OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Proteome Research is 4. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-03-01 to 2024-03-01.)

Article	Citations
Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data	264
Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1	204
Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase, a Key Drug Target for COVID-19	190
Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning	175
Evidence of Structural Protein Damage and Membrane Lipid Remodeling in Red Blood Cells from COVID-19 Patients	168
Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics	163
TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing	156
Optimal Dissociation Methods Differ for N- and O-Glycopeptides	151
Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients	151
Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level	144
Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection	134
Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling	95
Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window	87
Advances and Utility of the Human Plasma Proteome	83
Mass-Spectrometric Detection of SARS-CoV-2 Virus in Scrapings of the Epithelium of the Nasopharynx of Infected Patients via Nucleocapsid N Protein	83
Incomplete Systemic Recovery and Metabolic Phenoreversion in Post-Acute-Phase Nonhospitalized COVID-19 Patients: Implications for Assessment of Post-Acute COVID-19 Syndrome	81
Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine	76
Systemic Perturbations in Amine and Kynurenine Metabolism Associated with Acute SARS-CoV-2 Infection and Inflammatory Cytokine Responses	73
Characterization of Urinary Exosomes Purified with Size Exclusion Chromatography and Ultracentrifugation	72
Current Methods for the Characterization of O-Glycans	71
Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins	70
Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches	67
Targeting Proteases for Treating COVID-19	66
lipidr: A Software Tool for Data Mining and Analysis of Lipidomics Datasets	66
iDPPIV-SCM: A Sequence-Based Predictor for Identifying and Analyzing Dipeptidyl Peptidase IV (DPP-IV) Inhibitory Peptides Using a Scoring Card Method	65

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data	62
MASH Explorer: A Universal Software Environment for Top-Down Proteomics	61
The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach	60
Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results	59
NMR Spectroscopic Windows on the Systemic Effects of SARS-CoV-2 Infection on Plasma Lipoproteins and Metabolites in Relation to Circulating Cytokines	58
Proteomics and Informatics for Understanding Phases and Identifying Biomarkers in COVID-19 Disease	58
Rapid and Quantitative Protein Precipitation for Proteome Analysis by Mass Spectrometry	57
Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo	55
Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification	52
Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage	51
Plasma-Derived Extracellular Vesicle Phosphoproteomics through Chemical Affinity Purification	50
Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2	48
Considerations for MALDI-Based Quantitative Mass Spectrometry Imaging Studies	48
PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry	47
Improved Prediction Model of Protein Lysine Crotonylation Sites Using Bidirectional Recurrent Neural Networks	47
Accelerated Lysis and Proteolytic Digestion of Biopsy-Level Fresh-Frozen and FFPE Tissue Samples Using Pressure Cycling Technology	47
In Silico Drug Repurposing for SARS-CoV-2 Main Proteinase and Spike Proteins	47
Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard	45
Triple Negative Breast Cancer Detection Using LC–MS/MS Lipidomic Profiling	44
A Preprocessing Tool for Enhanced Ion Mobility–Mass Spectrometry-Based Omics Workflows	44
Protein–DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era	43
Quantitative Proteomics Reveals the Mechanism of Silver Nanoparticles against Multidrug-Resistant Pseudomonas aeruginosa Biofilms	42
Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics	42
What Are We Missing by Using Hydrophilic Enrichment? Improving Bacterial Glycoproteome Coverage Using Total Proteome and FAIMS Analyses	41
Proteomics in Non-model Organisms: A New Analytical Frontier	40
Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV-2 Protease	40
Driving Single Cell Proteomics Forward with Innovation	39
Cell Metabolomics Reveals Berberine-Inhibited Pancreatic Cancer Cell Viability and Metastasis by Regulating Citrate Metabolism	39
Early Breast Cancer Detection Using Untargeted and Targeted Metabolomics	39
Comparative Analysis of the Extracellular Matrix Proteome across the Myotendinous Junction	38
Data Dependent–Independent Acquisition (DDIA) Proteomics	37
Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers	37
Peptidomics: A Review of Clinical Applications and Methodologies	37
Single-Shot 10K Proteome Approach: Over 10,000 Protein Identifications by Data-Independent Acquisition-Based Single-Shot Proteomics with Ion Mobility Spectrometry	37
PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation	37
Ubiquitin-Modified Proteome of SARS-CoV-2-Infected Host Cells Reveals Insights into Virus–Host Interaction and Pathogenesis	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
Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines	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
Glycopeptide Biomarkers in Serum Haptoglobin for Hepatocellular Carcinoma Detection in Patients with Nonalcoholic Steatohepatitis	36
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses	35
A Two-Way Interaction between Methotrexate and the Gut Microbiota of Male Sprague–Dawley Rats	35
Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation	35
Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides	35
Comprehensive Examination of the Mouse Lung Metabolome Following Mycobacterium tuberculosis Infection Using a Multiplatform Mass Spectrometry Approach	35
Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques	34
Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer’s Disease	34
Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro	34
ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry	34
Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay	34

Enhancing Top-Down Proteomics of Brain Tissue with FAIMS	33
Effect of Very-Low-Calorie Ketogenic Diet on Psoriasis Patients: A Nuclear Magnetic Resonance-Based Metabolomic Study	33
Enrichment of Neurodegenerative Microglia Signature in Brain-Derived Extracellular Vesicles Isolated from Alzheimer’s Disease Mouse Models	33
ACE-2-Derived Biomimetic Peptides for the Inhibition of Spike Protein of SARS-CoV-2	33
Mass Spectrometric Analysis of Urine from COVID-19 Patients for Detection of SARS-CoV-2 Viral Antigen and to Study Host Response	33
Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?	32
New Enzymatic Approach to Distinguish Fucosylation Isomers of N-Linked Glycans in Tissues Using MALDI Imaging Mass Spectrometry	32
Importance of Block Randomization When Designing Proteomics Experiments	32
Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome	31
Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses	31
In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods	30
Venom Peptide Repertoire of the European Myrmicine Ant Manica rubida: Identification of Insecticidal Toxins	30
Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project	30
Quantitative Longitudinal Inventory of the N-Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes	30
Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment	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
Prediction of Neuropeptides from Sequence Information Using Ensemble Classifier and Hybrid Features	30
Fingerprinting Alzheimer’s Disease by ¹H Nuclear Magnetic Resonance Spectroscopy of Cerebrospinal Fluid	30
Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts	30
Metabolic Profiling of Neocortical Tissue Discriminates Alzheimer’s Disease from Mild Cognitive Impairment, High Pathology Controls, and Normal Controls	30
Metabolomics of Milk Reflects a Negative Energy Balance in Cows	29
Use of Lectin-based Affinity Techniques in Breast Cancer Glycoproteomics: A Review	29
Overview of Targets and Potential Drugs of SARS-CoV-2 According to the Viral Replication	29
Gut Microbiota-Derived Metabolite Signature in Suckling and Weaned Piglets	29
Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags	29
Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks	28
PD-L1 Glycosylation and Its Impact on Binding to Clinical Antibodies	28
Perspective on Proteomics for Virus Detection in Clinical Samples	28
HILIC–MRM–MS for Linkage-Specific Separation of Sialylated Glycopeptides to Quantify Prostate-Specific Antigen Proteoforms	27
Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2	27
Bile Acid Profiles Are Distinct among Patients with Different Etiologies of Chronic Liver Disease	27
Interaction of Drug Candidates with Various SARS-CoV-2 Receptors: An in Silico Study to Combat COVID-19	27
An Introduction to Mass Spectrometry-Based Proteomics	26
Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC–MS/MS	26
Revealing Dynamic Protein Acetylation across Subcellular Compartments	26
Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology	26
Longitudinal Plasma Proteomics Analysis Reveals Novel Candidate Biomarkers in Acute COVID-19	26
Impact of Increased FUT8 Expression on the Extracellular Vesicle Proteome in Prostate Cancer Cells	26
Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools	26
A Review of Imputation Strategies for Isobaric Labeling-Based Shotgun Proteomics	26
MS Annika: A New Cross-Linking Search Engine	26
mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection	26
Parallel Reaction Monitoring Mass Spectrometry Method for Detection of Both Casein and Whey Milk Allergens from a Baked Food Matrix	26
The 2022 Report on the Human Proteome from the HUPO Human Proteome Project	25
Temporal Proteomic Profiling of SH-SY5Y Differentiation with Retinoic Acid Using FAIMS and Real-Time Searching	24
Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme	24
DeepPSP: A Global–Local Information-Based Deep Neural Network for the Prediction of Protein Phosphorylation Sites	24
Serum or Plasma (and Which Plasma), That Is the Question	24
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	24
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	24
Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data	24
Identification and Quantitation of Amylase Trypsin Inhibitors Across Cultivars Representing the Diversity of Bread Wheat	24
Optimized Proteomics Workflow for the Detection of Small Proteins	24
Genomics- and Peptidomics-Based Discovery of Conserved and Novel Neuropeptides in the American Cockroach	24
Metabolomic Profiling of the Aqueous Humor in Patients with Wet Age-Related Macular Degeneration Using UHPLC–MS/MS	24
Longitudinal Transcriptomic, Proteomic, and Metabolomic Analysis of Citrus limon Response to Graft Inoculation by Candidatus Liberibacter asiaticus	23
Low Volume in Vitro Diagnostic Proton NMR Spectroscopy of Human Blood Plasma for Lipoprotein and Metabolite Analysis: Application to SARS-CoV-2 Biomarkers	23
PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity	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
Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice	23
A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients	23
QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories	23
Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination	23
Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma	23
Features of Peptide Fragmentation Spectra in Single-Cell Proteomics	23
A Panel of Glycopeptides as Candidate Biomarkers for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation	23
Fast and Highly Efficient Affinity Enrichment of Azide-A-DSBSO Cross-Linked Peptides	23
Machine Learning-Enabled Renal Cell Carcinoma Status Prediction Using Multiplatform Urine-Based Metabolomics	22
Role of Multiomics Data to Understand Host–Pathogen Interactions in COVID-19 Pathogenesis	22
iGlu_AdaBoost: Identification of Lysine Glutarylation Using the AdaBoost Classifier	22
Generation of an Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability	22
Biological Functions and Large-Scale Profiling of Protein Glycosylation in Human Semen	22
Genetic Variability of the SARS-CoV-2 Pocketome	22
Physiological Tau Interactome in Brain and Its Link to Tauopathies	22
TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level	22
Urine Proteomics: Evaluation of Different Sample Preparation Workflows for Quantitative, Reproducible, and Improved Depth of Analysis	22
Rapid Prostate Cancer Noninvasive Biomarker Screening Using Segmented Flow Mass Spectrometry-Based Untargeted Metabolomics	22
Urinary Volatilomics Unveils a Candidate Biomarker Panel for Noninvasive Detection of Clear Cell Renal Cell Carcinoma	21
Site-Specific N-Linked Glycosylation Analysis of Human Carcinoembryonic Antigen by Sheathless Capillary Electrophoresis–Tandem Mass Spectrometry	21
Deep Profiling of Microgram-Scale Proteome by Tandem Mass Tag Mass Spectrometry	21

Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison	21
Simplified and Unified Access to Cancer Proteogenomic Data	21
A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases	21
Global Inventory of ClpP- and ClpX-Regulated Proteins in Staphylococcus aureus	21
Peptide Correlation Analysis (PeCorA) Reveals Differential Proteoform Regulation	21
Proteomic Analysis Identifies Prolonged Disturbances in Pathways Related to Cholesterol Metabolism and Myocardium Function in the COVID-19 Recovery Stage	21
Rapid Response to Pandemic Threats: Immunogenic Epitope Detection of Pandemic Pathogens for Diagnostics and Vaccine Development Using Peptide Microarrays	21
DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients	21
Defining the Caprin-1 Interactome in Unstressed and Stressed Conditions	20
Identification of Novel Adipokines through Proteomic Profiling of Small Extracellular Vesicles Derived from Adipose Tissue	20
Discovery Proteomics for COVID-19: Where We Are Now	20
Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area	20
Proteomic Investigation of the Antibacterial Mechanism of trans-Cinnamaldehyde against Escherichia coli	20
Toward a Sample Metadata Standard in Public Proteomics Repositories	20
Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes	20
Proteomic Workflows for High-Quality Quantitative Proteome and Post-Translational Modification Analysis of Clinically Relevant Samples from Formalin-Fixed Paraffin-Embedded Archives	19
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	19
Potential Use of Serum Proteomics for Monitoring COVID-19 Progression to Complement RT-PCR Detection	19
Spritz: A Proteogenomic Database Engine	19
Quantitative Top-Down Proteomics by Isobaric Labeling with Thiol-Directed Tandem Mass Tags	19
Comparative Glycomic Analysis of Exosome Subpopulations Derived from Pancreatic Cancer Cell Lines	19
Computational Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage and Applications to 15 Tumors	19
Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors	19
¹H NMR-Based Urine Metabolomics Reveals Signs of Enhanced Carbon and Nitrogen Recycling in Prostate Cancer	19
Tailor: A Nonparametric and Rapid Score Calibration Method for Database Search-Based Peptide Identification in Shotgun Proteomics	19
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite	19
Characterization of Monophasic Solvent-Based Tissue Extractions for the Detection of Polar Metabolites and Lipids Applying Ultrahigh-Performance Liquid Chromatography–Mass Spectrometry Clinical Metabo	19
Uncovering the Metabolic Mechanism of Salidroside Alleviating Microglial Hypoxia Inflammation Based on Microfluidic Chip-Mass Spectrometry	19
Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context	19
Shell Disorder Analysis Suggests That Pangolins Offered a Window for a Silent Spread of an Attenuated SARS-CoV-2 Precursor among Humans	19
Toward a Universal Sample Preparation Method for Denaturing Top-Down Proteomics of Complex Proteomes	19
Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine-N-oxide	19
¹H qNMR-Based Metabolomics Discrimination of Covid-19 Severity	18
Complement and Coagulation Cascades are Potentially Involved in Dopaminergic Neurodegeneration in α-Synuclein-Based Mouse Models of Parkinson’s Disease	18
Assessment of Streptavidin Bead Binding Capacity to Improve Quality of Streptavidin-based Enrichment Studies	18
Aquatic Decomposition of Mammalian Corpses: A Forensic Proteomic Approach	18
Structure-Based Screening to Discover New Inhibitors for Papain-like Proteinase of SARS-CoV-2: An In Silico Study	18
Oxidative Damage to the TCA Cycle Enzyme MDH1 Dysregulates Bioenergetic Enzymatic Activity in the Aged Murine Brain	18
Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins	18
Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient	18
Potential Regulatory Role of Human-Carboxylesterase-1 Glycosylation in Liver Cancer Cell Growth	18
Biochemical Tools for Tracking Proteolysis	18
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	18
Proteomic Analysis of Sri Lanka Echis carinatus Venom: Immunological Cross-Reactivity and Enzyme Neutralization Potency of Indian Polyantivenom	18
Discovery of Novel Protein Biomarkers in Urine for Diagnosis of Urothelial Cancer Using iTRAQ Proteomics	18
Column-based Technology for CD9-HPLC Immunoaffinity Isolation of Serum Extracellular Vesicles	18
Crystal-C: A Computational Tool for Refinement of Open Search Results	18
Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease	18
The O-Glycome of Human Nigrostriatal Tissue and Its Alteration in Parkinson’s Disease	18
CIMAGE2.0: An Expanded Tool for Quantitative Analysis of Activity-Based Protein Profiling (ABPP) Data	18
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers	17
Public LC-Orbitrap Tandem Mass Spectral Library for Metabolite Identification	17
Dried Blood Spot-Based Metabolomic Profiling in Adults with Cystic Fibrosis	17
Optimization of Ultrafast Proteomics Using an LC-Quadrupole-Orbitrap Mass Spectrometer with Data-Independent Acquisition	17
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	17
Reduced Nicotinamide Mononucleotide (NMNH) Potently Enhances NAD⁺ and Suppresses Glycolysis, the TCA Cycle, and Cell Growth	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
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
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
Ex Vivo Equine Cartilage Explant Osteoarthritis Model: A Metabolomics and Proteomics Study	17
Proteome-Scale Analysis of Protein S-Acylation Comes of Age	17
Comparison of Unit Resolution Versus High-Resolution Accurate Mass for Parallel Reaction Monitoring	17
Liquid Chromatography–Mass Spectrometry-Based Tissue Metabolic Profiling Reveals Major Metabolic Pathway Alterations and Potential Biomarkers of Lung Cancer	17
Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity	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
Metabolic Variations between Low-Grade and High-Grade Gliomas—Profiling by ¹H NMR Spectroscopy	17
Multiomics Integrative Analysis for Discovering the Potential Mechanism of Dioscin against Hyperuricemia Mice	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
Mapping the Proteoform Landscape of Five Human Tissues	17
InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information	17
Proteomic Profiling of Stem Cell Tissues during Regeneration of Deer Antler: A Model of Mammalian Organ Regeneration	17
Mass Spectrometry-Based Structural Analysis of Cysteine-Rich Metal-Binding Sites in Proteins with MetaOdysseus R Software	16
Proteomic Analysis Reveals Proteins and Pathways Associated with Lactation in Bovine Mammary Epithelial Cell-Derived Exosomes	16
Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial	16
Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire	16
Accurate Identification of Deamidation and Citrullination from Global Shotgun Proteomics Data Using a Dual-Search Delta Score Strategy	16
Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9	16
Influence of Age, Sex, and Diet on the Human Fecal Metabolome Investigated by ¹H NMR Spectroscopy	16
FAIMS Enhances the Detection of PTM Crosstalk Sites	16
Automated Ligand Purification Platform Accelerates Immunopeptidome Analysis by Mass Spectrometry	16
Integrated Multi-Omics Analysis of Mechanisms Underlying Yeast Ethanol Tolerance	16
COSS: A Fast and User-Friendly Tool for Spectral Library Searching	16
Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection	16
Stable Isotope-Resolved Metabolomics Reveals the Abnormal Brain Glucose Catabolism in Depression Based on Chronic Unpredictable Mild Stress Rats	16
How (Not) to Generate a Highly Predictive Biomarker Panel Using Machine Learning	16
Sequential Precipitation and Delipidation Enables Efficient Enrichment of Low-Molecular Weight Proteins and Peptides from Human Plasma	16
Molecular Profiling Associated with Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2)-Mediated Carcinogenesis in Gastric Cancer	16
In Vitro Characterization and Metabolomic Analysis of Cold-Stored Platelets	16
Comprehensive Intrinsic Disorder Analysis of 6108 Viral Proteomes: From the Extent of Intrinsic Disorder Penetrance to Functional Annotation of Disordered Viral Proteins	16
DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics	15
Comparative Blood and Urine Metabolomics Analysis of Healthy Elderly and Young Male Singaporeans	15
Detection of Tear Components Using Matrix-Assisted Laser Desorption Ionization/Time-of-Flight Mass Spectrometry for Rapid Dry Eye Diagnosis	15
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	15