Molecular & Cellular Proteomics

Article	Citations
Quantitative Proteomic Analysis Reveals Functional Alterations of the Peripheral Immune System in Colorectal Cancer	207
Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis	171
Table of Contents	131
PROTEOMIC CHANGES TO THE ANTERIOR CEREBRAL ARTERY IN ALZHEIMER’S DISEASE	94
Easier, More Robust, and Faster Low-flow Quantitative Proteomics Approach	88
Region- and Cell-type–Resolved Multiomic Atlas of the Heart	75
LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections	70
Prenylated PALM2 Promotes the Migration of Esophageal Squamous Cell Carcinoma Cells Through Activating Ezrin	69
Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression	62
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	62
Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p	60
A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development	58
Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation	58
Clinical Proteomics for Solid Organ Tissues	52
CellEKT: A Robust Chemical Proteomics Workflow to Profile Cellular Target Engagement of Kinase Inhibitors	50
Temporal Wheat Proteome Remodeling by Deoxynivalenol Reveals Novel Detoxification Signatures and Strategies Across Cultivars	48
Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid	45
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing	45
mTORC2 Regulates Non-homologous End Joining Through Modulating the Temporal Dynamics of 53BP1	44
Employing Expression-Matched Controls Enables High-Confidence Proximity-Based Interactome Classification	44
Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model	44
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	41
Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides	39
CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1	37
Spatial Proteomics Reveals Distinct Protein Patterns in Cortical Migration Disorders Caused by LIN28A Overexpression and WNT Activation	36

A Methanolic Urea-Enhanced Protein Extraction Enabling the Largest Bacterial Phosphorylation Resource	35
Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine	35
The rise of molecular glues and bifunctional compounds	35
WITHDRAWN	33
Developing Cross-linking Mass Spectrometry to Define Protein Interaction Landscapes	33
High-throughput subcellular proteomics reveals phospho-signaling dynamics	32
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	31
PRM-LIVE Accelerates Target Class-based Selectivity Profiling of Small Molecule Inhibitors	31
Toward Comprehensive, Single-molecule Proteomics: Protein Identification by Shortepitope Mapping	31
A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell	30
Recent Advances in Mass Spectrometry-Based Protein Interactome Studies	30
In Situ Cell-Surface Proteomics: Method Development and Applications in Neurobiology	30
Proteomics, Transcriptomics, and Phosphoproteomics Reveal the Mechanism of Talaroconvolutin-A Suppressing Bladder Cancer via Blocking Cell Cycle and Triggering Ferroptosis	29
Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate	29
Phosphoproteome Profiling of the Receptor Tyrosine Kinase MuSK Identifies Tyrosine Phosphorylation of Rab GTPases	29
Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics	29
Proximity Labeling and SILAC-Based Proteomic Approach Identifies Proteins at the Interface of Homotypic and Heterotypic Cancer Cell Interactions	28
Bridging the Gap From Proteomics Technology to Clinical Application: Highlights From the 68th Benzon Foundation Symposium	28
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions	28
Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development	28
Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification	27
DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis	27
Development of a Fit-For-Purpose Multi-Marker Panel for Early Diagnosis of Pancreatic Ductal Adenocarcinoma	27
Recent Advances in Mass Spectrometry-Based Studies of Post-Translational Modifications in Alzheimer’s Disease	27
The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation	26
Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates	26
HEXB Drives Raised Paucimannosylation in Colorectal Cancer and Stratifies Patient Risk	25
Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin	24
Phosphoproteome Analysis Identifies a Synaptotagmin-1-Associated Complex Involved in Ischemic Neuron Injury	24
The in vivo Interaction Landscape of Histones H3.1 and H3.3	24
Integrative Proteomics and N-Glycoproteomics Analyses of Rheumatoid Arthritis Synovium Reveal Immune-Associated Glycopeptides	23
Improved Mass Spectrometry–Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles	23
Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification	23
Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA	22
Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays	22
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	22
Filter-Aided Extracellular Vesicle Enrichment (FAEVEr) for Proteomics	22
Multi-Omics Analysis Unveils Nsun5-Mediated Molecular Alterations in the Somatosensory Cortex and Its Impact on Pain Sensation	22
Highly multiplexed label-free imaging of tissue proteoforms using individual ion mass spectrometry	21
Highly multiplexed proteome-wide quantitation of functional residues enabled by a novel 11plex-AzidoTMT reagent	21
Mapping diverse proteome responses with intelligent mass spectrometry	21
Proteomic Identification of Autophagy Cargo Using Novel Tools in Combination with Quantitative Proteomics.	21
Multi-nanoparticle Workflow Enables Deep Plasma Proteomics at Scale, with Enhanced Precision, and Depths of Coverage	21
The One Hour Human Proteome	21
Automated workflows for DIA data using DIA-NN on the PaSER platform	21
Mass spectrometry and SomaScan technologies to detect a plasma copper proteome in two human populations	21
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	20
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
The Role of Clinical Glyco(proteo)mics in Precision Medicine	20

TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics	19
A Time Point Proteomic Analysis Reveals Protein Dynamics of Plasmodium Oocysts	18
Accurate MS-Based Diagnostic Amyloid Typing Using Endogenously Normalized Protein Intensities in Formalin-Fixed Paraffin-Embedded Tissue	18
Prospective on Imaging Mass Spectrometry in Clinical Diagnostics	18
Computational challenges of identification and quantification algorithms in single-cell proteomic data.	18
An Automated Workflow to Address Proteome Complexity and the Large Search Space Problem in Proteomics and HLA-I Immunopeptidomics	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
Back Cover	18
From Discovery to Delivery: A Rapid and Targeted Proteomics Workflow for Monitoring Chinese Hamster Ovary Biomanufacturing	18
Yellow Fever Blood Proteomics Study by Trapped Ion Mobility Mass Spectrometry	18
Cover	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
Cover	17
Deciphering the highly complex cancer immunopeptidome	17
MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets	16
Chemical Proteomics Reveals Nε-Fatty-Acylation of Septins by Rho Inactivation Domain (RID) of the Vibrio MARTX Toxin to Alter Septin Localization and Organization	16
TEAD Proteins Associate With DNA Repair Proteins to Facilitate Cellular Recovery From DNA Damage	16
Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes	16
Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer	16
SIRT3 Functions as an Eraser of Histone H3K9 Lactylation to Modulate Transcription for Inhibiting the Progression of Esophageal Cancer	16
11th Asia Oceania Human Proteome Organization Congress Report	16
Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification	16
pXg: Comprehensive Identification of Noncanonical MHC-I–Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads	16
Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector	16
Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress	16
Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2–Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation	16
Causal Inference and Annotation of Phosphoproteomics Data in Multiomics Cancer Studies	16
Generation of a Deep Mouse Brain Spectral Library for Transmembrane Proteome Profiling in Mental Disease Models	16
Application of stable isotope labelingbased quantitative PTM proteomics and interactomics in study of Arabidopsis cell signaling	15
Elucidating Fibroblast Growth Factor–Induced Kinome Dynamics Using Targeted Mass Spectrometry and Dynamic Modeling	15
Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses	15
Trypanosoma cruzi cardiomyocyte infection promotes innate immune response and metabolic rewiring	15
Clinical Proteomics: A Promise Becoming Reality	15
WITHDRAWN	15
Tracking drug action at the cell surface and the secreted proteome	15
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling	15
Cover	15
Complexome profiling of mitochondrial oxidative phosphorylation knockout models.	14
Phosphorylation Dynamics in a flg22-Induced, G Protein–Dependent Network Reveals the AtRGS1 Phosphatase	14
Jolkinolide B Activates Mitophagy to Exhibit Anti-pancreatic Cancer Activity and Alleviate Cognitive Deficits in Alzheimer's Disease	14
Localized K63 Ubiquitin Signaling Is Regulated by VCP/p97 During Oxidative Stress	14
Phosphoproteomic Analysis of FLCN Inactivation Highlights Differential Kinase Pathways and Regulatory TFEB Phosphoserines	14
Multi-omics Characterization of Acquired Olaparib Resistance in BRCA1 and BRCA2 Mutant Breast Cancer Cell Lines	14
An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity	14
Sulconazole Induces PANoptosis by Triggering Oxidative Stress and Inhibiting Glycolysis to Increase Radiosensitivity in Esophageal Cancer	14
msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level	14
Early Life Exposure to Deltamethrin Impairs Synaptic Function by Altering the Brain-Derived Extracellular Vesicle Proteome	14
Quantification and Proteomic Characterization of β-Hydroxybutyrylation Modification in the Hearts of AMPKα2 Knockout Mice	14
MSstatsTMT Improves Accuracy of Thermal Proteome Profiling	13
Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades	13
AMPylation regulates 5’-3’ exonuclease PLD3 processing.	13
WITHDRAWN	13
Antibody-based enrichment of phosphotyrosine peptides using magnetic beads simplifies and outperforms results obtained using Protein A agarose beads	13
A New Monoclonal Antibody Enables BAR Analysis of Subcellular Importin β1 Interactomes	13
Proteogenomic Analysis of Breast Cancer Transcriptomic and Proteomic Data, Using De Novo Transcript Assembly: Genome-Wide Identification of Novel Peptides and Clinical Implications	13
Restrained Wnt signaling pathway by enha nced EsGSK3β activity facilitates the infection of Spiroplasma and leads to neuropathic diseases in crustaceans	13
Evaluating timsTOF Pro 2 for the analysis of histone PTMs measured in Global Chromatin Profiling using dia-PASEF and prm-PASEF	13
A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans	13
Large-Scale Plasma Proteome Epitome Profiling is an Efficient Tool for the Discovery of Cancer Biomarkers	13
Landscape of Steroid Dynamics in Pregnancy: Insights From the Maternal-Placental-Fetal Unit and Placental Models	13
Robust and accurate redox metabolomics and proteomics of clinical samples by in situ derivatization of free thiols	13
WITHDRAWN	13
Analyzing N-Glycosylation Biosynthetic Networks Using Mass Spectrometry	13
Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains	12
Integrated Proteomics to Understand the Role of Neuritin (NRN1) as a Mediator of Cognitive Resilience to Alzheimer’s Disease	12
Galectin-4 Antimicrobial Activity Primarily Occurs Through its C-Terminal Domain	12
Mass Spectrometry–Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes	12
Predicting Protein Pathways Associated to Tumor Heterogeneity by Correlating Spatial Lipidomics and Proteomics: The Dry Proteomic Concept	12
Exploring the Spatial Landscape of the Estrogen Receptor Proximal Proteome With Antibody-Based Proximity Labeling	12
Experience-Induced Remodeling of the Hippocampal Post-synaptic Proteome and Phosphoproteome	12
Challenges and Opportunities for Single-cell Computational Proteomics	12
Serum Exosomes From Epithelial Ovarian Cancer Patients Contain LRP1, Which Promotes the Migration of Epithelial Ovarian Cancer Cell	12
Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence	12
Integrated Multiomics Reveals Alterations in Paucimannose and Complex Type N-Glycans in Cardiac Tissue of Patients with COVID-19	11
Bioinertization of NanoLC/MS/MS Systems by Depleting Metal Ions From the Mobile Phases for Phosphoproteomics	11
Antibody Profiling of Pan-Cancer Viral Proteome Reveals Biomarkers for Nasopharyngeal Carcinoma Diagnosis and Prognosis	11
Insight Into the Dynamics of the Ixodes ricinus Nymphal Midgut Proteome	11
Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies	11
Editorial Board	11

WITHDRAWN	11
The Proteome and Phosphoproteome Uncovers Candidate Proteins Associated With Vacuolar Phosphate Signal Multipled by Vacuolar Phosphate Transporter 1 (VPT1) in Arabidopsis	11
Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice	11
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes	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
High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissues	11
Application of Liquid-Liquid Extraction for N-terminal Myristoylation Proteomics	11
An AI-driven leap forward in peptide identification through deconvolution of chimeric spectra	11
Cover	11
The Proteome of Large or Small Extracellular Vesicles in Pig Seminal Plasma Differs, Defining Sources and Biological Functions	11
Cover	11
Nucleolar Proteomics Revealed the Regulation of RNA Exosome Localization by MTR4	11
Cover	11
inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction	11
Cover	11
Post-translational Modifications and Their Effects on the Conformation and Function of Hsp90 in Embryonic Stem Cells	11
Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts	11
Insights Into Glycobiology and the Protein-Glycan Interactome Using Glycan Microarray Technologies	10
An Improved Method for Sampling and Quantitative Protein Analytics of Cerebrospinal Fluid of Individual Mice	10
Comprehensive evaluation of cleavable bioorthogonal probes for site-specific O-GlcNAc proteomics	10
Innovations Toward Immunopeptidomics	10
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics	10
WITHDRAWN	10
Intelligent Data Acquisition Approaches for Single Cell Proteomics	10
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals	10
Exploring Virus–Host Interactions Through Combined Proteomic Approaches Identifies BANF1 as a New Essential Factor for African Swine Fever Virus	10
Early Proteomic Characteristics and Changes in the Optic Nerve Head, Optic Nerve, and Retina in a Rat Model of Ocular Hypertension	10
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell–Derived Cells	10
Ciliopathy-Associated Missense Mutations in IFT140 are Tolerated by the Inherent Resilience of the IFT Machinery	10
Super Enhanced Purification of Denatured-Refolded Ubiquitinated Proteins by ThUBD Revealed Ubiquitinome Dysfunction in Liver Fibrosis	10
Correction: Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β	10
Proteogenomic analysis of multiple myeloma reveals therapeutic opportunities and predictive signatures	10
Proteomic Characterization of Renal Cell Carcinoma Using MALDI-MS Imaging	10
Global proteomics reveals distinct muscle adaptations to menstrual cycle phase-based sprint interval training in endurance-trained females	10
LncRNA MALAT1 Facilitates HIV-1 Replication by Upregulation of CHCHD2 and Downregulation of IFN-I Expression	10
Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay	10
An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics	10
Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities	10
Change in Publication Schedule	10
Proteome imaging of human pancreas with a novel microPOTS platform	10
BAMS: A Robust Analytical Platform for Quantifying Histone Modifications and Various Proteoforms by IP MALDI MS	10
MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics	9
Soluble VCAM-1 May Serve as a Pharmacodynamic CSF Marker to Monitor BACE2 Activity in Non-Human Primates	9
STK33 Phosphorylates Fibrous Sheath Protein AKAP3/4 to Regulate Sperm Flagella Assembly in Spermiogenesis	9
Proteomic Profiling of Muscular Adaptations to Short-Term Concentric Versus Eccentric Exercise Training in Humans	9
eEF2K Activity Determines Synergy to Cotreatment of Cancer Cells With PI3K and MEK Inhibitors	9
An Expanding Repertoire of Protein Acylations	9
Proteomics and β-hydroxybutyrylation Modification Characterization in the Hearts of Naturally Senescent Mice	9
iProPhos: A Web-Based Interactive Platform for Integrated Proteome and Phosphoproteome Analysis	9
Development of a Spectral Library for the Discovery of Altered Genomic Events in Mycobacterium avium Associated With Virulence Using Mass Spectrometry–Based Proteogenomic Analysis	9
Corrigendum for “Mass Spectrometry-Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease”	9
ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis	9
Identification of State-Specific Proteomic and Transcriptomic Signatures of Microglia-Derived Extracellular Vesicles	9
Navigating proteomics techniques for molecular profiling of clinical cancer cohorts	9
Impact of Bmal1 Rescue and Time-Restricted Feeding on Liver and Muscle Proteomes During the Active Phase in Mice	9
Proteomic Analysis Reveals Trilaciclib-Induced Senescence	9
Inducible Protein Degradation as a Strategy to Identify Phosphoprotein Phosphatase 6 Substrates in RAS-Mutant Colorectal Cancer Cells	9
Multiomic Analysis Reveals Disruption of Cholesterol Homeostasis by Cannabidiol in Human Cell Lines	9
Early Days in the Hunt Laboratory at UVA, 1969 to 1980	9
diaPASEF Analysis for HLA-I Peptides Enables Quantification of Common Cancer Neoantigens	9