OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Proteome Research is 8. 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 2020-11-01 to 2024-11-01.)

Article	Citations
TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing	193
Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling	123
Advances and Utility of the Human Plasma Proteome	116
Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine	108
Incomplete Systemic Recovery and Metabolic Phenoreversion in Post-Acute-Phase Nonhospitalized COVID-19 Patients: Implications for Assessment of Post-Acute COVID-19 Syndrome	90
Systemic Perturbations in Amine and Kynurenine Metabolism Associated with Acute SARS-CoV-2 Infection and Inflammatory Cytokine Responses	80
Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics	78
An Introduction to Mass Spectrometry-Based Proteomics	76
Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage	66
Single-Shot 10K Proteome Approach: Over 10,000 Protein Identifications by Data-Independent Acquisition-Based Single-Shot Proteomics with Ion Mobility Spectrometry	63
NMR Spectroscopic Windows on the Systemic Effects of SARS-CoV-2 Infection on Plasma Lipoproteins and Metabolites in Relation to Circulating Cytokines	63
Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo	63
A Preprocessing Tool for Enhanced Ion Mobility–Mass Spectrometry-Based Omics Workflows	60
Early Breast Cancer Detection Using Untargeted and Targeted Metabolomics	57
Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data-Independent Acquisition	55
Protein–DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era	55
Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard	54
Peptidomics: A Review of Clinical Applications and Methodologies	51
Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers	50
Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks	49
Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?	49
Improved Prediction Model of Protein Lysine Crotonylation Sites Using Bidirectional Recurrent Neural Networks	48
In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods	46
Ubiquitin-Modified Proteome of SARS-CoV-2-Infected Host Cells Reveals Insights into Virus–Host Interaction and Pathogenesis	46
Driving Single Cell Proteomics Forward with Innovation	44

Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation	43
ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry	43
Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro	42
Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer’s Disease	41
Enrichment of Neurodegenerative Microglia Signature in Brain-Derived Extracellular Vesicles Isolated from Alzheimer’s Disease Mouse Models	41
Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment	40
Effect of Very-Low-Calorie Ketogenic Diet on Psoriasis Patients: A Nuclear Magnetic Resonance-Based Metabolomic Study	40
Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques	40
mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection	39
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite	39
PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity	39
Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides	38
Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme	38
Enhancing Top-Down Proteomics of Brain Tissue with FAIMS	38
Mass Spectrometric Analysis of Urine from COVID-19 Patients for Detection of SARS-CoV-2 Viral Antigen and to Study Host Response	37
Serum or Plasma (and Which Plasma), That Is the Question	37
ACE-2-Derived Biomimetic Peptides for the Inhibition of Spike Protein of SARS-CoV-2	36
Gut Microbiota-Derived Metabolite Signature in Suckling and Weaned Piglets	36
Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts	36
Metabolic Profiling of Neocortical Tissue Discriminates Alzheimer’s Disease from Mild Cognitive Impairment, High Pathology Controls, and Normal Controls	35
Mild Acid Elution and MHC Immunoaffinity Chromatography Reveal Similar Albeit Not Identical Profiles of the HLA Class I Immunopeptidome	35
Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags	34
The 2022 Report on the Human Proteome from the HUPO Human Proteome Project	34
Comparative Evaluation of MaxQuant and Proteome Discoverer MS1-Based Protein Quantification Tools	33
Overview of Targets and Potential Drugs of SARS-CoV-2 According to the Viral Replication	33
Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology	33
Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project	33
Bile Acid Profiles Are Distinct among Patients with Different Etiologies of Chronic Liver Disease	32
QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories	32
TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level	31
Longitudinal Plasma Proteomics Analysis Reveals Novel Candidate Biomarkers in Acute COVID-19	30
MS Annika: A New Cross-Linking Search Engine	30
Site-Specific N-Linked Glycosylation Analysis of Human Carcinoembryonic Antigen by Sheathless Capillary Electrophoresis–Tandem Mass Spectrometry	30
Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial	30
Column-based Technology for CD9-HPLC Immunoaffinity Isolation of Serum Extracellular Vesicles	30
DeepPSP: A Global–Local Information-Based Deep Neural Network for the Prediction of Protein Phosphorylation Sites	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	29
MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale	29
Features of Peptide Fragmentation Spectra in Single-Cell Proteomics	29
Proteomic Investigation of the Antibacterial Mechanism of trans-Cinnamaldehyde against Escherichia coli	29
Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice	28
Mapping the Proteoform Landscape of Five Human Tissues	28
Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison	28
Evaluation of Spin Columns for Human Plasma Depletion to Facilitate MS-Based Proteomics Analysis of Plasma	28
Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient	28
Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine-N-oxide	28
A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients	28
Machine Learning-Enabled Renal Cell Carcinoma Status Prediction Using Multiplatform Urine-Based Metabolomics	27
Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2	27
Complement and Coagulation Cascades are Potentially Involved in Dopaminergic Neurodegeneration in α-Synuclein-Based Mouse Models of Parkinson’s Disease	27

A Panel of Glycopeptides as Candidate Biomarkers for Early Diagnosis of NASH Hepatocellular Carcinoma Using a Stepped HCD Method and PRM Evaluation	26
Defining the Caprin-1 Interactome in Unstressed and Stressed Conditions	26
Toward an Integrated Machine Learning Model of a Proteomics Experiment	26
How (Not) to Generate a Highly Predictive Biomarker Panel Using Machine Learning	26
Urinary Volatilomics Unveils a Candidate Biomarker Panel for Noninvasive Detection of Clear Cell Renal Cell Carcinoma	26
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
Generation of an Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability	25
Role of Multiomics Data to Understand Host–Pathogen Interactions in COVID-19 Pathogenesis	25
Simplified and Unified Access to Cancer Proteogenomic Data	25
Proteome-Scale Analysis of Protein S-Acylation Comes of Age	25
Peptide Correlation Analysis (PeCorA) Reveals Differential Proteoform Regulation	25
Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area	25
Genomics- and Peptidomics-Based Discovery of Conserved and Novel Neuropeptides in the American Cockroach	25
Optimization of Ultrafast Proteomics Using an LC-Quadrupole-Orbitrap Mass Spectrometer with Data-Independent Acquisition	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
Genetic Variability of the SARS-CoV-2 Pocketome	24
Characterization of Monophasic Solvent-Based Tissue Extractions for the Detection of Polar Metabolites and Lipids Applying Ultrahigh-Performance Liquid Chromatography–Mass Spectrometry Clinical Metabo	24
Comparison of Unit Resolution Versus High-Resolution Accurate Mass for Parallel Reaction Monitoring	23
Deep Profiling of Microgram-Scale Proteome by Tandem Mass Tag Mass Spectrometry	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
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	23
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	23
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work	23
Discovery Proteomics for COVID-19: Where We Are Now	23
Proteomic Workflows for High-Quality Quantitative Proteome and Post-Translational Modification Analysis of Clinically Relevant Samples from Formalin-Fixed Paraffin-Embedded Archives	23
DIA-Based Proteome Profiling of Nasopharyngeal Swabs from COVID-19 Patients	23
Biochemical Tools for Tracking Proteolysis	23
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	22
Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms	22
DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics	22
¹H qNMR-Based Metabolomics Discrimination of Covid-19 Severity	22
Potential Use of Serum Proteomics for Monitoring COVID-19 Progression to Complement RT-PCR Detection	22
Proteomic Analysis Identifies Prolonged Disturbances in Pathways Related to Cholesterol Metabolism and Myocardium Function in the COVID-19 Recovery Stage	22
In Vitro Characterization and Metabolomic Analysis of Cold-Stored Platelets	22
Potential Regulatory Role of Human-Carboxylesterase-1 Glycosylation in Liver Cancer Cell Growth	21
Sage: An Open-Source Tool for Fast Proteomics Searching and Quantification at Scale	21
Global Inventory of ClpP- and ClpX-Regulated Proteins in Staphylococcus aureus	21
Quantitative Top-Down Proteomics by Isobaric Labeling with Thiol-Directed Tandem Mass Tags	21
The rawrr R Package: Direct Access to Orbitrap Data and Beyond	21
Simple and Efficient Microsolid-Phase Extraction Tip-Based Sample Preparation Workflow to Enable Sensitive Proteomic Profiling of Limited Samples (200 to 10,000 Cells)	21
Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity	21
Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection	21
The O-Glycome of Human Nigrostriatal Tissue and Its Alteration in Parkinson’s Disease	21
Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets	21
Uncovering the Metabolic Mechanism of Salidroside Alleviating Microglial Hypoxia Inflammation Based on Microfluidic Chip-Mass Spectrometry	21
In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50–200 μm	21
Public LC-Orbitrap Tandem Mass Spectral Library for Metabolite Identification	21
CIMAGE2.0: An Expanded Tool for Quantitative Analysis of Activity-Based Protein Profiling (ABPP) Data	21
Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins	20
Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire	20
Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation	20
Discovery of Novel Protein Biomarkers in Urine for Diagnosis of Urothelial Cancer Using iTRAQ Proteomics	20
Reduced Nicotinamide Mononucleotide (NMNH) Potently Enhances NAD⁺ and Suppresses Glycolysis, the TCA Cycle, and Cell Growth	20
Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer’s Disease	20
Assessment of Streptavidin Bead Binding Capacity to Improve Quality of Streptavidin-based Enrichment Studies	20
OpenTIMS, TimsPy, and TimsR: Open and Easy Access to timsTOF Raw Data	20
Computational Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage and Applications to 15 Tumors	20
Serum Glycoprotein Markers in Nonalcoholic Steatohepatitis and Hepatocellular Carcinoma	20
Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool	20
Protein Adsorption Loss─The Bottleneck of Single-Cell Proteomics	19
Early Detection of Pancreatic Cancer in Type 2 Diabetes Mellitus Patients Based on ¹H NMR Metabolomics	19
Comprehensive Intrinsic Disorder Analysis of 6108 Viral Proteomes: From the Extent of Intrinsic Disorder Penetrance to Functional Annotation of Disordered Viral Proteins	19
Integrating Top-Down and Bottom-Up Mass Spectrometric Strategies for Proteomic Profiling of Iranian Saw-Scaled Viper, Echis carinatus sochureki, Venom	19
Untargeted Stable Isotope Probing of the Gut Microbiota Metabolome Using ¹³C-Labeled Dietary Fibers	19
Systematic Identification of Protein Phosphorylation-Mediated Interactions	19
Quantitative Interactomics of Lck-TurboID in Living Human T Cells Unveils T Cell Receptor Stimulation-Induced Proximal Lck Interactors	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
Is Current Practice Adhering to Guidelines Proposed for Metabolite Identification in LC-MS Untargeted Metabolomics? A Meta-Analysis of the Literature	19
Direct Comparison of N-Glycans and Their Isomers Derived from Spike Glycoprotein 1 of MERS-CoV, SARS-CoV-1, and SARS-CoV-2	19
Spatially Resolved Metabolomics Based on Air-Flow-Assisted Desorption Electrospray Ionization–Mass Spectrometry Imaging Reveals Region-Specific Metabolic Alterations in Diabetic Encephalopathy	19
A Simple Optimization Workflow to Enable Precise and Accurate Imputation of Missing Values in Proteomic Data Sets	19
High-Throughput Venomics	18
Molecular Profiling Associated with Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2)-Mediated Carcinogenesis in Gastric Cancer	18
Structure-Based Screening to Discover New Inhibitors for Papain-like Proteinase of SARS-CoV-2: An In Silico Study	18
FAIMS Enhances the Detection of PTM Crosstalk Sites	18
Metabolic Snapshot of Plasma Samples Reveals New Pathways Implicated in SARS-CoV-2 Pathogenesis	18
BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers	18
Improving Peptide-Level Mass Spectrometry Analysis via Double Competition	18
Benchmarking Cleavable Biotin Tags for Peptide-Centric Chemoproteomics	18
Integrated Multi-Omics Analysis of Mechanisms Underlying Yeast Ethanol Tolerance	18

Metabolic Profiling of Urinary Chiral Amino-Containing Biomarkers for Gastric Cancer Using a Sensitive Chiral Chlorine-Labeled Probe by HPLC-MS/MS	18
Untargeted Gut Metabolomics to Delve the Interplay between Selenium Supplementation and Gut Microbiota	18
Stable Isotope-Resolved Metabolomics Reveals the Abnormal Brain Glucose Catabolism in Depression Based on Chronic Unpredictable Mild Stress Rats	17
Mass Spectrometry Imaging of N-Linked Glycans in a Formalin-Fixed Paraffin-Embedded Human Prostate by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization	17
An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community	17
Insights into the Differential Preservation of Bone Proteomes in Inhumed and Entombed Cadavers from Italian Forensic Caseworks	17
Evaluation of Disposable Trap Column nanoLC–FAIMS–MS/MS for the Proteomic Analysis of FFPE Tissue	17
Enhancement of Proteome Coverage by Ion Mobility Fractionation Coupled to PASEF on a TIMS–QTOF Instrument	17
Comprehensive Serum Lipidomics for Detecting Incipient Dementia in Parkinson’s Disease	17
Influence of Age, Sex, and Diet on the Human Fecal Metabolome Investigated by ¹H NMR Spectroscopy	17
Proximity Labeling, Quantitative Proteomics, and Biochemical Studies Revealed the Molecular Mechanism for the Inhibitory Effect of Indisulam on the Proliferation of Gastric Cancer Cells	17
Comparison of Quantitative Mass Spectrometric Methods for Drug Target Identification by Thermal Proteome Profiling	17
Serum Bile Acid Profiles Improve Clinical Prediction of Nonalcoholic Fatty Liver in T2DM patients	17
Coupling High-Field Asymmetric Ion Mobility Spectrometry with Capillary Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry Improves Protein Identifications in Bottom-Up Proteomic Analysi	17
Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis	17
Myocardial Infarction Induces Cardiac Fibroblast Transformation within Injured and Noninjured Regions of the Mouse Heart	17
InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information	17
Multiomics Profiling of Alzheimer’s Disease Serum for the Identification of Autoantibody Biomarkers	17
Salivary Metabolomics Reveals that Metabolic Alterations Precede the Onset of Schizophrenia	17
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	17
Proteomic Analysis of Whole Blood Using Volumetric Absorptive Microsampling for Precision Medicine Biomarker Studies	17
Prevaccination Glycan Markers of Response to an Influenza Vaccine Implicate the Complement Pathway	16
Acetic Acid Ion Pairing Additive for Reversed-Phase HPLC Improves Detection Sensitivity in Bottom-up Proteomics Compared to Formic Acid	16
Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics	16
Straightforward N-Acyl Homoserine Lactone Discovery and Annotation by LC–MS/MS-based Molecular Networking	16
Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma	16
PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data	16
Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities	16
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	16
Proteomics of Human Milk: Definition of a Discovery Workflow for Clinical Research Studies	16
Mapping Angiotensin II Type 1 Receptor-Biased Signaling Using Proximity Labeling and Proteomics Identifies Diverse Actions of Biased Agonists	16
Proteomic Profiling of Mitochondrial-Derived Vesicles in Brain Reveals Enrichment of Respiratory Complex Sub-assemblies and Small TIM Chaperones	16
Mass Spectrometry-Based Atlas of Extracellular Matrix Proteins across 25 Mouse Organs	16
Automated Ligand Purification Platform Accelerates Immunopeptidome Analysis by Mass Spectrometry	16
Transparent Exploration of Machine Learning for Biomarker Discovery from Proteomics and Omics Data	16
Protein Expression Profile of ACE2 in the Normal and COVID-19-Affected Human Brain	16
Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA	16
Comparable Plasma Lipid Changes in Patients with High-Grade Cervical Intraepithelial Neoplasia and Patients with Cervical Cancer	16
Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50–1000 Mammalian Cells	16
Evolution of Mass Spectrometry Instruments and Techniques for Blood Proteomics	16
Development and Provisional Validation of a Multiplex LC-MRM-MS Test for Timely Kidney Injury Detection in Urine	16
A Lipidome Map of the Silkworm Bombyx mori: Influences of Viral Infection	16
Use of Hybrid Data-Dependent and -Independent Acquisition Spectral Libraries Empowers Dual-Proteome Profiling	16
Digital Microfluidics Supported Microproteomics for Quantitative Proteome Analysis of Single Caenorhabditis elegans Nematodes	16
Resveratrol Enhances Wound Healing in Type 1 Diabetes Mellitus by Promoting the Expression of Extracellular Vesicle-Carried MicroRNA-129 Derived from Mesenchymal Stem Cells	15
prolfqua: A Comprehensive R-Package for Proteomics Differential Expression Analysis	15
Multiomics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem-Cell-Derived Cardiomyocytes	15
Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms	15
Method for Independent Estimation of the False Localization Rate for Phosphoproteomics	15
Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection	15
Extracellular Matrix Proteome Remodeling in Human Glioblastoma and Medulloblastoma	15
COVID-19: The Effect of Host Genetic Variations on Host–Virus Interactions	15
Surveying the Vampire Bat (Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens	15
Comprehensive Metabolomics and Lipidomics Profiling of Prostate Cancer Tissue Reveals Metabolic Dysregulations Associated with Disease Development	15
Reproducible Determination of High-Density Lipoprotein Proteotypes	15
Adhesion Characteristics and Dual Transcriptomic and Proteomic Analysis of Lactobacillus reuteri SH23 upon Gastrointestinal Fluid Stress	15
Increasing Proteome Depth While Maintaining Quantitative Precision in Short-Gradient Data-Independent Acquisition Proteomics	15
BAC-DROP: Rapid Digestion of Proteome Fractionated via Dissolvable Polyacrylamide Gel Electrophoresis and Its Application to Bottom-Up Proteomics Workflow	15
Human Multisubunit E3 Ubiquitin Ligase Required for Heterotrimeric G-Protein β-Subunit Ubiquitination and Downstream Signaling	15
MicroPOTS Analysis of Barrett’s Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress	15
ProteaseGuru: A Tool for Protease Selection in Bottom-Up Proteomics	15
Detectability of Biotin Tags by LC–MS/MS	15
Inflect: Optimizing Computational Workflows for Thermal Proteome Profiling Data Analysis	15
Omics Untargeted Key Script: R-Based Software Toolbox for Untargeted Metabolomics with Bladder Cancer Biomarkers Discovery Case Study	15
Integration of Metabolomics and Transcriptomics Reveals Ketone Body and Lipid Metabolism Disturbance Related to ER Stress in the Liver	15
Metabolites in the TCA Cycle Promote Resistance to Chloramphenicol of Edwardsiella tarda	15
DIMA: Data-Driven Selection of an Imputation Algorithm	14
Cross-Species Proteomic Comparison of Outer Membrane Vesicles and Membranes of Francisella tularensis subsp. tularensis versus subsp. holarctica	14
Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance	14
High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins	14
LFQ-Based Peptide and Protein Intensity Differential Expression Analysis	14
Fecal Metabolomics and Network Pharmacology Reveal the Correlations between Constipation and Depression	14
Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics	14
Proteomic Analysis of the Promastigote Secretome of Seven Leishmania Species	14
Development of Parallel Reaction Monitoring Assays for the Detection of Aggressive Prostate Cancer Using Urinary Glycoproteins	14
Improving Phosphoproteomics Profiling Using Data-Independent Mass Spectrometry	14
Defining the Sarcomeric Proteoform Landscape in Ischemic Cardiomyopathy by Top-Down Proteomics	14
Distinct Histone Post-translational Modifications during Plasmodium falciparum Gametocyte Development	14
Deciphering the Interregional and Interhemisphere Proteome of the Human Brain in the Context of the Human Proteome Project	14
Bridging the Polar and Hydrophobic Metabolome in Single-Run Untargeted Liquid Chromatography-Mass Spectrometry Dried Blood Spot Metabolomics for Clinical Purposes	14
Hybrid QconCAT-Based Targeted Absolute and Data-Independent Acquisition-Based Label-Free Quantification Enables In-Depth Proteomic Characterization of Wheat Amylase/Trypsin Inhibitor Extracts	14
Functionally Integrated Top-Down Proteomics for Standardized Assessment of Human Induced Pluripotent Stem Cell-Derived Engineered Cardiac Tissues	14
Toward Zero Variance in Proteomics Sample Preparation: Positive-Pressure FASP in 96-Well Format (PF96) Enables Highly Reproducible, Time- and Cost-Efficient Analysis of Sample Cohorts	14
High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps	14
Mass-Spectrometry-Based Near-Complete Draft of theSaccharomyces cerevisiaeProteome	14
Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion	14
Targeted Metabolomic Approach to Assess the Reproducibility of Plasma Metabolites over a Four Month Period in a Free-Living Population	13
Confident Identification of Citrullination and Carbamylation Assisted by Peptide Retention Time Prediction	13
Comprehensive Lipidomic Workflow for Multicohort Population Phenotyping Using Stable Isotope Dilution Targeted Liquid Chromatography-Mass Spectrometry	13
Deep Time Paleoproteomics: Looking Forward	13
IreK-Mediated, Cell Wall-Protective Phosphorylation in Enterococcus faecalis	13
Top-Down Proteomics and the Challenges of True Proteoform Characterization	13
Proteome Coverage after Simultaneous Proteo-Metabolome Liquid–Liquid Extraction	13
MaxQuant.Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin	13
Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss	13