Journal of Proteome Research

Article	Citations
The Future of Proteomics is Up in the Air: Can Ion Mobility Replace Liquid Chromatography for High Throughput Proteomics?	147
Issue Publication Information	141
Canadian Proteomics: A Journey across the Country Highlights Discovery and Innovation	119
Sequential Proteomic and N-Glycoproteomic Analyses of Bronchoalveolar Lavage Fluids for Potential Biomarker Discovery of Lung Adenocarcinoma	112
Localization of Multiple O-Linked Glycans Exhibited in Isomeric Glycopeptides by Hot Electron Capture Dissociation	104
DiDBiT-TMT: A Novel Method to Quantify Changes in the Proteomic Landscape Induced by Neural Plasticity	95
Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics	83
Margaret Dayhoff: A Personal Memoir	71
A Method to Estimate the Distribution of Proteins across Multiple Compartments Using Data from Quantitative Proteomics Subcellular Fractionation Experiments	70
Systematic Survey of the Regulatory Networks of the Long Noncoding RNA BANCR in Cervical Cancer Cells	70
Quantitative Proteomic Analysis Revealed Broad Roles of N6-Methyladenosine in Heat Shock Response	69
The Novel Interplay between Commensal Gut Bacteria and Metabolites in Diet-Induced Hyperlipidemic Rats Treated with Simvastatin	67
Quantitative Proteomics Reveals a Novel Role of the E3 Ubiquitin-Protein Ligase FANCL in the Activation of the Innate Immune Response through Regulation of TBK1 Phosphorylation during Peste des Petits	62
Targeted Proteomics Profiling for Biomarker Discovery in Glaucoma Using the Olink Proteomics Platform	62
ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics Data Sets	60
Automated Assignment of Proteoform Classification Levels	56
Reverse Phase Proteomic Array Profiling of Asparagine Synthetase Expression in Newly Diagnosed Acute Myeloid Leukemia	55
Comparison of Microflow and Analytical Flow Liquid Chromatography Coupled to Mass Spectrometry Global Metabolomics Methods Using a Urea Cycle Disorder Mouse Model	53
Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics	52
Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling	51
Antioxidant Impact of Soft Knotwood Extracts on Human Keratinocytes Shown by NMR Metabolomic Analysis	50
Integration of Automatic Text Mining and Genomic and Proteomic Analysis to Unravel Prostate Cancer Biomarkers	49
Dynamic Phosphotyrosine-Dependent Signaling Profiling in Living Cells by Two-Dimensional Proximity Proteomics	46
Time-Resolved Multiomics Illustrates Host and Gut Microbe Interactions during Salmonella Infection	45
SWATH-MS Analysis of Blood Plasma and Circulating Small Extracellular Vesicles Enables Detection of Putative Protein Biomarkers of Fertility in Young and Aged Dairy Cows	45

Metabolomics Reveals Novel Serum Metabolic Signatures in Gastric Cancer by a Mass Spectrometry Platform	44
Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens	43
Protein–Protein Interaction Networks Derived from Classical and Machine Learning-Based Natural Language Processing Tools	43
Comprehensive Metabolomics and Lipidomics Profiling of Prostate Cancer Tissue Reveals Metabolic Dysregulations Associated with Disease Development	42
Evaluation of the Suitability of Dried Saliva Spots for In-Depth Proteome Analyses for Clinical Applications	40
Untargeted Metabolomic Study of Lung Cancer Patients after Surgery with Curative Intent	39
Issue Editorial Masthead	39
Issue Publication Information	38
Issue Editorial Masthead	37
An XIC-Centric Strategy for Improved Identification and Quantification in Proteomic Data Analyses	36
Comprehensive Identification of Regulatory Protein Networks	34
Establishment of a Mass-Spectrometry-Based Method for the Identification of the In Vivo Whole Blood and Plasma ADP-Ribosylomes	34
Scents and Flavors of Mass Spectrometry in Latin America	34
Issue Editorial Masthead	34
Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection	34
Back to the Future, from a Departing Editor	34
Dysregulation of Amino Acid, Lipid, and Acylpyruvate Metabolism in Idiopathic Intracranial Hypertension: A Non-targeted Case Control and Longitudinal Metabolomic Study	34
Systematic Assessment of Deep Learning-Based Predictors of Fragmentation Intensity Profiles	32
Incomplete Systemic Recovery and Metabolic Phenoreversion in Post-Acute-Phase Nonhospitalized COVID-19 Patients: Implications for Assessment of Post-Acute COVID-19 Syndrome	32
Defining Alzheimer’s Disease through Proteomic CSF Profiling	31
Open-Source and FAIR Research Software for Proteomics	31
Integrative Analysis of Lactylome and Proteome of Hypertrophic Scar To Identify Pathways or Proteins Associated with Disease Development	31
Oral Squamous Cell Carcinoma Lipid Evaluation in Gingiva Tissue Stored in TRIzol via Shotgun Lipidomics and MALDI Mass Spectrometry Imaging	31
Plasma Olink Proteomics Reveals Novel Biomarkers for Prediction and Diagnosis in Dilated Cardiomyopathy with Heart Failure	31
Integration of Metabolomics, Lipidomics, and Proteomics Reveals the Metabolic Characterization of Nonalcoholic Steatohepatitis	31
Complementary Nuclear Magnetic Resonance-Based Metabolomics Approaches for Glioma Biomarker Identification in a Drosophila melanogaster Model	31
Discovery of Oogenesis Biomarkers from Mouse Oocytes Using a Single-Cell Proteomics Approach	30
CHalf: Folding Stability Made Simple	30
Metabolomics Analysis of the Effect of GAT-2 Deficiency on Th1 Cells in Mice	30
MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses	29
Ovalbumin Antigen-Specific Activation of Human T Cell Receptor Closely Resembles Soluble Antibody Stimulation as Revealed by BOOST Phosphotyrosine Proteomics	28
ppx: Programmatic Access to Proteomics Data Repositories	28
Analysis of Vascular Smooth Muscle Cells from Thoracic Aortic Aneurysms Reveals DNA Damage and Cell Cycle Arrest as Hallmarks in Bicuspid Aortic Valve Patients	28
EPURISp: Combining Enzymatic Digestion, Ultrafiltration, and Rapid In Situ Sample Purification for High-performance Proteomics	27
Leveraging Supervised Machine Learning Algorithms for System Suitability Testing of Mass Spectrometry Imaging Platforms	27
Comparative Proteomics and N-Glycoproteomics Reveal the Effects of Different Plasma Protein Enrichment Technologies	26
Integrated Transcriptomics–Proteomics Analysis Identifies Molecular Phenotypic Alterations Associated with Colorectal Cancer	26
Alignment and Analysis of a Disparately Acquired Multibatch Metabolomics Study of Maternal Pregnancy Samples	25
Categorization and Characterization of Snake Venom Variability through Intact Toxin Analysis by Mass Spectrometry	25
Spatial Venomics─Cobra Venom System Reveals Spatial Differentiation of Snake Toxins by Mass Spectrometry Imaging	25
Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities	25
Molecular Mechanisms of Acanthamoeba castellanii Response to Different Sources of Oxidative Stress	25
MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides	25
TurnoveR: A Skyline External Tool for Analysis of Protein Turnover in Metabolic Labeling Studies	25
Automated High-Throughput Affinity Capture-Mass Spectrometry Platform with Data-Independent Acquisition	25
Machine Learning-Enhanced Cerebrospinal Fluid N-Glycome for the Diagnosis and Prognosis of Primary Central Nervous System Lymphoma	25
Evaluation of DDA Library-Free Strategies for Phosphoproteomics and Ubiquitinomics Data-Independent Acquisition Data	25
Untargeted Metabolomics Analysis of Gingival Tissue in Patients with Severe Periodontitis	24
EIF4G2 Promotes Hepatocellular Carcinoma Progression via IRES-dependent PLEKHA1 Translation Regulation	24
PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors	24

Issue Editorial Masthead	24
NMR Metabolomics Assessment of Osteogenic Differentiation of Adipose-Tissue-Derived Mesenchymal Stem Cells	24
Quantitative Proteomics Reveal the Mechanism of MiR-138–5p Suppressing Cervical Cancer via Targeting ZNF385A	24
Chronic Exposure to Petroleum-Derived Hydrocarbons Alters Human Skin Microbiome and Metabolome Profiles: A Pilot Study	24
HLA Allele-Specific Quantitative Profiling of Type 1 Diabetic B Lymphocyte Immunopeptidome	23
Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome	23
Cerebrospinal Fluid Protein Biomarker Discovery in CLN3	23
Tbx18 Orchestrates Cytostructural Transdifferentiation of Cardiomyocytes to Pacemaker Cells by Recruiting the Epithelial–Mesenchymal Transition Program	23
Discovering the N-Terminal Methylome by Repurposing of Proteomic Datasets	23
Spatial Omics Reveals that Cancer-Associated Glycan Changes Occur Early in Liver Disease Development in a Western Diet Mouse Model of MASLD	23
Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples	23
A Sensitive and Controlled Data-Independent Acquisition Method for Proteomic Analysis of Cell Therapies	22
Identification of FGG as a Biomarker in Early Gastric Cancer via Tissue Proteomics and Clinical Verification	22
High Throughput UHPLC-MS-Based Lipidomics Using Vacuum Jacketed Columns	22
A Plasma Proteomics-Based Model for Identifying the Risk of Postpartum Depression Using Machine Learning	22
HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search	22
Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-Down Proteomics	22
Issue Editorial Masthead	22
Identification of LMAN1- and SURF4-Dependent Secretory Cargoes	22
Applying Log-Normal Peak Fitting to Parallel Reaction Monitoring Data Analysis	22
A Rapid One-Pot Workflow for Sensitive Microscale Phosphoproteomics	22
Quantitative Proteomics Reveal the Inherent Antibiotic Resistance Mechanism against Norfloxacin Resistance in Aeromonas hydrophila	22
Detection and Isolation of Circulating Tumor Cells from Breast Cancer Patients Using CUB Domain-Containing Protein 1	21
Quantitative Proteomics for the Development and Manufacturing of Human-Induced Pluripotent Stem Cell-Derived Neural Stem Cells Using Data-Independent Acquisition Mass Spectrometry	21
Development of a Simple and Stable NanoESI Spray System Using Suction Wind from the MS Inlet	21
Simultaneous Quantification of Apolipoprotein C-III O-Glycoforms by Protein-MRM	21
ClusterSheep: A Graphics Processing Unit-Accelerated Software Tool for Large-Scale Clustering of Tandem Mass Spectra from Shotgun Proteomics	21
Proteogenomics Study of Blastobotrys adeninivorans TMCC 70007—A Dominant Yeast in the Fermentation Process of Pu-erh Tea	20
AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation	20
IQMMA: Efficient MS1 Intensity Extraction Pipeline Using Multiple Feature Detection Algorithms for DDA Proteomics	20
Quantitative Phosphoproteomics and Acetylomics of Safranal Anticancer Effects in Triple-Negative Breast Cancer Cells	20
HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space	20
Proteomics Analysis of Knee Subchondral Bone Identifies Differentially Expressed Proteins Associated with Osteoarthritis	20
Deep, Unbiased, and Quantitative Mass Spectrometry-Based Plasma Proteome Analysis of Individual Responses to mRNA COVID-19 Vaccine	20
Issue Editorial Masthead	20
De Novo Linear Phosphorylation Site Motifs for BCR-ABL Kinase Revealed by Phospho-Proteomics in Yeast	20
Caspase-9 Is a Positive Regulator of Osteoblastic Cell Migration Identified by diaPASEF Proteomics	20
Electrochemically Etched Tapered-Tip Stainless-Steel Electrospray-Ionization Emitters for Capillary Electrophoresis–Mass Spectrometry	20
Fit for Purpose Approach To Evaluate Detection of Amino Acid Substitutions in Shotgun Proteomics	20
The Combination of Quantitative Proteomics and Systems Genetics Analysis Reveals that PTN Is Associated with Sleep-Loss-Induced Cognitive Impairment	20
Potential Use of Serum Proteomics for Monitoring COVID-19 Progression to Complement RT-PCR Detection	20
RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control	20
Normal Alpha-1-Antitrypsin Variants Display in Serum Allele-Specific Protein Levels	20
MSLibrarian: Optimized Predicted Spectral Libraries for Data-Independent Acquisition Proteomics	19
Insights into the Differential Preservation of Bone Proteomes in Inhumed and Entombed Cadavers from Italian Forensic Caseworks	19
Identification of Blood Biomarkers in Ischemic Stroke by Integrated Analysis of Metabolomics and Proteomics	19
Multiplex Assay to Determine Acute Phase Proteins in Modified Live PRRSV Vaccinated Pigs	19
Proteomics of Serum Samples for the Exploration of the Pathological Mechanism of Obstetric Antiphospholipid Syndrome	19
One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles	18
Issue Publication Information	18
Size-Dependent Separation of Extracellular Vesicle Subtypes with Exodisc Enabling Proteomic Analysis in Prostate Cancer	18
Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases	18
How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate	18
AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function	18
IL18R1-Related Molecules as Biomarkers for Asthma Severity and Prognostic Markers for Idiopathic Pulmonary Fibrosis	18
Issue Editorial Masthead	18
Plasma Proteomics to Identify Drug Targets and Potential Drugs for Retinal Artery Occlusion: An Integrated Analysis in the UK Biobank	18
Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals	18
Distinct Regions within SAP25 Recruit O-Linked Glycosylation, DNA Demethylation, and Ubiquitin Ligase and Hydrolase Activities to the Sin3/HDAC Complex	17
Toward an Ultimate Solution for Peptide Retention Time Prediction: The Effect of Column Temperature on Separation Selectivity	17
Software-Assisted Data Processing Workflow for Intact Glycoprotein Mass Spectrometry	17
Nonsevere Burn Induces a Prolonged Systemic Metabolic Phenotype Indicative of a Persistent Inflammatory Response Postinjury	17
Identifying Sex-Specific Serum Patterns of Alzheimer’s Mice through Deep TMT Profiling and a Concentration-Dependent Concatenation Strategy	17
Quantitative Acetylomics Reveals Substrates of Lysine Acetyltransferase GCN5 in Adult and Aging Drosophila	17
Valuable Contributions and Lessons Learned from Proteomics and Metabolomics Studies of COVID-19	17
Alternative LC–MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping of Human Hair Shafts	17
Multiplet-Assisted Peak Alignment for 1H NMR-Based Metabolomics	17
Metabolomics Meets Clinics: A Multivariate Analysis of Plasma and Urine Metabolic Signatures in Pulmonary Arterial Hypertension	16
Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags	16
SpectiCal: m/z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions	16
Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics	16
Impact of Internal Fragments on Top-Down Analysis of Intact Proteins by 193 nm UVPD	16
Nanoscale Solid-Phase Isobaric Labeling for Multiplexed Quantitative Phosphoproteomics	16
Novel Deep Eutectic Solvent-Based Protein Extraction Method for Pottery Residues and Archeological Implications	16
NovoRank: Refinement for De Novo Peptide Sequencing Based on Spectral Clustering and Deep Learning	16
Subchronic Graphene Exposure Reshapes Skin Cell Metabolism	16
Impact of Static Myoblast Loading on Protein Secretion Linked to Tenocyte Migration	16
Adaptive Metabolism of Staphylococcus aureus Revealed by Untargeted Metabolomics	16
Hybrid Quadrupole Mass Filter–Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics	16
Merging Full-Spectrum and Fragment Ion Intensity Predictions from Deep Learning for High-Quality Spectral Libraries	16

Precision Structural Interpretation of Site-Specific N-Glycans in Seminal Plasma	16
MGVB: a New Proteomics Toolset for Fast and Efficient Data Analysis	16
Multidimensional Cross-Linking and Real-Time Informatics for Multiprotein Interaction Studies	16
S-Palmitoylation during Retinoic Acid-Induced Neuronal Differentiation of SH-SY5Y Neuroblastoma Cells	16
N-Terminomic Identification of Intracellular MMP-2 Substrates in Cardiac Tissue	16
LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems	16
Profiling Glutathionylome in CD38-Mediated Epithelial–Mesenchymal Transition	15
Spatial Proteomic Profiling of Colorectal Cancer Revealed Its Tumor Microenvironment Heterogeneity	15
MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale	15
Issue Editorial Masthead	15
Ultrahigh-Resolution NMR with Water Signal Suppression for a Deeper Understanding of the Action of Antimetabolic Drugs on Diffuse Large B-Cell Lymphoma	15
MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments	15
Comparative Proteomics Reveals Prolonged Corneal Preservation Impaired Ocular Surface Immunity Accompanied by Fibrosis in Human Stroma	15
PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity	15
Targeted Mass Spectrometry of Longitudinal Patient Sera Reveals LTBP1 as a Potential Surveillance Biomarker for High-Grade Serous Ovarian Carcinoma	15
Issue Publication Information	15
SpaceANOVA: Spatial Co-occurrence Analysis of Cell Types in Multiplex Imaging Data Using Point Process and Functional ANOVA	15
Sulfoproteomics Workflow with Precursor Ion Accurate Mass Shift Analysis Reveals Novel Tyrosine Sulfoproteins in the Golgi	15
A Python Package for the Localization of Protein Modifications in Mass Spectrometry Data	15
1DE-MS Profiling for Proteoform-Correlated Proteomic Analysis, by Combining SDS-PAGE, Whole-Gel Slicing, Quantitative LC–MS/MS, and Reconstruction of Gel Distributions of Several Thousands of Proteins	15
LineageFilter: Improved Proteotyping of Complex Samples Using Metaproteomics and Machine Learning	15
Correction to “The Curiosity of the Young”	15
Irradiation Causes Alterations of Polyamine, Purine, and Sulfur Metabolism in Red Blood Cells and Multiple Organs	15
Non-Small Cell Lung Cancer Detection and Subtyping by UPLC-HRMS-Based Tissue Metabolomics	14
Analysis of Brain Protein Stability Changes in a Mouse Model of Alzheimer’s Disease	14
Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod	14
Evaluation of a Proteomics-Guided Protein Signature for Breast Cancer Detection in Breast Tissue	14
O-GlcNAcylation: Sagacious Orchestrator of Bone-, Joint-, and Spine-Related Diseases	14
Use and Comparison of Machine Learning Techniques to Discern the Protein Patterns of Autoantibodies Present in Women with and without Breast Pathology	14
Bacterial Immobilization and Toxicity Induced by a Bean Plant Immune System	14
Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins	14
Fasciola hepatica Cathepsin L Zymogens: Immuno-Proteomic Evidence for Highly Immunogenic Zymogen-Specific Conformational Epitopes to Support Diagnostics Development	14
LC-Orbitrap HRMS-Based Proteomics Reveals Novel Mitochondrial Dynamics Regulatory Proteins Associated with RasV12-Induced Glioblastoma (GBM) of Drosophila	14
AzidoTMT Enables Direct Enrichment and Highly Multiplexed Quantitation of Proteome-Wide Functional Residues	14
Proteomics and Metabolic Characteristics of Boar Seminal Plasma Extracellular Vesicles Reveal Biomarker Candidates Related to Sperm Motility	14
Gel-Based Sample Fractionation with SP3-Purification for Top-Down Proteomics	14
Placental Proteomics Reveals an Elevated Level of Aldo-Keto Reductase 1-B1, Highlighting Its Potential Role in Spontaneous Preterm Birth	14
Single Cell Analysis of Proteoforms	14
Coupling Proximity Biotinylation with Genomic Targeting to Characterize Locus-Specific Changes in Chromatin Environments	14
Second Special Issue on Methods for Omics Research: Proteome Research and Beyond	13
SPE-CZE-MS Quantifies Zeptomole Amounts of Phosphorylated Peptides	13
Metabolomic, Proteomic, and Single-Cell Proteomic Analysis of Cancer Cells Treated with the KRASG12D Inhibitor MRTX1133	13
Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N-Glycocapture Data	13
High-Coverage Metabolomics Reveals Gut Microbiota-Related Metabolic Traits of Type-2 Diabetes in Serum	13
Multiomics Analyses Reveal that Fatty Acid Metabolism and TCA Cycle Contribute to the Achievement of Functional Cure in Chronic Hepatitis B	13
Typic: A Practical and Robust Tool to Rank Proteotypic Peptides for Targeted Proteomics	13
Optimizing a Diagnostic Model of Periodontitis by Using Targeted Proteomics	13
Delineating Bovine Milk Derived Microvesicles from Exosomes Using Proteomics	13
NMR-Based Metabolomics Revealed the Underlying Inflammatory Pathology in Reactive Arthritis Synovial Joints	13
Accelerating Proteomics Using Broad Specificity Proteases	13
Orbitrap Mass Spectrometry and High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Enable the in-Depth Analysis of Human Serum Proteoforms	13
Proteomics and Metabolomics Reveal that an Abundant α-Glucosidase Drives Sorghum Fermentability for Beer Brewing	13
Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics	13
Untargeted Gut Metabolomics to Delve the Interplay between Selenium Supplementation and Gut Microbiota	13
Development of an Optimized LC-MS Workflow for Host Cell Protein Characterization to Support Upstream Process Development	13
Proteomics Platform Reveals Broad-Spectrum Nanobodies for SARS-CoV-2 Variant Neutralization	13
Tumor Lipid Signatures Are Descriptive of Acquisition of Therapy Resistance in an Endocrine-Related Breast Cancer Mouse Model	13
Quantitative Proteomics Reveals the Protein Regulatory Network of Anabaena sp. PCC 7120 under Nitrogen Deficiency	13
Human Serum Alters the Metabolism and Antibiotic Susceptibility of Staphylococcus aureus	13
FIGS: Featured Ion-Guided Stoichiometry for Data-Independent Proteomics through Dynamic Deconvolution	13
Traveling Wave Ion Mobility-Derived Collision Cross Section Database for Plant Specialized Metabolites: An Application to Ventilago harmandiana Pierre	13
Dynamic Responses of Chromosome-Binding Protein Complexes to Meiotic Prophase I of Mouse Spermatocyte	13
Proximity Labeling, Quantitative Proteomics, and Biochemical Studies Revealed the Molecular Mechanism for the Inhibitory Effect of Indisulam on the Proliferation of Gastric Cancer Cells	13
Novel Diagnostic Biomarkers for High-Grade Serous Ovarian Cancer Uncovered by Data-Independent Acquisition Mass Spectrometry	13
RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein–RNA Cross-Linking/Mass Spectrometry Data	13
Lysine Trimethylation in Planktonic and Pellicle Modes of Growth in Acinetobacter baumannii	13
Physiological Temperature and Osmotic Changes Drive Dynamic Proteome Alterations in the Leptospiral Outer Membrane and Enhance Protein Export Systems	13
Issue Editorial Masthead	12
Plasma Metabolomic Changes in Children with Cerebral Palsy Exposed to Botulinum Neurotoxin	12
Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme	12
Inactivation of Coronaviruses during Sample Preparation for Proteomics Experiments	12
Deep Saliva Proteomics Elucidating the Pathogenesis of Early Childhood Caries and Identifying Biomarkers for Early Prediction	12
Issue Publication Information	12
Efficient Indexing of Peptides for Database Search Using Tide	12
Optimized and Robust Workflow for Quantifying the Canonical Histone Ubiquitination Marks H2AK119ub and H2BK120ub by LC–MS/MS	12
Serum Metabolomics Profiling Coupled with Machine Learning Identifies Potential Diagnostic and Prognostic Candidate Markers in Meningioma Using Raman Spectroscopy, ATR-FTIR, and LC–MS/MS	12
Proteomic Analysis of the Promastigote Secretome of Seven Leishmania Species	12
Variability of 7K and 11K SomaScan Plasma Proteomics Assays	12
Flashlight into the Function of Unannotated C11orf52 using Affinity Purification Mass Spectrometry	12
Issue Editorial Masthead	12
Issue Editorial Masthead	12
Impact of Local Air Pressure on Ion Mobilities and Data Consistency in diaPASEF-Based High Throughput Proteomics	12
Analysis of Stratifin Expression and Proteome Variation in a Rat Model of Acute Lung Injury	12
Shared Proteins and Pathways of Cardiovascular and Cognitive Diseases: Relation to Vascular Cognitive Impairment	12
Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline	12
High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF	12
Proximity Proteomics and Biochemical Analysis Reveal a Noncanonical Function for UFM1-Specific Protease 1 in the p62 Body Formation	12
Correction to “Mannose-6-Phosphate Isomerase Functional Status Shapes a Rearrangement in the Proteome and Degradome of Mannose-Treated Melanoma Cells”	12
Issue Publication Information	12
Characterization of the Functional Interplay between the BRD7 and BRD9 Homologues in mSWI/SNF Complexes	12
Proteomic Evolution from Acute to Post-COVID-19 Conditions	12
Evaluating Proteomics Imputation Methods with Improved Criteria	12
Exploring Top-Down Mass Spectrometric Approaches To Probe Forest Cobra (Naja melanoleuca) Venom Proteoforms	11
IP-LC-MSMS Enables Identification of Three Tau O-GlcNAcylation Sites as O-GlcNAcase Inhibition Pharmacodynamic Readout in Transgenic Mice Overexpressing Human Tau	11
Online Alkaline-pH Reverse Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Conventional Low-pH Method for Global Proteomic Analysis	11