ Spatial Proteomics by Effective Combination of MALDI Imaging and LC-MS/MS	20
Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection	20
Multi-Omics Analysis Unveils Nsun5-Mediated Molecular Alterations in the Somatosensory Cortex and Its Impact on Pain Sensation	20
Recent Advances in Mass Spectrometry-Based Studies of Post-translational Modifications in Alzheimer’s Disease	20
Mapping diverse proteome responses with intelligent mass spectrometry	20
Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays	20
Multi-nanoparticle Workflow Enables Deep Plasma Proteomics at Scale, with Enhanced Precision, and Depths of Coverage	19
Highly multiplexed label-free imaging of tissue proteoforms using individual ion mass spectrometry	19
Automated workflows for DIA data using DIA-NN on the PaSER platform	19
Proteomic Identification of Autophagy Cargo Using Novel Tools in Combination with Quantitative Proteomics.	19
Mass spectrometry and SomaScan technologies to detect a plasma copper proteome in two human populations	19
Highly multiplexed proteome-wide quantitation of functional residues enabled by a novel 11plex-AzidoTMT reagent	19
TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics	18
Prospective on Imaging Mass Spectrometry in Clinical Diagnostics	18
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	18
(Sialyl)Lewis Antigen Expression on Glycosphingolipids, N-, and O-Glycans in Colorectal Cancer Cell Lines is Linked to a Colon-Like Differentiation Program	18
Three-dimensional feature matching improves the sensitivity of single-cell and spatial proteomics	17
Back Cover	17
The One Hour Human Proteome	17
Yellow Fever Blood Proteomics Study by Trapped Ion Mobility Mass Spectrometry	17

A Time Point Proteomic Analysis Reveals Protein Dynamics of Plasmodium Oocysts	17
Computational challenges of identification and quantification algorithms in single-cell proteomic data.	17
Deciphering the highly complex cancer immunopeptidome	17
The Role of Clinical Glyco(proteo)mics in Precision Medicine	17
pXg: Comprehensive Identification of Noncanonical MHC-I–Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads	16
Mapping the Degradable Kinome: A Resource for Expedited Degrader Development	16
Cover	16
Generation of a Deep Mouse Brain Spectral Library for Transmembrane Proteome Profiling in Mental Disease Models	16
Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector	16
Cover	16
Causal Inference and Annotation of Phosphoproteomics Data in Multiomics Cancer Studies	15
11th Asia Oceania Human Proteome Organization Congress Report	15
Chemical Proteomics Reveals Nε-Fatty-Acylation of Septins by Rho Inactivation Domain (RID) of the Vibrio MARTX Toxin to Alter Septin Localization and Organization	15
Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress	15
Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation	15
MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets	14
Clinical Proteomics: A Promise Becoming Reality	14
Elucidating Fibroblast Growth Factor–Induced Kinome Dynamics Using Targeted Mass Spectrometry and Dynamic Modeling	14
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling	14
TEAD Proteins Associate With DNA Repair Proteins to Facilitate Cellular Recovery From DNA Damage	14
Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification	14
Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses	14
Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes	14
SIRT3 Functions as an Eraser of Histone H3K9 Lactylation to Modulate Transcription for Inhibiting the Progression of Esophageal Cancer	14
Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer	14
WITHDRAWN	13
Early Life Exposure to Deltamethrin Impairs Synaptic Function by Altering the Brain-Derived Extracellular Vesicle Proteome	13
Complexome profiling of mitochondrial oxidative phosphorylation knockout models.	13
Cover	13
Trypanosoma cruzi cardiomyocyte infection promotes innate immune response and metabolic rewiring	13
Localized K63 Ubiquitin Signaling Is Regulated by VCP/p97 During Oxidative Stress	13
Tracking drug action at the cell surface and the secreted proteome	13
Application of stable isotope labelingbased quantitative PTM proteomics and interactomics in study of Arabidopsis cell signaling	13
Phosphorylation Dynamics in a flg22-Induced, G Protein–Dependent Network Reveals the AtRGS1 Phosphatase	13
A New Monoclonal Antibody Enables BAR Analysis of Subcellular Importin β1 Interactomes	12
Quantification and Proteomic Characterization of β-Hydroxybutyrylation Modification in the Hearts of AMPKα2 Knockout Mice	12
Sulconazole Induces PANoptosis by Triggering Oxidative Stress and Inhibiting Glycolysis to Increase Radiosensitivity in Esophageal Cancer	12
An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity	12
msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level	12
Large-Scale Plasma Proteome Epitome Profiling is an Efficient Tool for the Discovery of Cancer Biomarkers	12
Proteogenomic Analysis of Breast Cancer Transcriptomic and Proteomic Data, Using De Novo Transcript Assembly: Genome-Wide Identification of Novel Peptides and Clinical Implications	12
Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades	12
Phosphoproteomic Analysis of FLCN Inactivation Highlights Differential Kinase Pathways and Regulatory TFEB Phosphoserines	12
Landscape of Steroid Dynamics in Pregnancy: Insights From the Maternal-Placental-Fetal Unit and Placental Models	12
MSstatsTMT improves accuracy of thermal proteome profiling by trading off temperature treatments and biological replicates	12
Analyzing N-Glycosylation Biosynthetic Networks Using Mass Spectrometry	12
Experience-Induced Remodeling of the Hippocampal Post-synaptic Proteome and Phosphoproteome	11
Exploring the Spatial Landscape of the Estrogen Receptor Proximal Proteome With Antibody-Based Proximity Labeling	11
Mass Spectrometry–Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes	11
Antibody Profiling of Pan-Cancer Viral Proteome Reveals Biomarkers for Nasopharyngeal Carcinoma Diagnosis and Prognosis	11
A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans	11
Evaluating timsTOF Pro 2 for the analysis of histone PTMs measured in Global Chromatin Profiling using dia-PASEF and prm-PASEF	11
Predicting Protein Pathways Associated to Tumor Heterogeneity by Correlating Spatial Lipidomics and Proteomics: The Dry Proteomic Concept	11
Challenges and Opportunities for Single-cell Computational Proteomics	11
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	11
Robust and accurate redox metabolomics and proteomics of clinical samples by in situ derivatization of free thiols	11
WITHDRAWN	11
Antibody-based enrichment of phosphotyrosine peptides using magnetic beads simplifies and outperforms results obtained using Protein A agarose beads	11
Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence	11
Integrated Proteomics to Understand the Role of Neuritin (NRN1) as a Mediator of Cognitive Resilience to Alzheimer’s Disease	11
WITHDRAWN	11
Bioinertization of NanoLC/MS/MS Systems by Depleting Metal Ions From the Mobile Phases for Phosphoproteomics	10
Application of Liquid-Liquid Extraction for N-terminal Myristoylation Proteomics	10
Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains	10
inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction	10
Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice	10
An AI-driven leap forward in peptide identification through deconvolution of chimeric spectra	10
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes	10
Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies	10
Serum Exosomes From Epithelial Ovarian Cancer Patients Contain LRP1, Which Promotes the Migration of Epithelial Ovarian Cancer Cell	10
Integrated Multiomics Reveals Alterations in Paucimannose and Complex Type N-Glycans in Cardiac Tissue of Patients with COVID-19	10
Cover	10
WITHDRAWN	10
Early Proteomic Characteristics and Changes in the Optic Nerve Head, Optic Nerve, and Retina in a Rat Model of Ocular Hypertension	10
Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts	10
Cover	10
Insight Into the Dynamics of the Ixodes ricinus Nymphal Midgut Proteome	10
Galectin-4 Antimicrobial Activity Primarily Occurs Through its C-Terminal Domain	10
Cover	10
The Proteome of Large or Small Extracellular Vesicles in Pig Seminal Plasma Differs, Defining Sources and Biological Functions	10

Post-translational Modifications and Their Effects on the Conformation and Function of Hsp90 in Embryonic Stem Cells	10
Cover	10
Editorial Board	10
Inducible Protein Degradation as a Strategy to Identify Phosphoprotein Phosphatase 6 Substrates in RAS-Mutant Colorectal Cancer Cells	9
Proteome imaging of human pancreas with a novel microPOTS platform	9
The Proteome and Phosphoproteome Uncovers Candidate Proteins Associated With Vacuolar Phosphate Signal Multipled by Vacuolar Phosphate Transporter 1 (VPT1) in Arabidopsis	9
Super Enhanced Purification of Denatured-Refolded Ubiquitinated Proteins by ThUBD Revealed Ubiquitinome Dysfunction in Liver Fibrosis	9
Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay	9
Proteogenomic analysis of multiple myeloma reveals therapeutic opportunities and predictive signatures	9
Change in Publication Schedule	9
Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities	9
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals	9
Insights Into Glycobiology and the Protein-Glycan Interactome Using Glycan Microarray Technologies	9
Ciliopathy-Associated Missense Mutations in IFT140 are Tolerated by the Inherent Resilience of the IFT Machinery	9
An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics	9
Innovations Toward Immunopeptidomics	9
Correction: Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β	9
ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis	9
WITHDRAWN	9
An Improved Method for Sampling and Quantitative Protein Analytics of Cerebrospinal Fluid of Individual Mice	9
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell–Derived Cells	9
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics	9
LncRNA MALAT1 facilitates HIV-1 replication by upregulation of CHCHD2 and downregulation of IFN-I expression	9
iProPhos: A Web-Based Interactive Platform for Integrated Proteome and Phosphoproteome Analysis	9
eEF2K Activity Determines Synergy to Cotreatment of Cancer Cells With PI3K and MEK Inhibitors	8
Impact of Bmal1 Rescue and Time-Restricted Feeding on Liver and Muscle Proteomes During the Active Phase in Mice	8
Intelligent Data Acquisition Approaches for Single Cell Proteomics	8
Proteomic Analysis Reveals Trilaciclib-Induced Senescence	8
Development of a Spectral Library for the Discovery of Altered Genomic Events in Mycobacterium avium Associated With Virulence Using Mass Spectrometry–Based Proteogenomic Analysis	8
Proteomic Profiling of Muscular Adaptations to Short-Term Concentric Versus Eccentric Exercise Training in Humans	8
Corrigendum for “Mass Spectrometry-Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease”	8
Proteomics and β-hydroxybutyrylation Modification Characterization in the Hearts of Naturally Senescent Mice	8
Proteomic Characterization of Renal Cell Carcinoma Using MALDI-MS Imaging	8
Early Days in the Hunt Laboratory at UVA, 1969 to 1980	8
diaPASEF Analysis for HLA-I Peptides Enables Quantification of Common Cancer Neoantigens	8
MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics	8
STK33 Phosphorylates Fibrous Sheath Protein AKAP3/4 to Regulate Sperm Flagella Assembly in Spermiogenesis	8
Navigating proteomics techniques for molecular profiling of clinical cancer cohorts	8
An Expanding Repertoire of Protein Acylations	8
BAMS: A Robust Analytical Platform for Quantifying Histone Modifications and Various Proteoforms by IP MALDI MS	8
Multiomic Analysis Reveals Disruption of Cholesterol Homeostasis by Cannabidiol in Human Cell Lines	8
Identification of State-Specific Proteomic and Transcriptomic Signatures of Microglia-Derived Extracellular Vesicles	8