Molecular & Cellular Proteomics

Article	Citations
Single-cell Proteomics: Progress and Prospects	255
IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs	222
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis	169
A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics	143
Proximity Extension Assay in Combination with Next-Generation Sequencing for High-throughput Proteome-wide Analysis	132
The Peptide Vaccine of the Future	120
Decoding Post-Translational Modification Crosstalk With Proteomics	117
Trapped Ion Mobility Spectrometry and Parallel Accumulation–Serial Fragmentation in Proteomics	104
Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins	93
Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF	83
Quantitative Proteomics Identifies Proteins Enriched in Large and Small Extracellular Vesicles	81
Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives	79
Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis	78
Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein	73
Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication	72
PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results	71
An Introduction to Advanced Targeted Acquisition Methods	69
Multi-Omics Profiling for Health	68
Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction	62
Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics	61
Imaging Mass Spectrometry and Lectin Analysis of N-Linked Glycans in Carbohydrate Antigen–Defined Pancreatic Cancer Tissues	61
Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation	60
Proteome Profiling of Recombinant DNase Therapy in Reducing NETs and Aiding Recovery in COVID-19 Patients	57
MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates	55
In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease	54

Proteomic Landscape of Exosomes Reveals the Functional Contributions of CD151 in Triple-Negative Breast Cancer	49
Interspecies Differences in Proteome Turnover Kinetics Are Correlated With Life Spans and Energetic Demands	47
N-Glycomic Signature of Stage II Colorectal Cancer and Its Association With the Tumor Microenvironment	47
Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification	46
Scaling Up Single-Cell Proteomics	45
Serum Protein Profiling Reveals a Landscape of Inflammation and Immune Signaling in Early-stage COVID-19 Infection	44
The Complexity and Dynamics of the Tissue Glycoproteome Associated With Prostate Cancer Progression	43
An Expanding Repertoire of Protein Acylations	43
The Role of Data-Independent Acquisition for Glycoproteomics	43
Evaluation and Refinement of Sample Preparation Methods for Extracellular Matrix Proteome Coverage	40
Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples	37
Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry–Based Approaches	37
Ethical Principles, Constraints, and Opportunities in Clinical Proteomics	36
MHC Class I Immunopeptidome: Past, Present, and Future	36
An Automated Nanowell-Array Workflow for Quantitative Multiplexed Single-Cell Proteomics Sample Preparation at High Sensitivity	34
MS-Based Proteomics of Body Fluids: The End of the Beginning	34
Age-Associated Proteomic Signatures and Potential Clinically Actionable Targets of Colorectal Cancer	34
High-Throughput and Site-Specific N-Glycosylation Analysis of Human Alpha-1-Acid Glycoprotein Offers a Great Potential for New Biomarker Discovery	34
Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics	33
Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run	32
Integrated Glycoproteomics Identifies a Role of N-Glycosylation and Galectin-1 on Myogenesis and Muscle Development	32
ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping	32
Systematic Proteome and Lysine Succinylome Analysis Reveals Enhanced Cell Migration by Hyposuccinylation in Esophageal Squamous Cell Carcinoma	31
Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives	31
Glycomics, Glycoproteomics, and Glycogenomics: An Inter-Taxa Evolutionary Perspective	31
Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries	30
Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition	29
Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress	29
Proteomic Signature of Host Response to SARS-CoV-2 Infection in the Nasopharynx	29
Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review	29
Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites	28
Simple But Efficacious Enrichment of Integral Membrane Proteins and Their Interactions for In-Depth Membrane Proteomics	28
Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides	28
Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs	28
Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand	28
Subcellular Transcriptomics and Proteomics: A Comparative Methods Review	27
Quantitative Consequences of Protein Carriers in Immunopeptidomics and Tyrosine Phosphorylation MS2 Analyses	27
Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA	27
Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning	27
Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics	27
Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years	26
Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy	26
Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future	26
Plasma Proteomes Can Be Reidentifiable and Potentially Contain Personally Sensitive and Incidental Findings	26
Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation	25
Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs	25
Sulconazole Induces PANoptosis by Triggering Oxidative Stress and Inhibiting Glycolysis to Increase Radiosensitivity in Esophageal Cancer	25
PaxDb 5.0: Curated Protein Quantification Data Suggests Adaptive Proteome Changes in Yeasts	25
Isolation of Acetylated and Unmodified Protein N-Terminal Peptides by Strong Cation Exchange Chromatographic Separation of TrypN-Digested Peptides	25
Are There Indeed Spliced Peptides in the Immunopeptidome?	25

AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization	25
CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens	24
In-Depth Characterization of the Staphylococcus aureus Phosphoproteome Reveals New Targets of Stk1	24
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	24
Thyroglobulin Interactome Profiling Defines Altered Proteostasis Topology Associated With Thyroid Dyshormonogenesis	24
Multiattribute Glycan Identification and FDR Control for Glycoproteomics	23
Region-Specific Cell Membrane N-Glycome of Functional Mouse Brain Areas Revealed by nanoLC-MS Analysis	23
In-Depth Matrisome and Glycoproteomic Analysis of Human Brain Glioblastoma Versus Control Tissue	23
Proteomics, Lipidomics, Metabolomics, and 16S DNA Sequencing of Dental Plaque From Patients With Diabetes and Periodontal Disease	23
Comparative Proteome Signatures of Trace Samples by Multiplexed Data-Independent Acquisition	22
SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines	22
The Circadian Clock Gene Circuit Controls Protein and Phosphoprotein Rhythms in Arabidopsis thaliana	22
A Mouse Brain-based Multi-omics Integrative Approach Reveals Potential Blood Biomarkers for Ischemic Stroke	22
Mass Spectrometry–Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease	22
Structural Investigations of Human A2M Identify a Hollow Native Conformation That Underlies Its Distinctive Protease-Trapping Mechanism	22
Glycoproteomics Landscape of Asymptomatic and Symptomatic Human Alzheimer’s Disease Brain	21
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals	21
Sensitive and Quantitative Detection of MHC-I Displayed Neoepitopes Using a Semiautomated Workflow and TOMAHAQ Mass Spectrometry	21
Proteomic Dissection of the Impact of Environmental Exposures on Mouse Seminal Vesicle Function	21
Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multiomics Data	21
Enabling Photoactivated Cross-Linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-Cleavable Cross-Linkers	21
Quantitative Proteomic and Metabolomic Profiling Reveals Altered Mitochondrial Metabolism and Folate Biosynthesis Pathways in the Aging Drosophila Eye	21
Prediction and Validation of Mouse Meiosis-Essential Genes Based on Spermatogenesis Proteome Dynamics	20
Precision Glycoproteomics Reveals Distinctive N-Glycosylation in Human Spermatozoa	20
Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs	20
Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis	20
New Views of Old Proteins: Clarifying the Enigmatic Proteome	20
A Novel Mechanism for NF-κB-activation via IκB-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation	20
Global Proteome and Phosphoproteome Characterization of Sepsis-induced Kidney Injury	20
The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires	20
Proteomics-Based Insights Into the SARS-CoV-2–Mediated COVID-19 Pandemic: A Review of the First Year of Research	20
Separation and Identification of Permethylated Glycan Isomers by Reversed Phase NanoLC-NSI-MSn	20
Mass Spectrometric and Glycan Microarray–Based Characterization of the Filarial Nematode Brugia malayi Glycome Reveals Anionic and Zwitterionic Glycan Antigens	19
Integrated Proteomics to Understand the Role of Neuritin (NRN1) as a Mediator of Cognitive Resilience to Alzheimer’s Disease	19
Integrated Liver and Plasma Proteomics in Obese Mice Reveals Complex Metabolic Regulation	19
Integrated Systems Analysis of the Murine and Human Pancreatic Cancer Glycomes Reveals a Tumor-Promoting Role for ST6GAL1	19
Assessing the Preanalytical Variability of Plasma and Cerebrospinal Fluid Processing and Its Effects on Inflammation-Related Protein Biomarkers	18
Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma	18
Citrus Vascular Proteomics Highlights the Role of Peroxidases and Serine Proteases during Huanglongbing Disease Progression	18
Multisample Mass Spectrometry-Based Approach for Discovering Injury Markers in Chronic Kidney Disease	18
What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?	18
Prospective on Imaging Mass Spectrometry in Clinical Diagnostics	18
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics	18
Global Insights Into Lysine Acylomes Reveal Crosstalk Between Lysine Acetylation and Succinylation in Streptomyces coelicolor Metabolic Pathways	18
An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism	17
Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β	17
Mapping Isoform Abundance and Interactome of the Endogenous TMPRSS2-ERG Fusion Protein by Orthogonal Immunoprecipitation–Mass Spectrometry Assays	17
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes	17
Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury	17
Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups	17
Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities	17
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling	17
Oxonium Ion–Guided Optimization of Ion Mobility–Assisted Glycoproteomics on the timsTOF Pro	17
High Diversity of Glycosphingolipid Glycans of Colorectal Cancer Cell Lines Reflects the Cellular Differentiation Phenotype	16
In-Depth Comparison of Matrigel Dissolving Methods on Proteomic Profiling of Organoids	16
Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane	16
Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells	16
A Universal Peptide Matrix Interactomics Approach to Disclose Motif-Dependent Protein Binding	16
A Dynamic and Combinatorial Histone Code Drives Malaria Parasite Asexual and Sexual Development	16
Protein Modification Characteristics of the Malaria Parasite Plasmodium falciparum and the Infected Erythrocytes	16
Identification of Novel Serological Autoantibodies in Takayasu Arteritis Patients Using HuProt Arrays	16
Sensitive, High-Throughput HLA-I and HLA-II Immunopeptidomics Using Parallel Accumulation-Serial Fragmentation Mass Spectrometry	16
Pronounced Postmating Response in the Drosophila Female Reproductive Tract Fluid Proteome	15
Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome	15
MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies	15
Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2) Is Upregulated in Breast Epithelial–Mesenchymal Transition and Responds to Oxidative Stress	15
Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment	15
Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT	15
Single-Cell Quantitative Proteomic Analysis of Human Oocyte Maturation Revealed High Heterogeneity in In Vitro–Matured Oocytes	15
A New Parallel High-Pressure Packing System Enables Rapid Multiplexed Production of Capillary Columns	15
Proteome Characterization of Glaucoma Aqueous Humor	15
Integrated Redox Proteomic Analysis Highlights New Mechanisms of Sensitivity to Silver Nanoparticles	15
The Lysine Acetylation Modification in the Porin Aha1 of Aeromonas hydrophila Regulates the Uptake of Multidrug Antibiotics	15
A Comparative Analysis of Data Analysis Tools for Data-Independent Acquisition Mass Spectrometry	15
MHC Phosphopeptides: Promising Targets for Immunotherapy of Cancer and Other Chronic Diseases	14
Kinome Profiling of Primary Endometrial Tumors Using Multiplexed Inhibitor Beads and Mass Spectrometry Identifies SRPK1 as Candidate Therapeutic Target	14
Benchmarking Bioinformatics Pipelines in Data-Independent Acquisition Mass Spectrometry for Immunopeptidomics	14
Functional Diversity and Evolution of the Drosophila Sperm Proteome	14
Interactome Analysis of Human Phospholipase D and Phosphatidic Acid-Associated Protein Network	14
TMEM67, TMEM237, and Embigin in Complex With Monocarboxylate Transporter MCT1 Are Unique Components of the Photoreceptor Outer Segment Plasma Membrane	14

MRG Proteins Are Shared by Multiple Protein Complexes With Distinct Functions	14
Oxidative Modifications Switch Modulatory Activities of Urinary Proteins From Inhibiting to Promoting Calcium Oxalate Crystallization, Growth, and Aggregation	14
OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS	14
The Insufficient Activation of RIG-I–Like Signaling Pathway Contributes to Highly Efficient Replication of Porcine Picornaviruses in IBRS-2 Cells	14
Characterization of R-Loop–Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression	14
Slight Deuterium Enrichment in Water Acts as an Antioxidant: Is Deuterium a Cell Growth Regulator?	14
Novel Proteomic Profiling of Epididymal Extracellular Vesicles in the Domestic Cat Reveals Proteins Related to Sequential Sperm Maturation with Differences Observed between Normospermic and Teratosper	14
The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases	13
Proteome-wide Analysis Reveals Substrates of E3 Ligase RNF146 Targeted for Degradation	13
Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes	13
Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023	13
Proteomic Identification of Coxiella burnetii Effector Proteins Targeted to the Host Cell Mitochondria During Infection	13
MSstatsPTM: Statistical Relative Quantification of Posttranslational Modifications in Bottom-Up Mass Spectrometry-Based Proteomics	13
Multi–Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins	13
Increased Wheat Protein Content via Introgression of an HMW Glutenin Selectively Reshapes the Grain Proteome	13
A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis	13
Proteomic Analysis of Huntington’s Disease Medium Spiny Neurons Identifies Alterations in Lipid Droplets	13
Plasma Proteomic Kinetics in Response to Acute Exercise	13
SCASP: A Simple and Robust SDS-Aided Sample Preparation Method for Proteomic Research	13
Serum Proteomics Identifies Biomarkers Associated With the Pathogenesis of Idiopathic Pulmonary Fibrosis	12
Comprehensive Glycoprofiling of Oral Tumors Associates N-Glycosylation With Lymph Node Metastasis and Patient Survival	12
Proteomics: Progress and Promise of High-Throughput Proteomics in Chronic Kidney Disease	12
The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides	12
Decellularization Enables Characterization and Functional Analysis of Extracellular Matrix in Planarian Regeneration	12
Proteomic Profiling Reveals the Molecular Control of Oocyte Maturation	12
Commentary: Are There Indeed Spliced Peptides in the Immunopeptidome?	12
Domain Mapping of Chondroitin/Dermatan Sulfate Glycosaminoglycans Enables Structural Characterization of Proteoglycans	12
Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling	12
Quantitative Data-Independent Acquisition Glycoproteomics of Sparkling Wine	12
Peptidomics-Driven Strategy Reveals Peptides and Predicted Proteases Associated With Oral Cancer Prognosis	12
Multiomics Reveals Ectopic ATP Synthase Blockade Induces Cancer Cell Death via a lncRNA-mediated Phospho-signaling Network	11
Carboxylate-Modified Magnetic Bead (CMMB)-Based Isopropanol Gradient Peptide Fractionation (CIF) Enables Rapid and Robust Off-Line Peptide Mixture Fractionation in Bottom-Up Proteomics	11
A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos	11
Integrated Application of Multiomics Strategies Provides Insights Into the Environmental Hypoxia Response in Pelteobagrus vachelli Muscle	11
MicroID2: A Novel Biotin Ligase Enables Rapid Proximity-Dependent Proteomics	11
Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor	11
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner	11
Proteomic Analyses Identify Differentially Expressed Proteins and Pathways Between Low-Risk and High-Risk Subtypes of Early-Stage Lung Adenocarcinoma and Their Prognostic Impacts	11
Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol	11
Adipose Triglyceride Lipase Loss Promotes a Metabolic Switch in A549 Non–Small Cell Lung Cancer Cell Spheroids	11
New Proteomic Signatures to Distinguish Between Zika and Dengue Infections	11
SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering	11
Temporal Quantitative Proteomics of mGluR-induced Protein Translation and Phosphorylation in Neurons	11
Temporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-Dependent Mitophagy	11
Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform	11
Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias	11
Asparagine Hydroxylation is a Reversible Post-translational Modification	11
Blockade of High-Fat Diet Proteomic Phenotypes Using Exercise as Prevention or Treatment	11
Mass Spectrometry Identification of Biomarkers in Extracellular Vesicles From Plasmodium vivax Liver Hypnozoite Infections	11
Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate	10
Multiple Reaction Monitoring-Mass Spectrometry Enables Robust Quantitation of Plasma Proteins Regardless of Whole Blood Processing Delays That May Occur in the Clinic	10
CoolTip: Low-Temperature Solid-Phase Extraction Microcolumn for Capturing Hydrophilic Peptides and Phosphopeptides	10
Multiomic Analysis Reveals Disruption of Cholesterol Homeostasis by Cannabidiol in Human Cell Lines	10
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes	10
DeepHistoClass: A Novel Strategy for Confident Classification of Immunohistochemistry Images Using Deep Learning	10
Calculating Sample Size Requirements for Temporal Dynamics in Single-Cell Proteomics	10
Proteomic Analysis of Trichomonas vaginalis Phagolysosome, Lysosomal Targeting, and Unconventional Secretion of Cysteine Peptidases	10
Quantitative Proteomics and Phosphoproteomics Support a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis	10
Serum Exosomes From Epithelial Ovarian Cancer Patients Contain LRP1, Which Promotes the Migration of Epithelial Ovarian Cancer Cell	10
Low Cell Number Proteomic Analysis Using In-Cell Protease Digests Reveals a Robust Signature for Cell Cycle State Classification	10
Calculating Glycoprotein Similarities From Mass Spectrometric Data	10
Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells	10
An in-depth Comparison of the Pediatric and Adult Urinary N-glycomes	10
On the Robustness of Graph-Based Clustering to Random Network Alterations	9
Phosphoproteome Analysis Identifies a Synaptotagmin-1-Associated Complex Involved in Ischemic Neuron Injury	9
inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction	9
Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network	9
Temporal and Sex-Linked Protein Expression Dynamics in a Familial Model of Alzheimer’s Disease	9
A Complex Connection Between the Diversity of Human Gastric Mucin O-Glycans, Helicobacter pylori Binding, Helicobacter Infection and Fucosylation	9
Proteogenomic Analysis of Breast Cancer Transcriptomic and Proteomic Data, Using De Novo Transcript Assembly: Genome-Wide Identification of Novel Peptides and Clinical Implications	9
Soluble ANPEP Released From Human Astrocytes as a Positive Regulator of Microglial Activation and Neuroinflammation: Brain Renin–Angiotensin System in Astrocyte–Microglia Crosstalk	9
The One Hour Human Proteome	9
IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics	9
Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification	9
Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine	9
Large-Scale Immunopeptidome Analysis Reveals Recurrent Posttranslational Splicing of Cancer- and Immune-Associated Genes	9
Ionizing Radiation Drives Key Regulators of Antigen Presentation and a Global Expansion of the Immunopeptidome	9
TEAD Proteins Associate With DNA Repair Proteins to Facilitate Cellular Recovery From DNA Damage	9
Imaging Mass Spectrometry Reveals Alterations in N-Linked Glycosylation That Are Associated With Histopathological Changes in Nonalcoholic Steatohepatitis in Mouse and Human	9
Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones	9
The Proteome of Large or Small Extracellular Vesicles in Pig Seminal Plasma Differs, Defining Sources and Biological Functions	9
Personalized Drug Therapy: Innovative Concept Guided With Proteoformics	9
Identification of SUMO Targets Associated With the Pluripotent State in Human Stem Cells	9
Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits	9
MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets	9
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions	8
The in vivo Interaction Landscape of Histones H3.1 and H3.3	8
Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients	8
Proteins in Tumor-Derived Plasma Extracellular Vesicles Indicate Tumor Origin	8
Proteomic Profiling of Gastric Signet Ring Cell Carcinoma Tissues Reveals Characteristic Changes of the Complement Cascade Pathway	8
Spatially Resolved Activity-based Proteomic Profiles of the Murine Small Intestinal Lipases	8
Lysine Succinylation of VBS Contributes to Sclerotia Development and Aflatoxin Biosynthesis in Aspergillus flavus	8
Comparative Proteomic Analysis Identifies Key Metabolic Regulators of Gemcitabine Resistance in Pancreatic Cancer	8
Cellular Proteomic Profiling Using Proximity Labeling by TurboID-NES in Microglial and Neuronal Cell Lines	8
Tissue-Characteristic Expression of Mouse Proteome	8