Proteomics

Article	Citations
Editorial Board: Proteomics 11–12'21	153
	73
Front Cover	68
Contents: Proteomics 9'22	65
Editorial Board: Proteomics 10'22	57
Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three‐dimensional culture	50
	49
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	43
	41
Front Cover	41
	37
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	37
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	36
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	34
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	34
Standard abbreviations	34
Eye proteome of Drosophila melanogaster	33
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	32
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	32
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	32
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	32
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation	31
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	29
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	28

Contents: Proteomics 19–20'22	27
Front Cover	24
Front Cover	24
Standard abbreviations	24
Editorial Board: Proteomics 8'22	23
Editorial Board: Proteomics 21–22'23	22
Editorial Board: Proteomics 11–12'22	22
Contents: Proteomics 5'24	22
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis inOreochromis mossambicus	21
Proteome characterisation of extracellular vesicles isolated from heart	21
Standard abbreviations	21
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	21
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	21
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs	21
Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	20
Direct‐MS analysis of antibody‐antigen complexes	20
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	20
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	20
Analyzing domain features of small proteins using a machine‐learning method	19
Review of predicting protein stability changes upon variations	19
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	19
Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	19
A novel role for milk fat globule‐EGF factor 8 protein (MFGE8) in the mediation of mouse sperm–extracellular vesicle interactions	18
Omics insights into the responses to dietary selenium	17
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	17
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	16
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	16
Front Cover	16
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	15
Standard abbreviations	15
Proteomic changes associated with the development of açaí (Euterpe oleracea Mart.) seeds	15
Global profiling of protein lactylation in Caenorhabditis elegans	14
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	14
Universal and cross‐cancer prognostic biomarkers for predicting survival risk of cancer patients from expression profile of apoptotic pathway genes	14
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	14
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	14
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Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	14
An antibody‐free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis	14
Standard abbreviations	13
In‐silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases	13
Front Cover	13
Front Cover	13
Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry	13
Editorial Board: Proteomics 5'24	13
Standard abbreviations	13
Standard abbreviations	13
Standard abbreviations	13
Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development	12
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	12

Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	12
Front Cover	12
Passages in culture and stimulation conditions influence protein expression of primary fibroblasts	12
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	12
Immune capture and protein profiling of small extracellular vesicles from human plasma	12
Understanding extracellular vesicles	11
Editorial Board: Proteomics 13–14'21	11
Contents: Proteomics 13–14'23	11
Standard abbreviations	11
	11
Triple extraction method enables high quality mass spectrometry‐based proteomics and phospho‐proteomics for eventual multi‐omics integration studies	11
Contents: Proteomics 11–12'22	11
Front Cover	11
	11
Standard abbreviations	11
Editorial Board: Proteomics 10'21	11
Standard abbreviations	11
A Tandem Mass Tags (TMTs) labeling approach highlights differences between the shoot proteome of two Arabidopsis thaliana ecotypes, Col‐0 and Ws	11
Insights into the vision of the hadal snailfish Pseudoliparis swirei through proteomic analysis of the eye	10
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	10
Contents: Proteomics 9'23	10
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	10
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Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	10
Contents: Proteomics 7'25	9
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	9
Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin	9
Front Cover	9
A peptidoform based proteomic strategy for studying functions of post‐translational modifications	9
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Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	9
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	9
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	9
Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	9
The cuticle proteome of a planktonic crustacean	9
Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma	9
The utility of proteases in proteomics, from sequence profiling to structure and function analysis	9
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	9
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	9
Front Cover	9
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	9
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	8
A dataset resource for clinically associated phosphosites in hepatocellular carcinoma	8
Editorial Board: Proteomics 19–20'22	8
Contents: Proteomics 15–16'22	8
Standard abbreviations	8
Characterization of HLA‐A*33:03 epitopes via immunoprecipitation and LC‐MS/MS	8
Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients	8
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	8
Editorial Board: Proteomics 15'21	8
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	8
Contents: Proteomics 8'24	8
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Front Cover	8
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	8
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	8
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	8
Contents: Proteomics 17–18'21	8
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DDASSQ: An open‐source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform	8
Standard abbreviations	8
Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	8
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	8
Contents: Proteomics 17'24	8
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	8
Front Cover	7
Towards deciphering glioblastoma intra‐tumoral heterogeneity: The importance of integrating multidimensional models	7
Back Cover: Protein‐enabled detection of ibuprofen and sulfamethoxazole using solid‐state nanopores	7
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics	7
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Editorial Board: Proteomics 8'24	7
Standard abbreviations	7
Front Cover	7
Single‐molecule, hybridization‐based strategies for short nucleic acids detection and recognition with nanopores	7
Editorial Board: Proteomics 9'21	7
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	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
Standard abbreviations	7
Standard abbreviations	7
Molecular methods to study protein trafficking between organs	7

Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	7
Immunoproteome profiling of Listeria monocytogenes under mild acid and salt stress conditions	7
Editorial Board: Proteomics 9'22	7
Improving SWATH‐MS analysis by deep‐learning	7
Editorial Board: Proteomics 20'21	7
Front Cover	6
A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	6
Editorial Board: Proteomics 7–8'23	6
Standard abbreviations	6
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	6
Microproteins—Discovery, structure, and function	6
Toward proteome‐wide exploration of proteins in dried blood spots using liquid chromatography‐coupled mass spectrometry	6
Computational systems approach towards phosphoproteomics and their downstream regulation	6
Proteome Analysis of Corynebacterium diphtheriae–Macrophage Interaction	6
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	6
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Standard abbreviations	6
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	6
Automation of single‐cell proteomic sample preparation	6
Contents: Proteomics 8'25	6
Drug hapten‐specific T‐cell activation: Current status and unanswered questions	6
Potential of deep representative learning features to interpret the sequence information in proteomics	6
Computational tools for inferring transcription factor activity	6
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	6
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	6
Editorial Board: Proteomics 5–6'22	6
Contents: Proteomics 13–14'21	6
Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	6
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	6
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	6
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	5
Transforming peptide hormone prediction: The role of AI in modern proteomics	5
Human peripheral blood mononuclear cells: A review of recent proteomic applications	5
Contents: Proteomics 19'24	5
	5
An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus	5
Front Cover	5
Contents: Proteomics 16'21	5
Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics	5
Systematic analysis of the ubiquitome in mouse testis	5
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	5
Editorial Board: Proteomics 7'24	5
	5
Omics and systems view of innate immune pathways	5
Contents: Proteomics 18'24	5
Contents: Proteomics 11–12'21	5
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	5
DREAMweb: An online tool for graph‐based modeling of NMR protein structure	5
Specialised skin cancer spectral library for use in data‐independent mass spectrometry	5
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	5
Standard abbreviations	5
Editorial Board: Proteomics 17'24	5
	5
Standard abbreviations	5
Contents: Proteomics 23–24'24	5
Contents: Proteomics 11'23	4
What proteomics has taught us about honey bee (Apis mellifera) health and disease	4
Proteome reprogramming of endometrial epithelial cells by human trophectodermal small extracellular vesicles reveals key insights into embryo implantation	4
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	4
Novel histone modifications in microglia derived from a mouse model of chronic pain	4
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	4
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Standard abbreviations	4
Standard abbreviations	4
Contents: Proteomics 16'24	4
Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	4
Editorial Board: Proteomics 3–4'23	4
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	4
Spectral entropy as a measure of the metaproteome complexity	4
AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures	4
Editorial Board: Proteomics 14'24	4
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Editorial Board: Proteomics 15'24	4
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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
Standard abbreviations	4
Genetic and epigenetic control of the plant metabolome	4
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	4
Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	4
Challenges in computational discovery of bioactive peptides in ’omics data	4
Optimizing the PROTREC network‐based missing protein prediction algorithm	4
	4
Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects	4
Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	4
Contents: Proteomics 20'24	4
Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens	4