OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Proteome Research is 44. 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
Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients	151
Optimal Dissociation Methods Differ for N- and O-Glycopeptides	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
lipidr: A Software Tool for Data Mining and Analysis of Lipidomics Datasets	66
Targeting Proteases for Treating COVID-19	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
Considerations for MALDI-Based Quantitative Mass Spectrometry Imaging Studies	48
Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2	48
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
PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry	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