Proteomics

Article	Citations
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	102
Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three‐dimensional culture	86
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	83
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	63
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	57
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Front Cover	55
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	53
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	48
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation	46
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	45
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	45
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Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	36
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	36
Editorial Board: Proteomics 10'22	33
Front Cover	33
SIMPLEX Enriches Hydrophobic and Lipidated Proteins in Membrane Proteomics Experiments	32
LC‐MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain‐Tetanus Toxoid Conjugate Vaccine Against SARS‐CoV‐2	32
Contents: Proteomics 9'22	32
Standard abbreviations	31
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	31
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	30
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Eye proteome of Drosophila melanogaster	28
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	28
Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles	25
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Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	25
Front Cover	24
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	24
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	24
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs	24
Editorial Board: Proteomics 8'22	24
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	23
Contents: Proteomics 19–20'22	23
Standard abbreviations	23
Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	22
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	22
Contents: Proteomics 5'24	21
Editorial Board: Proteomics 21–22'23	21
Analyzing domain features of small proteins using a machine‐learning method	20
Editorial Board: Proteomics 11–12'22	19
Front Cover	19
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	19
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	19
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus	18
Omics insights into the responses to dietary selenium	18
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	18
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	18
Review of predicting protein stability changes upon variations	18
Standard abbreviations	17
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	17
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In‐silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases	16
Front Cover	16
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	15
Editorial Board: Proteomics 5'24	15
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	15
Front Cover	15
Front Cover	15
Proteomic changes associated with the development of açaí ( Euterpe oleracea Mart.) seeds	14
Standard abbreviations	14
Standard abbreviations	14
Front Cover	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
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Standard abbreviations	14
Standard abbreviations	14
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	13
Passages in culture and stimulation conditions influence protein expression of primary fibroblasts	13
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	13
Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry	13

An antibody‐free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis	13
Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	13
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	13
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	13
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	13
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	13
A peptidoform based proteomic strategy for studying functions of post‐translational modifications	12
Metaproteomic Analysis to Assess the Impact of Storage Media on Human Gut Microbiome in Fecal Samples	12
Contents: Proteomics 13–14'23	12
The cuticle proteome of a planktonic crustacean	12
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	12
Standard abbreviations	12
Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	12
The utility of proteases in proteomics, from sequence profiling to structure and function analysis	12
SLB‐msSIM: A Spectral Library‐Based Multiplex Segmented SIM Platform for Single‐Cell Proteomic Analysis	12
Contents: Proteomics 9'23	12
Contents: Proteomics 7'25	12
Standard abbreviations	12
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Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	11
Immune capture and protein profiling of small extracellular vesicles from human plasma	11
Standard abbreviations	11
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	11
Front Cover	11
Contents: Proteomics 11–12'22	11
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	11
Contents: Proteomics 15–16'22	11
Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin	11
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	11
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Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	11
Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma	11
Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	11
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	11
Front Cover	11
Contents: Proteomics 17'24	10
Contents: Proteomics 8'24	10
Standard abbreviations	10
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	10
Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients	10
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	10
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	10
Front Cover	10
Data‐Driven Proteomics for Post‐Translational Modification Discovery	10
Editorial Board: Proteomics 19–20'22	10
A dataset resource for clinically associated phosphosites in hepatocellular carcinoma	10
Immunoproteome profiling of Listeria monocytogenes under mild acid and salt stress conditions	10
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	10
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	10
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Front Cover	10
A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	9
Towards deciphering glioblastoma intra‐tumoral heterogeneity: The importance of integrating multidimensional models	9
Editorial Board: Proteomics 8'24	9
Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	9
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics	9
Issue Information: Proteomics 14'25	9
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	9
Back Cover: Protein‐enabled detection of ibuprofen and sulfamethoxazole using solid‐state nanopores	9
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
Standard abbreviations	9
Proteome Analysis of Corynebacterium diphtheriae–Macrophage Interaction	9
Targeted Quantitation of Phosphotyrosine‐Containing Proteins in T‐Cell Receptor Signaling Using a SureQuant‐Based Mass Spectrometry Approach	9
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	9
Microproteins—Discovery, structure, and function	9
Front Cover	9
Standard abbreviations	9
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Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	9
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	9
A Survey of Annotated smORF‐Encoded Polypeptides in Bacteria Interacting With Eukaryotic Hosts	9
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	9
Contents: Proteomics 8'25	8
Molecular methods to study protein trafficking between organs	8
Computational systems approach towards phosphoproteomics and their downstream regulation	8
Human peripheral blood mononuclear cells: A review of recent proteomic applications	8
Standard abbreviations	8
Improving SWATH‐MS analysis by deep‐learning	8
Computational tools for inferring transcription factor activity	8
Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	8

Editorial Board: Proteomics 9'22	8
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	8
Issue Information: Proteomics 19'25	8
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	8
Front Cover	8
Potential of deep representative learning features to interpret the sequence information in proteomics	8
Proteoform Identification Using Multiplexed Top‐Down Mass Spectra	8
Front Cover	8
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	7
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	7
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	7
Standard abbreviations	7
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	7
Contents: Proteomics 23–24'24	7
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	7
Editorial Board: Proteomics 17'24	7
DREAMweb: An online tool for graph‐based modeling of NMR protein structure	7
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	7
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	7
Editorial Board: Proteomics 5–6'22	7
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	7
Challenges in computational discovery of bioactive peptides in ’omics data	7
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Editorial Board: Proteomics 7'24	7
Front Cover	7
Contents: Proteomics 19'24	7
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	7
QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry‐Based Proteomics Datasets	7
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	7
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Editorial Board: Proteomics 7–8'23	7
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Spectral entropy as a measure of the metaproteome complexity	7
Transforming peptide hormone prediction: The role of AI in modern proteomics	7
Omics and systems view of innate immune pathways	6
An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus	6
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Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	6
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	6
Optimizing the PROTREC network‐based missing protein prediction algorithm	6
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Standard abbreviations	6
From Discovery to Implementation: Bringing Proteomics to the Clinic	6
Standard abbreviations	6
Issue Information: Proteomics 15'25	6
What proteomics has taught us about honey bee ( Apis mellifera ) health and disease	6
Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens	6
Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	6
Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	6
Editorial Board: Proteomics 14'24	6
Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology	6
Genetic and epigenetic control of the plant metabolome	6
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	6
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Contents: Proteomics 18'24	6
An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources	6
Metaproteomics and Meta‐Omics to Decrypt Microbiome Functionality	6
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Novel histone modifications in microglia derived from a mouse model of chronic pain	6
MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications	6
Editorial Board: Proteomics 3'22	5
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Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients	5
Standard abbreviations	5
Contents: Proteomics 11'23	5
Contents: Proteomics 20'24	5
Tissue‐Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency	5
Proteome profiling of vascular sap regarding Eucalyptus grandis, Eucalyptus urophylla, and Eucalyptus camaldulensis	5
Front Cover: Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing	5
Editorial Board: Proteomics 6'23	5
Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	5
Editorial Board: Proteomics 3–4'23	5
Editorial Board: Proteomics 15'24	5
Quantitative proteomic analysis of hepatic tissue in allotetraploid hybridized from red crucian carp and common carp identified crucial proteins and pathways associated with metabolism and growth rate	5
Standard abbreviations	5
Prediction of peptide hormones using an ensemble of machine learning and similarity‐based methods	5
Proteomics analysis of C2C12 myotubes treated with atrophy inducing cancer cell‐derived factors	5
Standard abbreviations	5
A crustacean neuropeptide spectral library for data‐independent acquisition (DIA) mass spectrometry applications	5
Sensitive Profiling of Mouse Liver Membrane Proteome Dysregulation Following a High‐Fat and Alcohol Diet Treatment	5
Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects	5
AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures	5
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Contents: Proteomics 16'24	5
Protein‐protein interaction networks as miners of biological discovery	5
Isolation and Characterization of Extracellular Vesicles From Ascochyta rabiei, a Necrotrophic Fungal Chickpea Pathogen	5
Standard abbreviations	5
Front Cover	5