Proteomics

Article	Citations
Editorial Board: Proteomics 11–12'21	160
	80
Front Cover	74
Contents: Proteomics 9'22	70
Editorial Board: Proteomics 10'22	52
	51
Front Cover	44
	43
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	42
	40
Standard abbreviations	38
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	36
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation	35
Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three‐dimensional culture	35
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	33
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	33
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	33
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	32
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	32
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	31
Eye proteome of Drosophila melanogaster	31
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	29
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	27
Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	27
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	25

A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	24
Contents: Proteomics 19–20'22	23
Front Cover	23
Front Cover	22
Editorial Board: Proteomics 21–22'23	22
Standard abbreviations	22
Contents: Proteomics 5'24	22
Editorial Board: Proteomics 8'22	22
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	21
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	21
Standard abbreviations	21
Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	21
Editorial Board: Proteomics 11–12'22	21
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	20
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	20
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	19
Direct‐MS analysis of antibody‐antigen complexes	19
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	18
Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	17
Review of predicting protein stability changes upon variations	17
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis inOreochromis mossambicus	17
Analyzing domain features of small proteins using a machine‐learning method	17
Front Cover	16
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs	16
Omics insights into the responses to dietary selenium	16
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	16
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	16
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Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development	15
Proteomic changes associated with the development of açaí (Euterpe oleracea Mart.) seeds	15
Standard abbreviations	15
Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	15
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	15
Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry	15
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	15
Global profiling of protein lactylation in Caenorhabditis elegans	15
Universal and cross‐cancer prognostic biomarkers for predicting survival risk of cancer patients from expression profile of apoptotic pathway genes	14
Passages in culture and stimulation conditions influence protein expression of primary fibroblasts	14
An antibody‐free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis	14
In‐silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases	14
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	14
Standard abbreviations	13
Standard abbreviations	13
Front Cover	13
Standard abbreviations	13
Front Cover	13
Standard abbreviations	13
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	12
Front Cover	12
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	12

Editorial Board: Proteomics 5'24	12
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	12
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	12
Contents: Proteomics 13–14'23	11
Standard abbreviations	11
Contents: Proteomics 11–12'22	11
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Front Cover	11
Standard abbreviations	11
Editorial Board: Proteomics 13–14'21	11
Contents: Proteomics 9'23	11
Standard abbreviations	11
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	10
Triple extraction method enables high quality mass spectrometry‐based proteomics and phospho‐proteomics for eventual multi‐omics integration studies	10
Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	10
Immune capture and protein profiling of small extracellular vesicles from human plasma	10
Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma	10
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JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	10
Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin	10
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	10
Contents: Proteomics 7'25	10
Front Cover	10
The cuticle proteome of a planktonic crustacean	9
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	9
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	9
Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	9
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A peptidoform based proteomic strategy for studying functions of post‐translational modifications	9
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	9
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	9
Understanding extracellular vesicles	9
Front Cover	9
Contents: Proteomics 8'24	9
Insights into the vision of the hadal snailfish Pseudoliparis swirei through proteomic analysis of the eye	9
The utility of proteases in proteomics, from sequence profiling to structure and function analysis	9
Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	9
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	9
Contents: Proteomics 15–16'22	9
Editorial Board: Proteomics 19–20'22	9
Immunoproteome profiling of Listeria monocytogenes under mild acid and salt stress conditions	8
Editorial Board: Proteomics 9'22	8
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	8
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	8
Characterization of HLA‐A*33:03 epitopes via immunoprecipitation and LC‐MS/MS	8
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	8
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	8
Standard abbreviations	8
Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients	8
Data‐Driven Proteomics for Post‐Translational Modification Discovery	8
Standard abbreviations	8
Standard abbreviations	8
Towards deciphering glioblastoma intra‐tumoral heterogeneity: The importance of integrating multidimensional models	8
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	8
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A dataset resource for clinically associated phosphosites in hepatocellular carcinoma	8
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	8
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	8
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	8
Editorial Board: Proteomics 15'21	8
Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	8
Front Cover	8
Standard abbreviations	8
Editorial Board: Proteomics 8'24	8
Back Cover: Protein‐enabled detection of ibuprofen and sulfamethoxazole using solid‐state nanopores	8
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics	8
DDASSQ: An open‐source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform	8
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	8
Contents: Proteomics 17'24	8
Standard abbreviations	8
Contents: Proteomics 17–18'21	8
Front Cover	8
Front Cover	8
Editorial Board: Proteomics 20'21	8
Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	7
Molecular methods to study protein trafficking between organs	7
Toward proteome‐wide exploration of proteins in dried blood spots using liquid chromatography‐coupled mass spectrometry	7
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	7

Proteome Analysis of Corynebacterium diphtheriae–Macrophage Interaction	7
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	7
A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	7
Computational systems approach towards phosphoproteomics and their downstream regulation	7
Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	7
Contents: Proteomics 8'25	7
Potential of deep representative learning features to interpret the sequence information in proteomics	7
Single‐molecule, hybridization‐based strategies for short nucleic acids detection and recognition with nanopores	7
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	7
Automation of single‐cell proteomic sample preparation	7
Improving SWATH‐MS analysis by deep‐learning	7
Drug hapten‐specific T‐cell activation: Current status and unanswered questions	7
Microproteins—Discovery, structure, and function	7
Front Cover	7
Computational tools for inferring transcription factor activity	7
Contents: Proteomics 19'24	6
Editorial Board: Proteomics 7'24	6
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	6
Editorial Board: Proteomics 7–8'23	6
Specialised skin cancer spectral library for use in data‐independent mass spectrometry	6
Systematic analysis of the ubiquitome in mouse testis	6
DREAMweb: An online tool for graph‐based modeling of NMR protein structure	6
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	6
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	6
Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics	6
Transforming peptide hormone prediction: The role of AI in modern proteomics	6
Standard abbreviations	6
Contents: Proteomics 13–14'21	6
Human peripheral blood mononuclear cells: A review of recent proteomic applications	6
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	6
Standard abbreviations	6
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	6
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	6
Contents: Proteomics 23–24'24	6
	6
Editorial Board: Proteomics 5–6'22	6
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	6
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	6
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Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	6
What proteomics has taught us about honey bee (Apis mellifera) health and disease	5
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Contents: Proteomics 16'21	5
Editorial Board: Proteomics 17'24	5
Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	5
Contents: Proteomics 11'23	5
Standard abbreviations	5
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	5
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	5
Contents: Proteomics 18'24	5
Contents: Proteomics 11–12'21	5
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	5
Spectral entropy as a measure of the metaproteome complexity	5
Editorial Board: Proteomics 3–4'23	5
Omics and systems view of innate immune pathways	5
An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus	5
Standard abbreviations	5
From Discovery to Implementation: Bringing Proteomics to the Clinic	5
Front Cover	5
Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens	5
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Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	5
Genetic and epigenetic control of the plant metabolome	5
Challenges in computational discovery of bioactive peptides in ’omics data	5
Standard abbreviations	4
Prediction of peptide hormones using an ensemble of machine learning and similarity‐based methods	4
Editorial Board: Proteomics 6'23	4
	4
Standard abbreviations	4
Contents: Proteomics 20'24	4
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	4
Contents: Proteomics 20'21	4
Proteomics analysis of C2C12 myotubes treated with atrophy inducing cancer cell‐derived factors	4
Front Cover: Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing	4
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Front Cover	4
MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications	4
Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects	4
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Editorial Board: Proteomics 14'24	4
Contents: Proteomics 16'24	4
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Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	4
Charge site manipulation to enhance top‐down fragmentation efficiency	4
Front Cover	4
Standard abbreviations	4
Editorial Board: Proteomics 3'22	4
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	4
Editorial Board: Proteomics 15'24	4
Standard abbreviations	4
	4
Novel histone modifications in microglia derived from a mouse model of chronic pain	4
An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources	4
Contents: Proteomics 20'23	4
Editorial Board: Proteomics 19'21	4