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	155
Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine	131
LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections	112
CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1	77
Clinical Proteomics for Solid Organ Tissues	69
Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model	66
Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid	56
Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis	53
A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development	53
Quantitative Proteomic Analysis Reveals Functional Alterations of the Peripheral Immune System in Colorectal Cancer	52
Region and cell-type resolved multi-omic altas of the heart	48
Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression	48
Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p	44
Table of Contents	43
PROTEOMIC CHANGES TO THE ANTERIOR CEREBRAL ARTERY IN ALZHEIMER’S DISEASE	43
Easier, More Robust, and Faster Low-flow Quantitative Proteomics Approach	40
Prenylated PALM2 Promotes the Migration of Esophageal Squamous Cell Carcinoma Cells Through Activating Ezrin	37
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	37
CellEKT: a robust chemical proteomics workflow to profile cellular target engagement of kinase inhibitors	36
Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation	35
Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides	34
The rise of molecular glues and bifunctional compounds	33
Developing Cross-linking Mass Spectrometry to Define Protein Interaction Landscapes	33
WITHDRAWN	32
High-throughput subcellular proteomics reveals phospho-signaling dynamics	31

PRM-LIVE Accelerates Target Class-based Selectivity Profiling of Small Molecule Inhibitors	30
Toward Comprehensive, Single-molecule Proteomics: Protein Identification by Shortepitope Mapping	29
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
In Situ Cell-Surface Proteomics: Method Development and Applications in Neurobiology	28
Recent Advances in Mass Spectrometry-Based Protein Interactome Studies	28
Proteomics, Transcriptomics, and Phosphoproteomics Reveal the Mechanism of Talaroconvolutin-A Suppressing Bladder Cancer via Blocking Cell Cycle and Triggering Ferroptosis	27
A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell	27
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions	26
Bridging the Gap From Proteomics Technology to Clinical Application: Highlights From the 68th Benzon Foundation Symposium	26
Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification	26
DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis	25
HEXB Drives Raised Paucimannosylation in Colorectal Cancer and Stratifies Patient Risk	25
Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification	24
Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate	24
Development of a Fit-For-Purpose Multi-Marker Panel for Early Diagnosis of Pancreatic Ductal Adenocarcinoma	24
Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA	24
The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation	24
Phosphoproteome Analysis Identifies a Synaptotagmin-1-Associated Complex Involved in Ischemic Neuron Injury	23
Integrative Proteomics and N-Glycoproteomics Analyses of Rheumatoid Arthritis Synovium Reveal Immune-Associated Glycopeptides	22
Filter-Aided Extracellular Vesicle Enrichment (FAEVEr) for Proteomics	22
Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates	21
Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin	21
Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development	21
Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection	20
Phosphoproteome Profiling of the Receptor Tyrosine Kinase MuSK Identifies Tyrosine Phosphorylation of Rab GTPases	20
The in vivo Interaction Landscape of Histones H3.1 and H3.3	20
Improved Mass Spectrometry–Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles	20
Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics	20
Enhanced In Situ Spatial Proteomics by Effective Combination of MALDI Imaging and LC-MS/MS	19
Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays	19
(Sialyl)Lewis Antigen Expression on Glycosphingolipids, N-, and O-Glycans in Colorectal Cancer Cell Lines is Linked to a Colon-Like Differentiation Program	19
TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics	19
Multi-Omics Analysis Unveils Nsun5-Mediated Molecular Alterations in the Somatosensory Cortex and Its Impact on Pain Sensation	18
Multi-nanoparticle Workflow Enables Deep Plasma Proteomics at Scale, with Enhanced Precision, and Depths of Coverage	18
Proteomic Identification of Autophagy Cargo Using Novel Tools in Combination with Quantitative Proteomics.	18
Highly multiplexed proteome-wide quantitation of functional residues enabled by a novel 11plex-AzidoTMT reagent	18
Mapping diverse proteome responses with intelligent mass spectrometry	18
Prospective on Imaging Mass Spectrometry in Clinical Diagnostics	18
Highly multiplexed label-free imaging of tissue proteoforms using individual ion mass spectrometry	18
The One Hour Human Proteome	18
Mass spectrometry and SomaScan technologies to detect a plasma copper proteome in two human populations	18
Automated workflows for DIA data using DIA-NN on the PaSER platform	18
The Role of Clinical Glyco(proteo)mics in Precision Medicine	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	17
Back Cover	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
Generation of a Deep Mouse Brain Spectral Library for Transmembrane Proteome Profiling in Mental Disease Models	16
Three-dimensional feature matching improves the sensitivity of single-cell and spatial proteomics	16
Clinical Proteomics: A Promise Becoming Reality	16

Cover	16
Deciphering the highly complex cancer immunopeptidome	16
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
Yellow Fever Blood Proteomics Study by Trapped Ion Mobility Mass Spectrometry	16
Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector	15
11th Asia Oceania Human Proteome Organization Congress Report	15
Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress	15
Cover	14
Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer	14
Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation	14
TEAD Proteins Associate With DNA Repair Proteins to Facilitate Cellular Recovery From DNA Damage	14
Chemical Proteomics Reveals Nε-Fatty-Acylation of Septins by Rho Inactivation Domain (RID) of the Vibrio MARTX Toxin to Alter Septin Localization and Organization	14
MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets	14
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling	14
Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses	14
Elucidating Fibroblast Growth Factor–Induced Kinome Dynamics Using Targeted Mass Spectrometry and Dynamic Modeling	14
Causal Inference and Annotation of Phosphoproteomics Data in Multiomics Cancer Studies	13
Cover	13
SIRT3 functions as an eraser of histone H3K9 lactylation to modulate transcription for inhibiting the progression of esophageal cancer	13
A New Monoclonal Antibody Enables BAR Analysis of Subcellular Importin β1 Interactomes	13
Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes	13
Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification	13
Phosphorylation Dynamics in a flg22-Induced, G Protein–Dependent Network Reveals the AtRGS1 Phosphatase	12
Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades	12
Application of stable isotope labelingbased quantitative PTM proteomics and interactomics in study of Arabidopsis cell signaling	12
Complexome profiling of mitochondrial oxidative phosphorylation knockout models.	12
Landscape of steroid dynamics in pregnancy - insights from the maternal-placental-fetal unit and placental models	12
Phosphoproteomic Analysis of FLCN Inactivation Highlights Differential Kinase Pathways and Regulatory TFEB Phosphoserines	12
Localized K63 Ubiquitin Signaling Is Regulated by VCP/p97 During Oxidative Stress	12
Early Life Exposure to Deltamethrin Impairs Synaptic Function by Altering the Brain-Derived Extracellular Vesicle Proteome	12
Tracking drug action at the cell surface and the secreted proteome	12
msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level	12
Quantification and Proteomic Characterization of β-Hydroxybutyrylation Modification in the Hearts of AMPKα2 Knockout Mice	12
Large-Scale Plasma Proteome Epitome Profiling is an Efficient Tool for the Discovery of Cancer Biomarkers	12
WITHDRAWN	12
Trypanosoma cruzi cardiomyocyte infection promotes innate immune response and metabolic rewiring	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
Robust and accurate redox metabolomics and proteomics of clinical samples by in situ derivatization of free thiols	11
WITHDRAWN	11
Evaluating timsTOF Pro 2 for the analysis of histone PTMs measured in Global Chromatin Profiling using dia-PASEF and prm-PASEF	11
Sulconazole Induces PANoptosis by Triggering Oxidative Stress and Inhibiting Glycolysis to Increase Radiosensitivity in Esophageal Cancer	11
WITHDRAWN	11
Antibody-based enrichment of phosphotyrosine peptides using magnetic beads simplifies and outperforms results obtained using Protein A agarose beads	11
An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity	11
Analyzing N-Glycosylation Biosynthetic Networks Using Mass Spectrometry	11
Experience-Induced Remodeling of the Hippocampal Post-synaptic Proteome and Phosphoproteome	11
Serum Exosomes From Epithelial Ovarian Cancer Patients Contain LRP1, Which Promotes the Migration of Epithelial Ovarian Cancer Cell	10
Cover	10
Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts	10
Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies	10
Application of Liquid-Liquid Extraction for N-terminal Myristoylation Proteomics	10
Antibody Profiling of Pan-Cancer Viral Proteome Reveals Biomarkers for Nasopharyngeal Carcinoma Diagnosis and Prognosis	10
Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains	10
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	10
Integrated Proteomics to Understand the Role of Neuritin (NRN1) as a Mediator of Cognitive Resilience to Alzheimer’s Disease	10
Exploring the Spatial Landscape of the Estrogen Receptor Proximal Proteome With Antibody-Based Proximity Labeling	10
Bioinertization of NanoLC/MS/MS Systems by Depleting Metal Ions From the Mobile Phases for Phosphoproteomics	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
Challenges and Opportunities for Single-cell Computational Proteomics	10
Mass Spectrometry–Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes	10
A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans	10
inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction	10
Cover	10
The Proteome of Large or Small Extracellular Vesicles in Pig Seminal Plasma Differs, Defining Sources and Biological Functions	10
Predicting Protein Pathways Associated to Tumor Heterogeneity by Correlating Spatial Lipidomics and Proteomics: The Dry Proteomic Concept	10
Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence	10
The Proteome and Phosphoproteome Uncovers Candidate Proteins Associated With Vacuolar Phosphate Signal Multipled by Vacuolar Phosphate Transporter 1 (VPT1) in Arabidopsis	9
Cover	9
Post-translational Modifications and Their Effects on the Conformation and Function of Hsp90 in Embryonic Stem Cells	9
Integrated Multiomics Reveals Alterations in Paucimannose and Complex Type N-Glycans in Cardiac Tissue of Patients with COVID-19	9
Ciliopathy-Associated Missense Mutations in IFT140 are Tolerated by the Inherent Resilience of the IFT Machinery	9
Super Enhanced Purification of Denatured-Refolded Ubiquitinated Proteins by ThUBD Revealed Ubiquitinome Dysfunction in Liver Fibrosis	9
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes	9
Editorial Board	9
WITHDRAWN	9
Early Proteomic Characteristics and Changes in the Optic Nerve Head, Optic Nerve, and Retina in a Rat Model of Ocular Hypertension	9
Innovations Toward Immunopeptidomics	9
Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay	9

Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice	9
An AI-driven leap forward in peptide identification through deconvolution of chimeric spectra	9
Cover	9
Insights Into Glycobiology and the Protein-Glycan Interactome Using Glycan Microarray Technologies	9
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell–Derived Cells	9
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals	9
Proteomic Characterization of Renal Cell Carcinoma Using MALDI-MS Imaging	8
Proteogenomic analysis of multiple myeloma reveals therapeutic opportunities and predictive signatures	8
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics	8
Impact of Bmal1 Rescue and Time-Restricted Feeding on Liver and Muscle Proteomes During the Active Phase in Mice	8
Proteomics and β-hydroxybutyrylation Modification Characterization in the Hearts of Naturally Senescent Mice	8
ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis	8
Proteomic Analysis Reveals Trilaciclib-Induced Senescence	8
Intelligent Data Acquisition Approaches for Single Cell Proteomics	8
WITHDRAWN	8
An improved method for sampling and quantitative protein analytics of cerebrospinal fluid of individual mice	8
iProPhos: A Web-Based Interactive Platform for Integrated Proteome and Phosphoproteome Analysis	8
Inducible Protein Degradation as a Strategy to Identify Phosphoprotein Phosphatase 6 Substrates in RAS-Mutant Colorectal Cancer Cells	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
BAMS: A Robust Analytical Platform for Quantifying Histone Modifications and Various Proteoforms by IP MALDI MS	8
Early Days in the Hunt Laboratory at UVA, 1969 to 1980	8
Proteome imaging of human pancreas with a novel microPOTS platform	8
An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics	8
Correction: Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β	8
Change in Publication Schedule	8
Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities	8
eEF2K Activity Determines Synergy to Cotreatment of Cancer Cells With PI3K and MEK Inhibitors	8
MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics	7
Identification of State-Specific Proteomic and Transcriptomic Signatures of Microglia-Derived Extracellular Vesicles	7
From Patient Skin to Brain: Understanding Neurodegeneration with Fibroblast-iPSCNeuron Proteomics	7
Single-Cell Proteomic Characterization of Drug-Resistant Prostate Cancer Cells Reveals Molecular Signatures Associated with Morphological Changes	7
Native Size-Exclusion Chromatography–Based Mass Spectrometry Reveals New Components of the Early Heat Shock Protein 90 Inhibition Response Among Limited Global Changes	7
Characterization of Glycoproteoforms of Integrins α2 and β1 in Megakaryocytes in the Occurrence of JAK2V617F Mutation-Induced Primary Myelofibrosis	7
Development of a Spectral Library for the Discovery of Altered Genomic Events in Mycobacterium avium Associated With Virulence Using Mass Spectrometry–Based Proteogenomic Analysis	7
diaPASEF Analysis for HLA-I Peptides Enables Quantification of Common Cancer Neoantigens	7
Multiomic Analysis Reveals Disruption of Cholesterol Homeostasis by Cannabidiol in Human Cell Lines	7
Cover	7
Biomarkers Found in the Tumor Interstitial Fluid may Help Explain the Differential Behavior Among Keratinocyte Carcinomas	7
SpotLight Proteomics Identifies Variable Sequences of Blood Antibodies Specific Against Deamidated Human Serum Albumin	7
Proteomic and Cellular Characterization of Omicron Breakthrough Infections and a Third Homologous or Heterologous Boosting Vaccination in a Longitudinal Cohort	7
Proteomic Profiling of Muscular Adaptations to Short-Term Concentric Versus Eccentric Exercise Training in Humans	7
STK33 Phosphorylates Fibrous Sheath Protein AKAP3/4 to Regulate Sperm Flagella Assembly in Spermiogenesis	7
An Expanding Repertoire of Protein Acylations	7
PI3Kα Translocation Mediates Nuclear PtdIns(3,4,5)P3 Effector Signaling in Colorectal Cancer	7
Quantification Quality Control Emerges as a Crucial Factor to Enhance Single-Cell Proteomics Data Analysis	7
Identification of Proteome-Based Immune Subtypes of Early Hepatocellular Carcinoma and Analysis of Potential Metabolic Drivers	7
Navigating proteomics techniques for molecular profiling of clinical cancer cohorts	7