Journal of Proteome Research

Article	Citations
Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase, a Key Drug Target for COVID-19	194
Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning	183
Evidence of Structural Protein Damage and Membrane Lipid Remodeling in Red Blood Cells from COVID-19 Patients	180
TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing	167
Optimal Dissociation Methods Differ for N- and O-Glycopeptides	154
Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients	152
Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level	146
Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection	137
Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling	101
Advances and Utility of the Human Plasma Proteome	94
Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window	87
Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine	85
Incomplete Systemic Recovery and Metabolic Phenoreversion in Post-Acute-Phase Nonhospitalized COVID-19 Patients: Implications for Assessment of Post-Acute COVID-19 Syndrome	85
Mass-Spectrometric Detection of SARS-CoV-2 Virus in Scrapings of the Epithelium of the Nasopharynx of Infected Patients via Nucleocapsid N Protein	83
Systemic Perturbations in Amine and Kynurenine Metabolism Associated with Acute SARS-CoV-2 Infection and Inflammatory Cytokine Responses	75
Current Methods for the Characterization of O-Glycans	75
Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins	71
Targeting Proteases for Treating COVID-19	69
Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches	67
iDPPIV-SCM: A Sequence-Based Predictor for Identifying and Analyzing Dipeptidyl Peptidase IV (DPP-IV) Inhibitory Peptides Using a Scoring Card Method	66
Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results	65
MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data	64
MASH Explorer: A Universal Software Environment for Top-Down Proteomics	62
The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach	60
NMR Spectroscopic Windows on the Systemic Effects of SARS-CoV-2 Infection on Plasma Lipoproteins and Metabolites in Relation to Circulating Cytokines	60

Proteomics and Informatics for Understanding Phases and Identifying Biomarkers in COVID-19 Disease	59
Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage	58
Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification	57
Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo	57
Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics	56
Considerations for MALDI-Based Quantitative Mass Spectrometry Imaging Studies	54
Plasma-Derived Extracellular Vesicle Phosphoproteomics through Chemical Affinity Purification	52
PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry	50
Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2	50
In Silico Drug Repurposing for SARS-CoV-2 Main Proteinase and Spike Proteins	48
Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard	47
Improved Prediction Model of Protein Lysine Crotonylation Sites Using Bidirectional Recurrent Neural Networks	47
A Preprocessing Tool for Enhanced Ion Mobility–Mass Spectrometry-Based Omics Workflows	46
Triple Negative Breast Cancer Detection Using LC–MS/MS Lipidomic Profiling	45
Protein–DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era	45
Quantitative Proteomics Reveals the Mechanism of Silver Nanoparticles against Multidrug-Resistant Pseudomonas aeruginosa Biofilms	44
Peptidomics: A Review of Clinical Applications and Methodologies	43
What Are We Missing by Using Hydrophilic Enrichment? Improving Bacterial Glycoproteome Coverage Using Total Proteome and FAIMS Analyses	43
Proteomics in Non-model Organisms: A New Analytical Frontier	42
An Introduction to Mass Spectrometry-Based Proteomics	41
Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV-2 Protease	41
Comparative Analysis of the Extracellular Matrix Proteome across the Myotendinous Junction	41
Early Breast Cancer Detection Using Untargeted and Targeted Metabolomics	41
Cell Metabolomics Reveals Berberine-Inhibited Pancreatic Cancer Cell Viability and Metastasis by Regulating Citrate Metabolism	40
Single-Shot 10K Proteome Approach: Over 10,000 Protein Identifications by Data-Independent Acquisition-Based Single-Shot Proteomics with Ion Mobility Spectrometry	40
Driving Single Cell Proteomics Forward with Innovation	40
Glycopeptide Biomarkers in Serum Haptoglobin for Hepatocellular Carcinoma Detection in Patients with Nonalcoholic Steatohepatitis	39
Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers	39
Data Dependent–Independent Acquisition (DDIA) Proteomics	39
Ubiquitin-Modified Proteome of SARS-CoV-2-Infected Host Cells Reveals Insights into Virus–Host Interaction and Pathogenesis	39
Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines	38
PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation	38
Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques	37
Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks	37
A Two-Way Interaction between Methotrexate and the Gut Microbiota of Male Sprague–Dawley Rats	37
Quantitative In-Vitro Diagnostic NMR Spectroscopy for Lipoprotein and Metabolite Measurements in Plasma and Serum: Recommendations for Analytical Artifact Minimization with Special Reference to COVID-	37
Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project	37
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses	36
Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?	36
Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro	36
In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods	36
Enhancing Top-Down Proteomics of Brain Tissue with FAIMS	35
Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation	35
Mass Spectrometric Analysis of Urine from COVID-19 Patients for Detection of SARS-CoV-2 Viral Antigen and to Study Host Response	35
ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry	35
Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides	35
Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer’s Disease	35
Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts	34
Enrichment of Neurodegenerative Microglia Signature in Brain-Derived Extracellular Vesicles Isolated from Alzheimer’s Disease Mouse Models	34
New Enzymatic Approach to Distinguish Fucosylation Isomers of N-Linked Glycans in Tissues Using MALDI Imaging Mass Spectrometry	34

Importance of Block Randomization When Designing Proteomics Experiments	34
ACE-2-Derived Biomimetic Peptides for the Inhibition of Spike Protein of SARS-CoV-2	34
Effect of Very-Low-Calorie Ketogenic Diet on Psoriasis Patients: A Nuclear Magnetic Resonance-Based Metabolomic Study	33
Gut Microbiota-Derived Metabolite Signature in Suckling and Weaned Piglets	33
Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment	33
Metabolic Profiling of Neocortical Tissue Discriminates Alzheimer’s Disease from Mild Cognitive Impairment, High Pathology Controls, and Normal Controls	32
Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome	32
Prediction of Neuropeptides from Sequence Information Using Ensemble Classifier and Hybrid Features	31
Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses	31
Metabolomics of Milk Reflects a Negative Energy Balance in Cows	31
Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project	30
“A Chain Only as Strong as Its Weakest Link”: An Up-to-Date Literature Review on the Bidirectional Interaction of Pulmonary Fibrosis and COVID-19	30
Parallel Reaction Monitoring Mass Spectrometry Method for Detection of Both Casein and Whey Milk Allergens from a Baked Food Matrix	30
PD-L1 Glycosylation and Its Impact on Binding to Clinical Antibodies	30
Overview of Targets and Potential Drugs of SARS-CoV-2 According to the Viral Replication	30
Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme	30
Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags	30
mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection	30
Impact of Increased FUT8 Expression on the Extracellular Vesicle Proteome in Prostate Cancer Cells	29
The 2022 Report on the Human Proteome from the HUPO Human Proteome Project	29
Bile Acid Profiles Are Distinct among Patients with Different Etiologies of Chronic Liver Disease	29
Human Bone Proteomes before and after Decomposition: Investigating the Effects of Biological Variation and Taphonomic Alteration on Bone Protein Profiles and the Implications for Forensic Proteomics	28
Perspective on Proteomics for Virus Detection in Clinical Samples	28
Interaction of Drug Candidates with Various SARS-CoV-2 Receptors: An in Silico Study to Combat COVID-19	28
Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology	28
Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2	27
MS Annika: A New Cross-Linking Search Engine	27
Longitudinal Plasma Proteomics Analysis Reveals Novel Candidate Biomarkers in Acute COVID-19	27
Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools	27
Features of Peptide Fragmentation Spectra in Single-Cell Proteomics	26
PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity	26
Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition	26
QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories	26
A Review of Imputation Strategies for Isobaric Labeling-Based Shotgun Proteomics	26
Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma	26
Serum or Plasma (and Which Plasma), That Is the Question	26
TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level	25
A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients	25
Quantitative Assessment of SARS-CoV-2 Virus in Nasopharyngeal Swabs Stored in Transport Medium by a Straightforward LC-MS/MS Assay Targeting Nucleocapsid, Membrane, and Spike Proteins	25
Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data	25
Genomics- and Peptidomics-Based Discovery of Conserved and Novel Neuropeptides in the American Cockroach	25
Optimized Proteomics Workflow for the Detection of Small Proteins	25
DeepPSP: A Global–Local Information-Based Deep Neural Network for the Prediction of Protein Phosphorylation Sites	25
Temporal Proteomic Profiling of SH-SY5Y Differentiation with Retinoic Acid Using FAIMS and Real-Time Searching	25
Biological Functions and Large-Scale Profiling of Protein Glycosylation in Human Semen	24
Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison	24
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite	24
Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice	24
Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination	24
Site-Specific N-Linked Glycosylation Analysis of Human Carcinoembryonic Antigen by Sheathless Capillary Electrophoresis–Tandem Mass Spectrometry	24
Low Volume in Vitro Diagnostic Proton NMR Spectroscopy of Human Blood Plasma for Lipoprotein and Metabolite Analysis: Application to SARS-CoV-2 Biomarkers	24
Urinary Volatilomics Unveils a Candidate Biomarker Panel for Noninvasive Detection of Clear Cell Renal Cell Carcinoma	23
A Panel of Glycopeptides as Candidate Biomarkers for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation	23
Physiological Tau Interactome in Brain and Its Link to Tauopathies	23
Column-based Technology for CD9-HPLC Immunoaffinity Isolation of Serum Extracellular Vesicles	23
Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome	23
Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area	23
Genetic Variability of the SARS-CoV-2 Pocketome	23
Machine Learning-Enabled Renal Cell Carcinoma Status Prediction Using Multiplatform Urine-Based Metabolomics	22
A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases	22
iGlu_AdaBoost: Identification of Lysine Glutarylation Using the AdaBoost Classifier	22
Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient	22
Rapid Response to Pandemic Threats: Immunogenic Epitope Detection of Pandemic Pathogens for Diagnostics and Vaccine Development Using Peptide Microarrays	22
Proteomic Investigation of the Antibacterial Mechanism of trans-Cinnamaldehyde against Escherichia coli	22
Generation of an Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability	22
Role of Multiomics Data to Understand Host–Pathogen Interactions in COVID-19 Pathogenesis	22
Development of an Efficient and Sensitive Chemical Derivatization-Based LC–MS/MS Method for Quantifying Gut Microbiota-Derived Metabolites in Human Plasma and Its Application in Studying Cardiovascula	22
Characterization of Monophasic Solvent-Based Tissue Extractions for the Detection of Polar Metabolites and Lipids Applying Ultrahigh-Performance Liquid Chromatography–Mass Spectrometry Clinical Metabo	21
Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context	21
Deep Profiling of Microgram-Scale Proteome by Tandem Mass Tag Mass Spectrometry	21
Peptide Correlation Analysis (PeCorA) Reveals Differential Proteoform Regulation	21
Simplified and Unified Access to Cancer Proteogenomic Data	21
Liquid Chromatography–Mass Spectrometry-Based Tissue Metabolic Profiling Reveals Major Metabolic Pathway Alterations and Potential Biomarkers of Lung Cancer	21
Identification of Novel Adipokines through Proteomic Profiling of Small Extracellular Vesicles Derived from Adipose Tissue	21
Global Inventory of ClpP- and ClpX-Regulated Proteins in Staphylococcus aureus	21
Discovery Proteomics for COVID-19: Where We Are Now	21
Proteomic Analysis Identifies Prolonged Disturbances in Pathways Related to Cholesterol Metabolism and Myocardium Function in the COVID-19 Recovery Stage	21
Complement and Coagulation Cascades are Potentially Involved in Dopaminergic Neurodegeneration in α-Synuclein-Based Mouse Models of Parkinson’s Disease	21
1H NMR-Based Urine Metabolomics Reveals Signs of Enhanced Carbon and Nitrogen Recycling in Prostate Cancer	21
DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients	21

Shell Disorder Analysis Suggests That Pangolins Offered a Window for a Silent Spread of an Attenuated SARS-CoV-2 Precursor among Humans	20
Toward a Universal Sample Preparation Method for Denaturing Top-Down Proteomics of Complex Proteomes	20
Defining the Caprin-1 Interactome in Unstressed and Stressed Conditions	20
Computational Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage and Applications to 15 Tumors	20
Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors	20
In Vitro Characterization and Metabolomic Analysis of Cold-Stored Platelets	20
Proteome-Scale Analysis of Protein S-Acylation Comes of Age	20
Proteomic Workflows for High-Quality Quantitative Proteome and Post-Translational Modification Analysis of Clinically Relevant Samples from Formalin-Fixed Paraffin-Embedded Archives	20
Spritz: A Proteogenomic Database Engine	20
Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes	20
Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine-N-oxide	20
Toward a Sample Metadata Standard in Public Proteomics Repositories	20
Uncovering the Metabolic Mechanism of Salidroside Alleviating Microglial Hypoxia Inflammation Based on Microfluidic Chip-Mass Spectrometry	20
How (Not) to Generate a Highly Predictive Biomarker Panel Using Machine Learning	19
Quantitative Top-Down Proteomics by Isobaric Labeling with Thiol-Directed Tandem Mass Tags	19
DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics	19
1H qNMR-Based Metabolomics Discrimination of Covid-19 Severity	19
Potential Regulatory Role of Human-Carboxylesterase-1 Glycosylation in Liver Cancer Cell Growth	19
Biochemical Tools for Tracking Proteolysis	19
The O-Glycome of Human Nigrostriatal Tissue and Its Alteration in Parkinson’s Disease	19
In Stallion Spermatozoa, Superoxide Dismutase (Cu–Zn) (SOD1) and the Aldo-Keto-Reductase Family 1 Member b (AKR1B1) Are the Proteins Most Significantly Reduced by Cryopreservation	19
Potential Use of Serum Proteomics for Monitoring COVID-19 Progression to Complement RT-PCR Detection	19
Ultraperformance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Mass Spectrometry-Based Metabolomics and Lipidomics Identify Biomarkers for Efficacy Evaluation of Mesalazine in a Dextran	19
Structure-Based Screening to Discover New Inhibitors for Papain-like Proteinase of SARS-CoV-2: An In Silico Study	18
Discovery of Novel Protein Biomarkers in Urine for Diagnosis of Urothelial Cancer Using iTRAQ Proteomics	18
Reduced Nicotinamide Mononucleotide (NMNH) Potently Enhances NAD+ and Suppresses Glycolysis, the TCA Cycle, and Cell Growth	18
Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease	18
Toward an Integrated Machine Learning Model of a Proteomics Experiment	18
Proteomic Analysis of Sri Lanka Echis carinatus Venom: Immunological Cross-Reactivity and Enzyme Neutralization Potency of Indian Polyantivenom	18
Mapping the Proteoform Landscape of Five Human Tissues	18
Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial	18
Assessment of Streptavidin Bead Binding Capacity to Improve Quality of Streptavidin-based Enrichment Studies	18
Optimization of Ultrafast Proteomics Using an LC-Quadrupole-Orbitrap Mass Spectrometer with Data-Independent Acquisition	18
CIMAGE2.0: An Expanded Tool for Quantitative Analysis of Activity-Based Protein Profiling (ABPP) Data	18
Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins	18
Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets	18
Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection	18
Public LC-Orbitrap Tandem Mass Spectral Library for Metabolite Identification	18
Multiomics Integrative Analysis for Discovering the Potential Mechanism of Dioscin against Hyperuricemia Mice	18
Comparison of Unit Resolution Versus High-Resolution Accurate Mass for Parallel Reaction Monitoring	17
Computational Immune Proteomics Approach to Target COVID-19	17
Quantitative Interactomics of Lck-TurboID in Living Human T Cells Unveils T Cell Receptor Stimulation-Induced Proximal Lck Interactors	17
Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire	17
Early Detection of Pancreatic Cancer in Type 2 Diabetes Mellitus Patients Based on 1H NMR Metabolomics	17
Metabolic Variations between Low-Grade and High-Grade Gliomas—Profiling by 1H NMR Spectroscopy	17
Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery	17
Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms	17
Integrating Intact Mass Analysis and Middle-Down Mass Spectrometry Approaches to Effectively Characterize Trastuzumab and Adalimumab Structural Heterogeneity	17
InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information	17
Simple and Efficient Microsolid-Phase Extraction Tip-Based Sample Preparation Workflow to Enable Sensitive Proteomic Profiling of Limited Samples (200 to 10,000 Cells)	17
Sequential Precipitation and Delipidation Enables Efficient Enrichment of Low-Molecular Weight Proteins and Peptides from Human Plasma	17
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers	17
Metabolite Profiling Reveals Predictive Biomarkers and the Absence of β-Methyl Amino-l-alanine in Plasma from Individuals Diagnosed with Amyotrophic Lateral Sclerosis	17
Integrating Top-Down and Bottom-Up Mass Spectrometric Strategies for Proteomic Profiling of Iranian Saw-Scaled Viper, Echis carinatus sochureki, Venom	17
Stable Isotope-Resolved Metabolomics Reveals the Abnormal Brain Glucose Catabolism in Depression Based on Chronic Unpredictable Mild Stress Rats	17
The rawrr R Package: Direct Access to Orbitrap Data and Beyond	17
Optimized Sample Preparation and Data Processing of Data-Independent Acquisition Methods for the Robust Quantification of Trace-Level Host Cell Protein Impurities in Antibody Drug Products	17
Proteomic Analysis Reveals Proteins and Pathways Associated with Lactation in Bovine Mammary Epithelial Cell-Derived Exosomes	17
Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity	17
Molecular Profiling Associated with Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2)-Mediated Carcinogenesis in Gastric Cancer	17
Direct Comparison of N-Glycans and Their Isomers Derived from Spike Glycoprotein 1 of MERS-CoV, SARS-CoV-1, and SARS-CoV-2	17
COSS: A Fast and User-Friendly Tool for Spectral Library Searching	17
Influence of Age, Sex, and Diet on the Human Fecal Metabolome Investigated by 1H NMR Spectroscopy	17
Ex Vivo Equine Cartilage Explant Osteoarthritis Model: A Metabolomics and Proteomics Study	17
Mass Spectrometry-Based Structural Analysis of Cysteine-Rich Metal-Binding Sites in Proteins with MetaOdysseus R Software	17
An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community	16
Ultrahigh-Resolution Mass Spectrometry-Based Platform for Plasma Metabolomics Applied to Type 2 Diabetes Research	16
Automated Ligand Purification Platform Accelerates Immunopeptidome Analysis by Mass Spectrometry	16
Integrated Multi-Omics Analysis of Mechanisms Underlying Yeast Ethanol Tolerance	16
Deep Time Course Proteomics of SARS-CoV- and SARS-CoV-2-Infected Human Lung Epithelial Cells (Calu-3) Reveals Strong Induction of Interferon-Stimulated Gene Expression by SARS-CoV-2 in Contrast to SAR	16
Proteomic Analysis of Whole Blood Using Volumetric Absorptive Microsampling for Precision Medicine Biomarker Studies	16
Untargeted Gut Metabolomics to Delve the Interplay between Selenium Supplementation and Gut Microbiota	16
FAIMS Enhances the Detection of PTM Crosstalk Sites	16
MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale	16
Insights into the Differential Preservation of Bone Proteomes in Inhumed and Entombed Cadavers from Italian Forensic Caseworks	16
Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool	16
Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis	16
MS-DAP Platform for Downstream Data Analysis of Label-Free Proteomics Uncovers Optimal Workflows in Benchmark Data Sets and Increased Sensitivity in Analysis of Alzheimer’s Biomarker Data	16
Benchmarking Cleavable Biotin Tags for Peptide-Centric Chemoproteomics	16
Sensitive, Rapid, Robust, and Reproducible Workflow for Host Cell Protein Profiling in Biopharmaceutical Process Development	16
Helicobacter pylori Immunoproteomic Profiles in Gastric Cancer	16
Comprehensive Intrinsic Disorder Analysis of 6108 Viral Proteomes: From the Extent of Intrinsic Disorder Penetrance to Functional Annotation of Disordered Viral Proteins	16
Detection of Tear Components Using Matrix-Assisted Laser Desorption Ionization/Time-of-Flight Mass Spectrometry for Rapid Dry Eye Diagnosis	16
Metabolic Profiling of Urinary Chiral Amino-Containing Biomarkers for Gastric Cancer Using a Sensitive Chiral Chlorine-Labeled Probe by HPLC-MS/MS	15
Joint Synovial Fluid Metabolomics Method to Decipher the Metabolic Mechanisms of Adjuvant Arthritis and Geniposide Intervention	15
Metabolomic Nuclear Magnetic Resonance Studies at Presymptomatic and Symptomatic Stages of Huntington’s Disease on a Drosophila Model	15
Fragment Mass Spectrum Prediction Facilitates Site Localization of Phosphorylation	15
Hippocampus Proteomics and Brain Lipidomics Reveal Network Dysfunction and Lipid Molecular Abnormalities in APP/PS1 Mouse Model of Alzheimer’s Disease	15
Comparative Blood and Urine Metabolomics Analysis of Healthy Elderly and Young Male Singaporeans	15
Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling	15
Brain Lipid Dynamics in Amyloid Precursor Protein/Presenilin 1 Mouse Model of Early Alzheimer’s Disease by Desorption Electrospray Ionization and Matrix Assisted Laser Desorption Ionization–Mass Spect	15
Spatially Resolved Metabolomics Based on Air-Flow-Assisted Desorption Electrospray Ionization–Mass Spectrometry Imaging Reveals Region-Specific Metabolic Alterations in Diabetic Encephalopathy	15
Quantitative Proteomic Analysis of Chikungunya Virus-Infected Aedes aegypti Reveals Proteome Modulations Indicative of Persistent Infection	15
Serum Glycoprotein Markers in Nonalcoholic Steatohepatitis and Hepatocellular Carcinoma	15
Generation of SARS-CoV-2 S1 Spike Glycoprotein Putative Antigenic Epitopes in Vitro by Intracellular Aminopeptidases	15