Proteomics

Article	Citations
Editorial Board: Proteomics 10'22	109
Front Cover	92
Contents: Proteomics 9'22	84
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	65
SIMPLEX Enriches Hydrophobic and Lipidated Proteins in Membrane Proteomics Experiments	61
Eye proteome of Drosophila melanogaster	59
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Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	50
	47
Standard abbreviations	46
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	45
Front Cover	40
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	39
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	36
LC‐MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain‐Tetanus Toxoid Conjugate Vaccine Against SARS‐CoV‐2	35
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation	35
	35
Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	34
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
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	33
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	32
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	30
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	30
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	30

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	30
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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	26
Editorial Board: Proteomics 8'22	26
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs	26
Front Cover	25
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	25
Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	25
Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles	25
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	25
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	25
Contents: Proteomics 5'24	24
Contents: Proteomics 19–20'22	24
Standard abbreviations	24
Editorial Board: Proteomics 21–22'23	23
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	22
Editorial Board: Proteomics 11–12'22	22
Front Cover	21
Analyzing domain features of small proteins using a machine‐learning method	21
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus	20
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	20
Urinary Peptidomic Profiling In Post‐Acute Sequelae of SARS‐CoV‐2 Infection: A Case‐Control Study	20
Omics insights into the responses to dietary selenium	20
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	19
Review of predicting protein stability changes upon variations	19
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	19
An antibody‐free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis	18
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	18
Front Cover	17
Standard abbreviations	17
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Front Cover	16
Standard abbreviations	16
Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry	16
Editorial Board: Proteomics 5'24	16
Front Cover	16
Standard abbreviations	16
Proteomic changes associated with the development of açaí ( Euterpe oleracea Mart.) seeds	16
Standard abbreviations	16
In‐silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases	16
Standard abbreviations	15
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	15
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Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	15
Standard abbreviations	14
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	14
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	14
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	14
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	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
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	14
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	14
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	13
A peptidoform based proteomic strategy for studying functions of post‐translational modifications	13
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Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	13
Contents: Proteomics 13–14'23	13
Contents: Proteomics 7'25	13
Contents: Proteomics 9'23	13
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	13
The cuticle proteome of a planktonic crustacean	13
Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin	13
Standard abbreviations	13
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Contents: Proteomics 11–12'22	12
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	12
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	12
Front Cover	12
Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	12
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	12
Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	12
Front Cover	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
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	12
Standard abbreviations	11
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	11
Immune capture and protein profiling of small extracellular vesicles from human plasma	11
Metaproteomic Analysis to Assess the Impact of Storage Media on Human Gut Microbiome in Fecal Samples	11
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	11
Standard abbreviations	11
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Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	11
Contents: Proteomics 17'24	11
Contents: Proteomics 8'24	11
SLB‐msSIM: A Spectral Library‐Based Multiplex Segmented SIM Platform for Single‐Cell Proteomic Analysis	11
Data‐Driven Proteomics for Post‐Translational Modification Discovery	11
Editorial Board: Proteomics 19–20'22	11
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	11
Contents: Proteomics 15–16'22	11
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	11
Front Cover	11
Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients	11
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics	10
Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	10
Issue Information: Proteomics 14'25	10
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	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
Targeted Quantitation of Phosphotyrosine‐Containing Proteins in T‐Cell Receptor Signaling Using a SureQuant‐Based Mass Spectrometry Approach	10
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	10
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	10
Front Cover	10
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	10
Data Processing and Analysis in Positional Proteomics	10
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	10
A Survey of Annotated smORF‐Encoded Polypeptides in Bacteria Interacting With Eukaryotic Hosts	10
Standard abbreviations	9
Front Cover	9
Proteome Analysis of Corynebacterium diphtheriae–Macrophage Interaction	9
Standard abbreviations	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
Front Cover	9
	9
Editorial Board: Proteomics 8'24	9
Contents: Proteomics 8'25	9
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	9
Potential of deep representative learning features to interpret the sequence information in proteomics	9
Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	9
Standard abbreviations	9
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	9
Front Cover	9
Editorial Board: Proteomics 9'22	9
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
Microproteins—Discovery, structure, and function	8
A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	8
Computational tools for inferring transcription factor activity	8
Editorial Board: Proteomics 7'24	8

Contents: Proteomics 23–24'24	8
Transforming peptide hormone prediction: The role of AI in modern proteomics	8
Comparative Analysis of Proteoform Clean‐Up Methods for In‐Depth Top‐Down Proteomics	8
Computational systems approach towards phosphoproteomics and their downstream regulation	8
Improving SWATH‐MS analysis by deep‐learning	8
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DREAMweb: An online tool for graph‐based modeling of NMR protein structure	8
Contents: Proteomics 19'24	8
Molecular methods to study protein trafficking between organs	8
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	8
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	8
Editorial Board: Proteomics 7–8'23	8
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	8
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	8
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Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	7
From Discovery to Implementation: Bringing Proteomics to the Clinic	7
Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens	7
Standard abbreviations	7
QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry‐Based Proteomics Datasets	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 entropy as a measure of the metaproteome complexity	7
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Contents: Proteomics 18'24	7
Editorial Board: Proteomics 5–6'22	7
An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus	7
What proteomics has taught us about honey bee ( Apis mellifera ) health and disease	7
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	7
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Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	7
Challenges in computational discovery of bioactive peptides in ’omics data	7
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	7
Front Cover	7
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	7
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	7
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	7
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Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	7
Issue Information: Proteomics 15'25	7
Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	7
Genetic and epigenetic control of the plant metabolome	7
Omics and systems view of innate immune pathways	7
Issue Information: Proteomics 19'25	7
Human peripheral blood mononuclear cells: A review of recent proteomic applications	7
Editorial Board: Proteomics 17'24	7
Standard abbreviations	7
	7
Proteoform Identification Using Multiplexed Top‐Down Mass Spectra	7
Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology	6
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Standard abbreviations	6
Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	6
Standard abbreviations	6
Contents: Proteomics 16'24	6
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Novel histone modifications in microglia derived from a mouse model of chronic pain	6
See the Unseen: Rapid, Multiparametric Single‐Particle Analysis of Extracellular Vesicles With Nano‐Flow Cytometry	6
Optimizing the PROTREC network‐based missing protein prediction algorithm	6
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Editorial Board: Proteomics 15'24	6
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Metaproteomics and Meta‐Omics to Decrypt Microbiome Functionality	6
Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	6
Editorial Board: Proteomics 14'24	6
Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients	6
Editorial Board: Proteomics 3–4'23	6
Contents: Proteomics 11'23	6
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	6
Standard abbreviations	6