Proteomics

Article	Citations
Editorial Board: Proteomics 10'22	110
Front Cover	97
Contents: Proteomics 9'22	88
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	66
SIMPLEX Enriches Hydrophobic and Lipidated Proteins in Membrane Proteomics Experiments	61
Eye proteome of Drosophila melanogaster	60
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RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	49
Standard abbreviations	49
Front Cover	45
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	40
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LC‐MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain‐Tetanus Toxoid Conjugate Vaccine Against SARS‐CoV‐2	38
Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	37
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	36
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	36
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Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	34
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	33
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	33
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	33
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	32
Comparing and integrating TMT‐SPS‐MS3 and label‐free quantitative approaches for proteomics scrutiny in recalcitrant Mango (Mangifera indica L.) peel tissue during postharvest period	32

Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	32
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	29
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	29
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs	28
Omics insights into the responses to dietary selenium	27
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Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles	26
Urinary Peptidomic Profiling In Post‐Acute Sequelae of SARS‐CoV‐2 Infection: A Case‐Control Study	26
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	25
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	25
Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	25
Editorial Board: Proteomics 8'22	25
Standard abbreviations	24
Front Cover	24
Contents: Proteomics 19–20'22	24
Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	24
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	24
Contents: Proteomics 5'24	23
Analyzing domain features of small proteins using a machine‐learning method	21
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	21
Front Cover	21
Editorial Board: Proteomics 21–22'23	21
Review of predicting protein stability changes upon variations	20
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus	20
Editorial Board: Proteomics 11–12'22	20
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	19
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	18
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	18
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	18
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	18
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	17
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Standard abbreviations	17
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	17
Front Cover	17
Standard abbreviations	16
Front Cover	16
Proteomic changes associated with the development of açaí ( Euterpe oleracea Mart.) seeds	16
Front Cover	16
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Editorial Board: Proteomics 5'24	16
Standard abbreviations	15
Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry	15
An antibody‐free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis	15
Standard abbreviations	15
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	15
Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	15
Standard abbreviations	15
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	15
Contents: Proteomics 13–14'23	14

Standard abbreviations	14
Issue Information: Proteomics 23'25	14
Contents: Proteomics 7'25	14
Global profiling of protein lactylation in Caenorhabditis elegans	14
Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development	14
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	14
Contents: Proteomics 9'23	14
In‐silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases	14
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	13
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	13
Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	13
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	13
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Front Cover	13
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VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	13
Front Cover	13
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	13
Standard abbreviations	13
Contents: Proteomics 11–12'22	12
Metaproteomic Analysis to Assess the Impact of Storage Media on Human Gut Microbiome in Fecal Samples	12
Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	12
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	12
Proteomics Advances in Immunology and Infection Research	12
Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma	12
The utility of proteases in proteomics, from sequence profiling to structure and function analysis	12
Immune capture and protein profiling of small extracellular vesicles from human plasma	12
The cuticle proteome of a planktonic crustacean	12
SLB‐msSIM: A Spectral Library‐Based Multiplex Segmented SIM Platform for Single‐Cell Proteomic Analysis	12
Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	12
Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput	12
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	12
Issue Information: Proteomics 14'25	11
Editorial Board: Proteomics 19–20'22	11
Contents: Proteomics 8'24	11
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	11
Contents: Proteomics 17'24	11
Targeted Quantitation of Phosphotyrosine‐Containing Proteins in T‐Cell Receptor Signaling Using a SureQuant‐Based Mass Spectrometry Approach	11
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Front Cover	11
Standard abbreviations	11
Data‐Driven Proteomics for Post‐Translational Modification Discovery	11
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	11
Standard abbreviations	11
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	11
Contents: Proteomics 15–16'22	11
A dataset resource for clinically associated phosphosites in hepatocellular carcinoma	11
Front Cover	11
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	10
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	10
Immunoproteome profiling of Listeria monocytogenes under mild acid and salt stress conditions	10
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	10
Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	10
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	10
Data Processing and Analysis in Positional Proteomics	10
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	10
Assessing Discrepancies in miRNA Profiles of Mouse Blood‐Derived Extracellular Vesicles: A Systematic Review of Sequencing Data	10
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	10
Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients	10
A Survey of Annotated smORF‐Encoded Polypeptides in Bacteria Interacting With Eukaryotic Hosts	10
Progress of Deep Learning Prediction of CD8+ T‐Cell Epitopes	10
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics	10
Towards deciphering glioblastoma intra‐tumoral heterogeneity: The importance of integrating multidimensional models	9
Back Cover: Protein‐enabled detection of ibuprofen and sulfamethoxazole using solid‐state nanopores	9
Standard abbreviations	9
Improving SWATH‐MS analysis by deep‐learning	9
Front Cover	9
Contents: Proteomics 8'25	9
Front Cover	9
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Understanding bacterial pathogen diversity: A proteogenomic analysis and use of an array of genome assemblies to identify novel virulence factors of the honey bee bacterial pathogen Paenibacillus l	9
Editorial Board: Proteomics 9'22	9
Standard abbreviations	9
Computational tools for inferring transcription factor activity	9
Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	9
Standard abbreviations	9
Proteome Analysis of Corynebacterium diphtheriae–Macrophage Interaction	9
Potential of deep representative learning features to interpret the sequence information in proteomics	9
Front Cover	9
Molecular methods to study protein trafficking between organs	8

Computational systems approach towards phosphoproteomics and their downstream regulation	8
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	8
Editorial Board: Proteomics 5–6'22	8
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	8
Transforming peptide hormone prediction: The role of AI in modern proteomics	8
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	8
A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	8
Comparative Analysis of Proteoform Clean‐Up Methods for In‐Depth Top‐Down Proteomics	8
QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry‐Based Proteomics Datasets	8
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	8
Contents: Proteomics 19'24	8
Issue Information: Proteomics 19'25	8
Editorial Board: Proteomics 8'24	8
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	8
Microproteins—Discovery, structure, and function	8
Standard abbreviations	8
Editorial Board: Proteomics 7'24	8
DREAMweb: An online tool for graph‐based modeling of NMR protein structure	8
Front Cover	7
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Issue Information: Proteomics 15'25	7
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	7
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	7
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	7
Standard abbreviations	7
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	7
From Discovery to Implementation: Bringing Proteomics to the Clinic	7
Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	7
Editorial Board: Proteomics 17'24	7
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Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	7
Contents: Proteomics 23–24'24	7
Editorial Board: Proteomics 7–8'23	7
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Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens	7
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	7
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Genetic and epigenetic control of the plant metabolome	7
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	7
Spectral entropy as a measure of the metaproteome complexity	7
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	7
Contents: Proteomics 18'24	7
Proteoform Identification Using Multiplexed Top‐Down Mass Spectra	7
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	7
An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus	7
Human peripheral blood mononuclear cells: A review of recent proteomic applications	7
Challenges in computational discovery of bioactive peptides in ’omics data	7
What proteomics has taught us about honey bee ( Apis mellifera ) health and disease	7
Omics and systems view of innate immune pathways	7
Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients	6
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Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	6
Prediction of peptide hormones using an ensemble of machine learning and similarity‐based methods	6
Editorial Board: Proteomics 14'24	6
Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	6
Contents: Proteomics 16'24	6
Contents: Proteomics 11'23	6
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Standard abbreviations	6
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	6
See the Unseen: Rapid, Multiparametric Single‐Particle Analysis of Extracellular Vesicles With Nano‐Flow Cytometry	6
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Issue Information: Proteomics 24'25	6
Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	6
Standard abbreviations	6
Standard abbreviations	6
Novel histone modifications in microglia derived from a mouse model of chronic pain	6
Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology	6
AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures	6
A Proteomics Resource Investigating Fibrosis: Proof‐of‐Concept for Identifying Novel Drug Candidates	6
Optimizing the PROTREC network‐based missing protein prediction algorithm	6
Editorial Board: Proteomics 15'24	6
Sensitive Profiling of Mouse Liver Membrane Proteome Dysregulation Following a High‐Fat and Alcohol Diet Treatment	5
Isolation and Characterization of Extracellular Vesicles From Ascochyta rabiei , a Necrotrophic Fungal Chickpea Pathogen	5
Protein‐protein interaction networks as miners of biological discovery	5
Proteomic Profiling of Myofiber Repair Annexins and Their Role in Duchenne Muscular Dystrophy	5
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Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt‐Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica)	5
Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells	5
Capillary blood self‐collection for high‐throughput proteomics	5
Microglia Display Altered Spatial Morphology and Proteome After Stroke	5
Charge site manipulation to enhance top‐down fragmentation efficiency	5
In‐Depth Proteome Profiling of the Hippocampus of LDLR Knockout Mice Reveals Alternation in Synaptic Signaling Pathway	5
Editorial Board: Proteomics 3–4'23	5
Contents: Proteomics 20'23	5
Editorial Board: Proteomics 20'24	5
Identification of proteoforms by top‐down proteomics using two‐dimensional low/low pH reversed‐phase liquid chromatography‐mass spectrometry	5
A comprehensive revisit of the machine‐learning tools developed for the identification of enhancers in the human genome	5
Proteomics analysis of C2C12 myotubes treated with atrophy inducing cancer cell‐derived factors	5
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MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications	5
Front Cover	5