Molecular & Cellular Proteomics

Article	Citations
Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine	195
Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model	162
Quantitative Proteomic Analysis Reveals Functional Alterations of the Peripheral Immune System in Colorectal Cancer	127
Table of Contents	87
Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis	87
PROTEOMIC CHANGES TO THE ANTERIOR CEREBRAL ARTERY IN ALZHEIMER’S DISEASE	73
Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression	66
Easier, More Robust, and Faster Low-flow Quantitative Proteomics Approach	66
NovoBoard: A Comprehensive Framework for Evaluating the False Discovery Rate and Accuracy of De Novo Peptide Sequencing	59
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	58
Temporal Wheat Proteome Remodeling by Deoxynivalenol Reveals Novel Detoxification Signatures and Strategies Across Cultivars	57
Prenylated PALM2 Promotes the Migration of Esophageal Squamous Cell Carcinoma Cells Through Activating Ezrin	54
Exploring the Early Molecular Pathogenesis of Osteoarthritis Using Differential Network Analysis of Human Synovial Fluid	54
LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections	52
Region- and Cell-type–Resolved Multiomic Atlas of the Heart	48
A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development	45
Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p	45
Employing Expression-Matched Controls Enables High-Confidence Proximity-Based Interactome Classification	44
Discovery Proteomics Analysis Determines That Driver Oncogenes Suppress Antiviral Defense Pathways Through Reduction in Interferon-β Autocrine Stimulation	43
CellEKT: A Robust Chemical Proteomics Workflow to Profile Cellular Target Engagement of Kinase Inhibitors	40
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	40
Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides	38
Clinical Proteomics for Solid Organ Tissues	37
CREB-Regulated Transcriptional Coactivator 2 Proteome Landscape is Modulated by SREBF1	36
mTORC2 regulates non-homologous end joining through modulating the temporal dynamics of 53BP1	36

A Methanolic Urea-enhanced Protein Extraction Enabling the Largest Bacterial Phosphorylation Resource	35
The rise of molecular glues and bifunctional compounds	33
WITHDRAWN	33
Spatial proteomics reveals distinct protein patterns in cortical migration disorders caused by LIN28A overexpression and WNT activation.	33
Developing Cross-linking Mass Spectrometry to Define Protein Interaction Landscapes	33
High-throughput subcellular proteomics reveals phospho-signaling dynamics	31
PRM-LIVE Accelerates Target Class-based Selectivity Profiling of Small Molecule Inhibitors	31
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	30
Toward Comprehensive, Single-molecule Proteomics: Protein Identification by Shortepitope Mapping	29
A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell	28
Development of a Fit-For-Purpose Multi-Marker Panel for Early Diagnosis of Pancreatic Ductal Adenocarcinoma	28
Recent Advances in Mass Spectrometry-Based Studies of Post-Translational Modifications in Alzheimer’s Disease	28
Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification	28
In Situ Cell-Surface Proteomics: Method Development and Applications in Neurobiology	28
Recent Advances in Mass Spectrometry-Based Protein Interactome Studies	28
Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development	28
Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin	27
Phosphoproteome Profiling of the Receptor Tyrosine Kinase MuSK Identifies Tyrosine Phosphorylation of Rab GTPases	27
Phosphoproteome Analysis Identifies a Synaptotagmin-1-Associated Complex Involved in Ischemic Neuron Injury	27
HEXB Drives Raised Paucimannosylation in Colorectal Cancer and Stratifies Patient Risk	27
The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation	27
The in vivo Interaction Landscape of Histones H3.1 and H3.3	27
Cerebrospinal Fluid Protein Markers Indicate Neuro-Damage in SARS-CoV-2-Infected Nonhuman Primates	27
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions	26
Proximity Labeling and SILAC-Based Proteomic Approach Identifies Proteins at the Interface of Homotypic and Heterotypic Cancer Cell Interactions	26
Filter-Aided Extracellular Vesicle Enrichment (FAEVEr) for Proteomics	26
Proteomics, Transcriptomics, and Phosphoproteomics Reveal the Mechanism of Talaroconvolutin-A Suppressing Bladder Cancer via Blocking Cell Cycle and Triggering Ferroptosis	25
Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA	24
Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification	23
DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis	23
Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate	22
Bridging the Gap From Proteomics Technology to Clinical Application: Highlights From the 68th Benzon Foundation Symposium	22
Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics	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
Improved Mass Spectrometry–Based Methods Reveal Abundant Propionylation and Tissue-Specific Histone Propionylation Profiles	22
Integrative Proteomics and N-Glycoproteomics Analyses of Rheumatoid Arthritis Synovium Reveal Immune-Associated Glycopeptides	22
Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays	21
Multi-nanoparticle Workflow Enables Deep Plasma Proteomics at Scale, with Enhanced Precision, and Depths of Coverage	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	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
Multi-Omics Analysis Unveils Nsun5-Mediated Molecular Alterations in the Somatosensory Cortex and Its Impact on Pain Sensation	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
Highly multiplexed label-free imaging of tissue proteoforms using individual ion mass spectrometry	20
Proteomic Identification of Autophagy Cargo Using Novel Tools in Combination with Quantitative Proteomics.	20
(Sialyl)Lewis Antigen Expression on Glycosphingolipids, N-, and O-Glycans in Colorectal Cancer Cell Lines is Linked to a Colon-Like Differentiation Program	19
From Discovery to Delivery: A Rapid and Targeted Proteomics Workflow for Monitoring Chinese Hamster Ovary Biomanufacturing	19
Enhanced In Situ Spatial Proteomics by Effective Combination of MALDI Imaging and LC-MS/MS	19
Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection	19

The Role of Clinical Glyco(proteo)mics in Precision Medicine	18
TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics	18
An automated workflow to address proteome complexity and the large search space problem in proteomics and HLA-I immunopeptidomics	18
Prospective on Imaging Mass Spectrometry in Clinical Diagnostics	18
Accurate MS-based diagnostic amyloid typing using endogenously normalized protein intensities in formalin-fixed paraffin-embedded tissue	18
A Time Point Proteomic Analysis Reveals Protein Dynamics of Plasmodium Oocysts	17
Three-dimensional feature matching improves the sensitivity of single-cell and spatial proteomics	17
Yellow Fever Blood Proteomics Study by Trapped Ion Mobility Mass Spectrometry	17
Computational challenges of identification and quantification algorithms in single-cell proteomic data.	17
Deciphering the highly complex cancer immunopeptidome	17
The One Hour Human Proteome	17
Back Cover	17
Mapping the Degradable Kinome: A Resource for Expedited Degrader Development	17
Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer	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
Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress	16
Deep Learning Enhances Precision of Citrullination Identification in Human and Plant Tissue Proteomes	16
Cover	16
Generation of a Deep Mouse Brain Spectral Library for Transmembrane Proteome Profiling in Mental Disease Models	16
Causal Inference and Annotation of Phosphoproteomics Data in Multiomics Cancer Studies	16
Cover	16
Clinical Proteomics: A Promise Becoming Reality	15
SIRT3 Functions as an Eraser of Histone H3K9 Lactylation to Modulate Transcription for Inhibiting the Progression of Esophageal Cancer	15
MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets	15
Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector	15
11th Asia Oceania Human Proteome Organization Congress Report	15
pXg: Comprehensive Identification of Noncanonical MHC-I–Associated Peptides From De Novo Peptide Sequencing Using RNA-Seq Reads	15
Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification	15
Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses	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
Elucidating Fibroblast Growth Factor–Induced Kinome Dynamics Using Targeted Mass Spectrometry and Dynamic Modeling	15
TEAD Proteins Associate With DNA Repair Proteins to Facilitate Cellular Recovery From DNA Damage	14
Tracking drug action at the cell surface and the secreted proteome	14
Trypanosoma cruzi cardiomyocyte infection promotes innate immune response and metabolic rewiring	14
Early Life Exposure to Deltamethrin Impairs Synaptic Function by Altering the Brain-Derived Extracellular Vesicle Proteome	14
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling	14
WITHDRAWN	14
Landscape of Steroid Dynamics in Pregnancy: Insights From the Maternal-Placental-Fetal Unit and Placental Models	14
Complexome profiling of mitochondrial oxidative phosphorylation knockout models.	14
Cover	14
Application of stable isotope labelingbased quantitative PTM proteomics and interactomics in study of Arabidopsis cell signaling	14
An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity	14
Localized K63 Ubiquitin Signaling Is Regulated by VCP/p97 During Oxidative Stress	13
A New Monoclonal Antibody Enables BAR Analysis of Subcellular Importin β1 Interactomes	13
Multi-omics characterization of acquired Olaparib resistance in BRCA1 and BRCA2 mutant breast cancer cell lines	13
Robust and accurate redox metabolomics and proteomics of clinical samples by in situ derivatization of free thiols	13
Phosphoproteomic Analysis of FLCN Inactivation Highlights Differential Kinase Pathways and Regulatory TFEB Phosphoserines	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
Large-Scale Plasma Proteome Epitome Profiling is an Efficient Tool for the Discovery of Cancer Biomarkers	13
Sulconazole Induces PANoptosis by Triggering Oxidative Stress and Inhibiting Glycolysis to Increase Radiosensitivity in Esophageal Cancer	13
WITHDRAWN	13
Quantification and Proteomic Characterization of β-Hydroxybutyrylation Modification in the Hearts of AMPKα2 Knockout Mice	13
msqrob2PTM: Differential Abundance and Differential Usage Analysis of MS-Based Proteomics Data at the Posttranslational Modification and Peptidoform Level	13
MSstatsTMT Improves Accuracy of Thermal Proteome Profiling	13
Analyzing N-Glycosylation Biosynthetic Networks Using Mass Spectrometry	13
Uncommon N-Glycan Structures in Anhydrobiotic Tardigrades	13
Phosphorylation Dynamics in a flg22-Induced, G Protein–Dependent Network Reveals the AtRGS1 Phosphatase	13
Antibody-based enrichment of phosphotyrosine peptides using magnetic beads simplifies and outperforms results obtained using Protein A agarose beads	12
Galectin-4 Antimicrobial Activity Primarily Occurs Through its C-Terminal Domain	12
Evaluating timsTOF Pro 2 for the analysis of histone PTMs measured in Global Chromatin Profiling using dia-PASEF and prm-PASEF	12
A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans	12
Antibody Profiling of Pan-Cancer Viral Proteome Reveals Biomarkers for Nasopharyngeal Carcinoma Diagnosis and Prognosis	12
WITHDRAWN	12
Exploring the Spatial Landscape of the Estrogen Receptor Proximal Proteome With Antibody-Based Proximity Labeling	12
High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissues	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
Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains	11
Cover	11
Integrated Multiomics Reveals Alterations in Paucimannose and Complex Type N-Glycans in Cardiac Tissue of Patients with COVID-19	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
Bioinertization of NanoLC/MS/MS Systems by Depleting Metal Ions From the Mobile Phases for Phosphoproteomics	11
Integrated Proteomics to Understand the Role of Neuritin (NRN1) as a Mediator of Cognitive Resilience to Alzheimer’s Disease	11
Challenges and Opportunities for Single-cell Computational Proteomics	11
Mass Spectrometry–Driven Discovery of Neuropeptides Mediating Nictation Behavior of Nematodes	11
Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence	11
Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts	11
inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction	11
Application of Liquid-Liquid Extraction for N-terminal Myristoylation Proteomics	11
Nucleolar proteomics revealed the regulation of RNA exosome localization by MTR4	11

Experience-Induced Remodeling of the Hippocampal Post-synaptic Proteome and Phosphoproteome	11
Predicting Protein Pathways Associated to Tumor Heterogeneity by Correlating Spatial Lipidomics and Proteomics: The Dry Proteomic Concept	11
Serum Exosomes From Epithelial Ovarian Cancer Patients Contain LRP1, Which Promotes the Migration of Epithelial Ovarian Cancer Cell	11
Cover	11
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes	11
The Proteome of Large or Small Extracellular Vesicles in Pig Seminal Plasma Differs, Defining Sources and Biological Functions	11
Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice	11
Super Enhanced Purification of Denatured-Refolded Ubiquitinated Proteins by ThUBD Revealed Ubiquitinome Dysfunction in Liver Fibrosis	10
WITHDRAWN	10
Editorial Board	10
Insights Into Glycobiology and the Protein-Glycan Interactome Using Glycan Microarray Technologies	10
The Proteome and Phosphoproteome Uncovers Candidate Proteins Associated With Vacuolar Phosphate Signal Multipled by Vacuolar Phosphate Transporter 1 (VPT1) in Arabidopsis	10
LncRNA MALAT1 Facilitates HIV-1 Replication by Upregulation of CHCHD2 and Downregulation of IFN-I Expression	10
An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry–Based Secretomics	10
Exploring virus-host interactions through combined proteomic approaches identifies BANF1 as a new essential factor for African Swine Fever Virus	10
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics	10
Cover	10
Innovations Toward Immunopeptidomics	10
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals	10
Ciliopathy-Associated Missense Mutations in IFT140 are Tolerated by the Inherent Resilience of the IFT Machinery	10
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell–Derived Cells	10
Correction: Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β	10
Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay	10
Cover	10
An AI-driven leap forward in peptide identification through deconvolution of chimeric spectra	10
Post-translational Modifications and Their Effects on the Conformation and Function of Hsp90 in Embryonic Stem Cells	10
ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis	10
An Improved Method for Sampling and Quantitative Protein Analytics of Cerebrospinal Fluid of Individual Mice	10
Early Proteomic Characteristics and Changes in the Optic Nerve Head, Optic Nerve, and Retina in a Rat Model of Ocular Hypertension	10
Change in Publication Schedule	10
STK33 Phosphorylates Fibrous Sheath Protein AKAP3/4 to Regulate Sperm Flagella Assembly in Spermiogenesis	9
Multiomic Analysis Reveals Disruption of Cholesterol Homeostasis by Cannabidiol in Human Cell Lines	9
Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities	9
WITHDRAWN	9
Early Days in the Hunt Laboratory at UVA, 1969 to 1980	9
iProPhos: A Web-Based Interactive Platform for Integrated Proteome and Phosphoproteome Analysis	9
Soluble VCAM-1 May Serve as a Pharmacodynamic CSF Marker to Monitor BACE2 Activity in Non-Human Primates	9
Proteomics and β-hydroxybutyrylation Modification Characterization in the Hearts of Naturally Senescent Mice	9
BAMS: A Robust Analytical Platform for Quantifying Histone Modifications and Various Proteoforms by IP MALDI MS	9
Identification of State-Specific Proteomic and Transcriptomic Signatures of Microglia-Derived Extracellular Vesicles	9
Proteome imaging of human pancreas with a novel microPOTS platform	9
Intelligent Data Acquisition Approaches for Single Cell Proteomics	9
diaPASEF Analysis for HLA-I Peptides Enables Quantification of Common Cancer Neoantigens	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
Proteomic Profiling of Muscular Adaptations to Short-Term Concentric Versus Eccentric Exercise Training in Humans	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
Proteomic Characterization of Renal Cell Carcinoma Using MALDI-MS Imaging	9
Proteogenomic analysis of multiple myeloma reveals therapeutic opportunities and predictive signatures	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
eEF2K Activity Determines Synergy to Cotreatment of Cancer Cells With PI3K and MEK Inhibitors	9