Molecular & Cellular Proteomics

Article	Citations
A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients	273
Single-cell Proteomics: Progress and Prospects	218
Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries	160
IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs	159
Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant	142
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis	139
Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches	135
MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics	125
DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis	122
An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics	119
A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics	114
The Peptide Vaccine of the Future	93
Decoding Post-Translational Modification Crosstalk With Proteomics	89
MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures	86
Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins	86
Trapped Ion Mobility Spectrometry and Parallel Accumulation–Serial Fragmentation in Proteomics	82
Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing	77
Proximity Extension Assay in Combination with Next-Generation Sequencing for High-throughput Proteome-wide Analysis	74
Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis	68
Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication	63
Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives	62
Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein	58
Imaging Mass Spectrometry and Lectin Analysis of N-Linked Glycans in Carbohydrate Antigen–Defined Pancreatic Cancer Tissues	53
PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results	52
Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation	52

Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing	51
An Introduction to Advanced Targeted Acquisition Methods	51
Proteome Profiling of Recombinant DNase Therapy in Reducing NETs and Aiding Recovery in COVID-19 Patients	50
Quantitative Proteomics Identifies Proteins Enriched in Large and Small Extracellular Vesicles	47
Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF	47
In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease	46
Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction	45
Accurate MS-based Rab10 Phosphorylation Stoichiometry Determination as Readout for LRRK2 Activity in Parkinson's Disease	44
Serum Protein Profiling Reveals a Landscape of Inflammation and Immune Signaling in Early-stage COVID-19 Infection	42
Developments and Applications of Functional Protein Microarrays	42
N-Glycomic Signature of Stage II Colorectal Cancer and Its Association With the Tumor Microenvironment	41
Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics	41
Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search	40
Phenotypic Adaption of Pseudomonas aeruginosa by Hacking Siderophores Produced by Other Microorganisms	39
The Complexity and Dynamics of the Tissue Glycoproteome Associated With Prostate Cancer Progression	39
Proteomic Landscape of Exosomes Reveals the Functional Contributions of CD151 in Triple-Negative Breast Cancer	38
Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue	38
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity	37
The Role of Data-Independent Acquisition for Glycoproteomics	37
Interspecies Differences in Proteome Turnover Kinetics Are Correlated With Life Spans and Energetic Demands	37
A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria	36
Robust Summarization and Inference in Proteome-wide Label-free Quantification	36
Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome	36
Scaling Up Single-Cell Proteomics	35
HIGD2A is Required for Assembly of the COX3 Module of Human Mitochondrial Complex IV	35
Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification	35
Evaluation and Refinement of Sample Preparation Methods for Extracellular Matrix Proteome Coverage	35
Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry	34
The CEP5 Peptide Promotes Abiotic Stress Tolerance, As Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis	33
Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker	33
MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates	32
Investigation of Inter- and Intratumoral Heterogeneity of Glioblastoma Using TOF-SIMS	32
An Expanding Repertoire of Protein Acylations	32
Organellar Maps Through Proteomic Profiling – A Conceptual Guide	32
Ethical Principles, Constraints, and Opportunities in Clinical Proteomics	32
Profiling Cell Signaling Networks at Single-cell Resolution	31
Arginine in C9ORF72 Dipolypeptides Mediates Promiscuous Proteome Binding and Multiple Modes of Toxicity	31
Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples	31
Decreased Immunoglobulin G Core Fucosylation, A Player in Antibody-dependent Cell-mediated Cytotoxicity, is Associated with Autoimmune Thyroid Diseases	30
Dysregulation of Exosome Cargo by Mutant Tau Expressed in Human-induced Pluripotent Stem Cell (iPSC) Neurons Revealed by Proteomics Analyses	30
Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical The	30
Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry–Based Approaches	30
Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics	30
Integrated Glycoproteomics Identifies a Role of N-Glycosylation and Galectin-1 on Myogenesis and Muscle Development	29
The DNA Sensor cGAS is Decorated by Acetylation and Phosphorylation Modifications in the Context of Immune Signaling	28
Human Hepatocyte Nuclear Factor 4-α Encodes Isoforms with Distinct Transcriptional Functions	28
Age-Associated Proteomic Signatures and Potential Clinically Actionable Targets of Colorectal Cancer	27
Systematic Proteome and Lysine Succinylome Analysis Reveals Enhanced Cell Migration by Hyposuccinylation in Esophageal Squamous Cell Carcinoma	27
Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines	27
High-Throughput and Site-Specific N-Glycosylation Analysis of Human Alpha-1-Acid Glycoprotein Offers a Great Potential for New Biomarker Discovery	27

Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to Searching	27
Glycomics, Glycoproteomics, and Glycogenomics: An Inter-Taxa Evolutionary Perspective	27
ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping	26
Peptidomic Analysis of Urine from Youths with Early Type 1 Diabetes Reveals Novel Bioactivity of Uromodulin Peptides In Vitro	26
Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation	26
Pitfalls in HLA Ligandomics—How to Catch a Li(e)gand	26
Discovery of a Redox Thiol Switch: Implications for Cellular Energy Metabolism	26
Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network	25
Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors	25
Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review	25
Are There Indeed Spliced Peptides in the Immunopeptidome?	25
Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future	25
Seminal Plasma Proteome as an Indicator of Sperm Dysfunction and Low Sperm Motility in Chickens	24
Mutation-independent Proteomic Signatures of Pathological Progression in Murine Models of Duchenne Muscular Dystrophy	24
Antibody Binding Epitope Mapping (AbMap) of Hundred Antibodies in a Single Run	24
Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs	24
Multi-Omics Profiling for Health	24
The Aspergillus fumigatus Secretome Alters the Proteome of Pseudomonas aeruginosa to Stimulate Bacterial Growth: Implications for Co-infection	24
Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments	24
Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries	23
Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years	23
Proteomic Signature of Host Response to SARS-CoV-2 Infection in the Nasopharynx	23
Molecular Dynamics Simulation-assisted Ionic Liquid Screening for Deep Coverage Proteome Analysis	23
Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides	23
Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics	23
Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation	22
Characterization of Signaling Pathways Associated with Pancreatic β-cell Adaptive Flexibility in Compensation of Obesity-linked Diabetes in db/db Mice	22
CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens	22
AlphaTims: Indexing Trapped Ion Mobility Spectrometry–TOF Data for Fast and Easy Accession and Visualization	22
Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics	22
MHC Class I Immunopeptidome: Past, Present, and Future	22
Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress	21
Isolation of Acetylated and Unmodified Protein N-Terminal Peptides by Strong Cation Exchange Chromatographic Separation of TrypN-Digested Peptides	21
Quantitative Proteomics of Human Heart Samples Collected In Vivo Reveal the Remodeled Protein Landscape of Dilated Left Atrium Without Atrial Fibrillation	21
Subcellular Transcriptomics and Proteomics: A Comparative Methods Review	21
Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping	21
In-Depth Characterization of the Staphylococcus aureus Phosphoproteome Reveals New Targets of Stk1	21
In-Depth Matrisome and Glycoproteomic Analysis of Human Brain Glioblastoma Versus Control Tissue	21
Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives	21
Quantitative Consequences of Protein Carriers in Immunopeptidomics and Tyrosine Phosphorylation MS2 Analyses	21
Simple But Efficacious Enrichment of Integral Membrane Proteins and Their Interactions for In-Depth Membrane Proteomics	21
Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites	21
Peptide-based Interaction Proteomics	21
Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung Cancer	20
Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition	20
Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA	20
Structural Investigations of Human A2M Identify a Hollow Native Conformation That Underlies Its Distinctive Protease-Trapping Mechanism	20
Plasma Proteomes Can Be Reidentifiable and Potentially Contain Personally Sensitive and Incidental Findings	20
PolySTest: Robust Statistical Testing of Proteomics Data with Missing Values Improves Detection of Biologically Relevant Features	20
The Circadian Clock Gene Circuit Controls Protein and Phosphoprotein Rhythms in Arabidopsis thaliana	20
The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis	20
A Mouse Brain-based Multi-omics Integrative Approach Reveals Potential Blood Biomarkers for Ischemic Stroke	20
Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning	19
Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs	19
Quantitative Proteomic and Metabolomic Profiling Reveals Altered Mitochondrial Metabolism and Folate Biosynthesis Pathways in the Aging Drosophila Eye	19
Thyroglobulin Interactome Profiling Defines Altered Proteostasis Topology Associated With Thyroid Dyshormonogenesis	19
Proteomics, Lipidomics, Metabolomics, and 16S DNA Sequencing of Dental Plaque From Patients With Diabetes and Periodontal Disease	19
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability	19
Comparative Proteome Signatures of Trace Samples by Multiplexed Data-Independent Acquisition	19
Enabling Photoactivated Cross-Linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-Cleavable Cross-Linkers	19
Kir2.1 Interactome Mapping Uncovers PKP4 as a Modulator of the Kir2.1-Regulated Inward Rectifier Potassium Currents	18
Depolarization-dependent Induction of Site-specific Changes in Sialylation on N-linked Glycoproteins in Rat Nerve Terminals	18
Citrus Vascular Proteomics Highlights the Role of Peroxidases and Serine Proteases during Huanglongbing Disease Progression	18
Separation and Identification of Permethylated Glycan Isomers by Reversed Phase NanoLC-NSI-MSn	18
Region-Specific Cell Membrane N-Glycome of Functional Mouse Brain Areas Revealed by nanoLC-MS Analysis	18
Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multiomics Data	18
The Secretome Profiling of a Pediatric Airway Epithelium Infected with hRSV Identified Aberrant Apical/Basolateral Trafficking and Novel Immune Modulating (CXCL6, CXCL16, CSF3) and Antiviral (CEACAM1)	17
A Novel Mechanism for NF-κB-activation via IκB-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation	17
Prediction and Validation of Mouse Meiosis-Essential Genes Based on Spermatogenesis Proteome Dynamics	17
Proteomics-Based Insights Into the SARS-CoV-2–Mediated COVID-19 Pandemic: A Review of the First Year of Research	17
Sensitive and Quantitative Detection of MHC-I Displayed Neoepitopes Using a Semiautomated Workflow and TOMAHAQ Mass Spectrometry	17
Examining and Fine-tuning the Selection of Glycan Compositions with GlyConnect Compozitor	17
Mass Spectrometric and Glycan Microarray–Based Characterization of the Filarial Nematode Brugia malayi Glycome Reveals Anionic and Zwitterionic Glycan Antigens	17
Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis	16
Integrated Systems Analysis of the Murine and Human Pancreatic Cancer Glycomes Reveals a Tumor-Promoting Role for ST6GAL1	16
MS-Based Proteomics of Body Fluids: The End of the Beginning	16
Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty	16
Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9	16
The Choice of Search Engine Affects Sequencing Depth and HLA Class I Allele-Specific Peptide Repertoires	16
Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma	16

Modulation of Natural HLA-B*27:05 Ligandome by Ankylosing Spondylitis-associated Endoplasmic Reticulum Aminopeptidase 2 (ERAP2)	15
Integrated Redox Proteomic Analysis Highlights New Mechanisms of Sensitivity to Silver Nanoparticles	15
Multisample Mass Spectrometry-Based Approach for Discovering Injury Markers in Chronic Kidney Disease	15
Multiattribute Glycan Identification and FDR Control for Glycoproteomics	15
Assessing the Preanalytical Variability of Plasma and Cerebrospinal Fluid Processing and Its Effects on Inflammation-Related Protein Biomarkers	15
SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines	15
Global Proteome and Phosphoproteome Characterization of Sepsis-induced Kidney Injury	15
A Universal Peptide Matrix Interactomics Approach to Disclose Motif-Dependent Protein Binding	15
Proteomic Dissection of the Impact of Environmental Exposures on Mouse Seminal Vesicle Function	15
Mapping Isoform Abundance and Interactome of the Endogenous TMPRSS2-ERG Fusion Protein by Orthogonal Immunoprecipitation–Mass Spectrometry Assays	15
Glycoproteomics Landscape of Asymptomatic and Symptomatic Human Alzheimer’s Disease Brain	14
Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane	14
Proteomic Analysis Reveals that Topoisomerase 2A is Associated with Defective Sperm Head Morphology	14
Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β	14
Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals	14
Flow-induced Reorganization of Laminin-integrin Networks Within the Endothelial Basement Membrane Uncovered by Proteomics	14
Perlecan Knockdown Significantly Alters Extracellular Matrix Composition and Organization During Cartilage Development	14
Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli	13
Characterization of R-Loop–Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression	13
An Interaction Network of RNA-Binding Proteins Involved in Drosophila Oogenesis	13
Identification of an Unconventional Subpeptidome Bound to the Behçet's Disease-associated HLA-B*51:01 that is Regulated by Endoplasmic Reticulum Aminopeptidase 1 (ERAP1)	13
A New Parallel High-Pressure Packing System Enables Rapid Multiplexed Production of Capillary Columns	13
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes	13
Proteomic Portraits Reveal Evolutionarily Conserved and Divergent Responses to Spinal Cord Injury	13
An Integrated Transcriptomics and Proteomics Analysis Implicates lncRNA MALAT1 in the Regulation of Lipid Metabolism	13
Sulconazole Induces PANoptosis by Triggering Oxidative Stress and Inhibiting Glycolysis to Increase Radiosensitivity in Esophageal Cancer	13
Mass Spectrometry–Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease	13
TMEM67, TMEM237, and Embigin in Complex With Monocarboxylate Transporter MCT1 Are Unique Components of the Photoreceptor Outer Segment Plasma Membrane	13
New Views of Old Proteins: Clarifying the Enigmatic Proteome	13
Protein Modification Characteristics of the Malaria Parasite Plasmodium falciparum and the Infected Erythrocytes	13
Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs	13
Precision Glycoproteomics Reveals Distinctive N-Glycosylation in Human Spermatozoa	13
Kinome Profiling of Primary Endometrial Tumors Using Multiplexed Inhibitor Beads and Mass Spectrometry Identifies SRPK1 as Candidate Therapeutic Target	12
Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface	12
Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities	12
Pronounced Postmating Response in the Drosophila Female Reproductive Tract Fluid Proteome	12
MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies	12
Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2) Is Upregulated in Breast Epithelial–Mesenchymal Transition and Responds to Oxidative Stress	12
Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment	12
Identification of Tumor Antigens in the HLA Peptidome of Patient-derived Xenograft Tumors in Mouse	12
Global Insights Into Lysine Acylomes Reveal Crosstalk Between Lysine Acetylation and Succinylation in Streptomyces coelicolor Metabolic Pathways	12
Quantitative Data-Independent Acquisition Glycoproteomics of Sparkling Wine	12
Oxidative Modifications Switch Modulatory Activities of Urinary Proteins From Inhibiting to Promoting Calcium Oxalate Crystallization, Growth, and Aggregation	12
The Challenge of Classifying Metastatic Cell Properties by Molecular Profiling Exemplified with Cutaneous Melanoma Cells and Their Cerebral Metastasis from Patient Derived Mouse Xenografts	12
A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis	12
Proteomic Identification of Coxiella burnetii Effector Proteins Targeted to the Host Cell Mitochondria During Infection	12
Integrative Metabolic Pathway Analysis Reveals Novel Therapeutic Targets in Osteoarthritis	12
Identification of Novel Serological Autoantibodies in Takayasu Arteritis Patients Using HuProt Arrays	12
Increased Wheat Protein Content via Introgression of an HMW Glutenin Selectively Reshapes the Grain Proteome	12
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner	11
Slight Deuterium Enrichment in Water Acts as an Antioxidant: Is Deuterium a Cell Growth Regulator?	11
Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol	11
Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling	11
Interactome Analysis of Human Phospholipase D and Phosphatidic Acid-Associated Protein Network	11
Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor	11
Proteome-wide Analysis Reveals Substrates of E3 Ligase RNF146 Targeted for Degradation	11
Proteomics of Campylobacter jejuni Growth in Deoxycholate Reveals Cj0025c as a Cystine Transport Protein Required for Wild-type Human Infection Phenotypes	11
Prospective on Imaging Mass Spectrometry in Clinical Diagnostics	11
Integrated Liver and Plasma Proteomics in Obese Mice Reveals Complex Metabolic Regulation	11
Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells	11
Commentary: Are There Indeed Spliced Peptides in the Immunopeptidome?	11
Multiomics Reveals Ectopic ATP Synthase Blockade Induces Cancer Cell Death via a lncRNA-mediated Phospho-signaling Network	11
Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT	11
Domain Mapping of Chondroitin/Dermatan Sulfate Glycosaminoglycans Enables Structural Characterization of Proteoglycans	11
A Dynamic and Combinatorial Histone Code Drives Malaria Parasite Asexual and Sexual Development	11
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	11
MHC Phosphopeptides: Promising Targets for Immunotherapy of Cancer and Other Chronic Diseases	11
Temporal Quantitative Proteomics of mGluR-induced Protein Translation and Phosphorylation in Neurons	11
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling	11
OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS	10
The Neuroproteomic Basis of Enhanced Perception and Processing of Brood Signals That Trigger Increased Reproductive Investment in Honeybee (Apis mellifera) Workers	10
Identification of Lysine Acetylation Sites on MERS-CoV Replicase pp1ab	10
Proteomic Analyses Identify Differentially Expressed Proteins and Pathways Between Low-Risk and High-Risk Subtypes of Early-Stage Lung Adenocarcinoma and Their Prognostic Impacts	10
In-Depth Comparison of Matrigel Dissolving Methods on Proteomic Profiling of Organoids	10
Agonists of Orally Expressed TRP Channels Stimulate Salivary Secretion and Modify the Salivary Proteome	10
SCASP: A Simple and Robust SDS-Aided Sample Preparation Method for Proteomic Research	10
New Proteomic Signatures to Distinguish Between Zika and Dengue Infections	10
N-glycosylation Site Analysis Reveals Sex-related Differences in Protein N-glycosylation in the Rice Brown Planthopper (Nilaparvata lugens)	10
The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides	10
Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups	10
Proteome Analysis Reveals a Significant Host-Specific Response in Rhizobium leguminosarum bv. viciae Endosymbiotic Cells	10
A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos	10
AMPK Interactome Reveals New Function in Non-homologous End Joining DNA Repair	10
DeepHistoClass: A Novel Strategy for Confident Classification of Immunohistochemistry Images Using Deep Learning	10
The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases	10
Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome	10
Carboxylate-Modified Magnetic Bead (CMMB)-Based Isopropanol Gradient Peptide Fractionation (CIF) Enables Rapid and Robust Off-Line Peptide Mixture Fractionation in Bottom-Up Proteomics	10
Single-Cell Quantitative Proteomic Analysis of Human Oocyte Maturation Revealed High Heterogeneity in In Vitro–Matured Oocytes	10
Asparagine Hydroxylation is a Reversible Post-translational Modification	10
Integrated Application of Multiomics Strategies Provides Insights Into the Environmental Hypoxia Response in Pelteobagrus vachelli Muscle	10
Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones	9
Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification	9
Oxonium Ion–Guided Optimization of Ion Mobility–Assisted Glycoproteomics on the timsTOF Pro	9
Adipose Triglyceride Lipase Loss Promotes a Metabolic Switch in A549 Non–Small Cell Lung Cancer Cell Spheroids	9
An in-depth Comparison of the Pediatric and Adult Urinary N-glycomes	9