Proteomics

Article	Citations
	131
	110
	104
Standard abbreviations	79
Front Cover	71
	69
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	65
Editorial Board: Proteomics 10'22	63
Front Cover	61
Contents: Proteomics 9'22	58
Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	54
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	53
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Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	43
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	42
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	42
Eye proteome of Drosophila melanogaster	40
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	40
LC‐MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain‐Tetanus Toxoid Conjugate Vaccine Against SARS‐CoV‐2	37
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	36
Single Extracellular Vesicles and Omics	36
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	36
SIMPLEX Enriches Hydrophobic and Lipidated Proteins in Membrane Proteomics Experiments	36
Proteomic Profiling of Primary Hippocampal Neurons Reveals Noncanonical GFAP Expression and Metabolic Adaptations in Glia‐Free Culture	33
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	31

Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	30
Omics insights into the responses to dietary selenium	30
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	30
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Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus	29
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	29
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	28
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	26
Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	26
Contents: Proteomics 19–20'22	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
Front Cover	25
Standard abbreviations	25
Editorial Board: Proteomics 21–22'23	24
Contents: Proteomics 5'24	24
Analyzing domain features of small proteins using a machine‐learning method	23
Front Cover	23
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	22
Editorial Board: Proteomics 11–12'22	22
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	22
Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles	21
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	21
Urinary Peptidomic Profiling In Post‐Acute Sequelae of SARS‐CoV‐2 Infection: A Case‐Control Study	21
Review of predicting protein stability changes upon variations	21
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	21
Standard abbreviations	20
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Editorial Board: Proteomics 5'24	20
Global profiling of protein lactylation in Caenorhabditis elegans	20
Front Cover	20
Standard abbreviations	19
Front Cover	19
	19
Standard abbreviations	19
Standard abbreviations	18
Standard abbreviations	18
Issue Information: Proteomics 23'25	17
Proteomic changes associated with the development of açaí ( Euterpe oleracea Mart.) seeds	17
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	17
An antibody‐free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis	17
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	17
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	17
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	17
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	17
Plasma Proteomics Across Three Generations of Mass Spectrometry Instruments: Lessons for Biofluid Method Optimisation	17
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	16
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	16
Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	16
Proteomics Advances in Immunology and Infection Research	16
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	16

Standard abbreviations	16
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	16
Front Cover	15
	15
Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	15
Front Cover	15
Metaproteomic Analysis to Assess the Impact of Storage Media on Human Gut Microbiome in Fecal Samples	15
SLB‐msSIM: A Spectral Library‐Based Multiplex Segmented SIM Platform for Single‐Cell Proteomic Analysis	15
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Contents: Proteomics 11–12'22	15
Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	15
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	14
Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput	14
Contents: Proteomics 9'23	14
The cuticle proteome of a planktonic crustacean	14
Contents: Proteomics 13–14'23	14
Contents: Proteomics 7'25	14
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	14
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	14
Standard abbreviations	14
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	14
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	13
Immune capture and protein profiling of small extracellular vesicles from human plasma	13
Contents: Proteomics 8'24	13
Data‐Driven Proteomics for Post‐Translational Modification Discovery	13
Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma	13
Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	13
Contents: Proteomics 15–16'22	13
Standard abbreviations	13
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The utility of proteases in proteomics, from sequence profiling to structure and function analysis	13
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	13
Contents: Proteomics 17'24	13
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	13
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	13
Front Cover	12
Standard abbreviations	12
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	12
Editorial Board: Proteomics 19–20'22	12
Progress of Deep Learning Prediction of CD8+ T‐Cell Epitopes	12
Targeted Quantitation of Phosphotyrosine‐Containing Proteins in T‐Cell Receptor Signaling Using a SureQuant‐Based Mass Spectrometry Approach	12
Front Cover	12
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	12
Immunoproteome profiling of Listeria monocytogenes under mild acid and salt stress conditions	12
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	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	11
Assessing Discrepancies in miRNA Profiles of Mouse Blood‐Derived Extracellular Vesicles: A Systematic Review of Sequencing Data	11
Standard abbreviations	11
Front Cover	11
Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	11
A Survey of Annotated smORF‐Encoded Polypeptides in Bacteria Interacting With Eukaryotic Hosts	11
Issue Information: Proteomics 14'25	11
Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	11
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	11
Standard abbreviations	11
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Contents: Proteomics 8'25	11
A dataset resource for clinically associated phosphosites in hepatocellular carcinoma	11
Data Processing and Analysis in Positional Proteomics	11
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	11
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	11
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	11
Editorial Board: Proteomics 8'24	11
Towards deciphering glioblastoma intra‐tumoral heterogeneity: The importance of integrating multidimensional models	11
Front Cover	11
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	11
Editorial Board: Proteomics 9'22	10
Proteome Analysis of Corynebacterium diphtheriae–Macrophage Interaction	10
Molecular methods to study protein trafficking between organs	10
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	10
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	10
Issue Information: Proteomics 19'25	10
Standard abbreviations	10
Front Cover	10
Comparative Analysis of Proteoform Clean‐Up Methods for In‐Depth Top‐Down Proteomics	10
Microproteins—Discovery, structure, and function	10
Quantitative Proteomics Reveals the Adaptive Mechanisms of Aeromonas hydrophila Under Cobalt Stress	10
A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	10
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	10

Computational systems approach towards phosphoproteomics and their downstream regulation	10
Optimization of Microfluidic Geometry for Extracellular Vesicle Capture Using an Automated Parallel Pattern Search	10
Improving SWATH‐MS analysis by deep‐learning	10
Computational tools for inferring transcription factor activity	10
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	10
DREAMweb: An online tool for graph‐based modeling of NMR protein structure	9
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	9
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Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	9
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	9
Editorial Board: Proteomics 7–8'23	9
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	9
Standard abbreviations	9
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	9
Contents: Proteomics 19'24	9
Editorial Board: Proteomics 7'24	9
Contents: Proteomics 23–24'24	9
Transforming peptide hormone prediction: The role of AI in modern proteomics	9
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	9
QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry‐Based Proteomics Datasets	9
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Contents: Proteomics 18'24	8
Imaging Mass Spectrometry‐Based Assessment of ER, PR, and HER2 Protein Expression in Breast Cancer	8
Proteoform Identification Using Multiplexed Top‐Down Mass Spectra	8
Hypoxia Modulates Nanovesicle Phenotype and Angiogenic Function From Human Pluripotent Stem Cells	8
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	8
Front Cover	8
What proteomics has taught us about honey bee ( Apis mellifera ) health and disease	8
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Issue Information: Proteomics 15'25	8
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	8
Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species	8
Proteomic Characterization of AS1411 Reveals ATP6AP1 as a Mediator of Triple‐Negative Breast Cancer Progression	8
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From Discovery to Implementation: Bringing Proteomics to the Clinic	8
Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	8
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Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	8
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	8
Spectral entropy as a measure of the metaproteome complexity	8
Challenges in computational discovery of bioactive peptides in ’omics data	8
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Editorial Board: Proteomics 17'24	8
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Standard abbreviations	8
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Omics and systems view of innate immune pathways	7
Editorial Board: Proteomics 3–4'23	7
Optimizing the PROTREC network‐based missing protein prediction algorithm	7
Contents: Proteomics 16'24	7
Contents: Proteomics 11'23	7
Editorial Board: Proteomics 14'24	7
Standard abbreviations	7
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	7
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Standard abbreviations	7
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Genetic and epigenetic control of the plant metabolome	7
Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	7
Editorial Board: Proteomics 15'24	7
Contents: Proteomics 20'24	7
Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	7
Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients	6
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	6
Proteomics analysis of C2C12 myotubes treated with atrophy inducing cancer cell‐derived factors	6
An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources	6
Metaproteomics and Meta‐Omics to Decrypt Microbiome Functionality	6
Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	6
MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications	6
Prediction of peptide hormones using an ensemble of machine learning and similarity‐based methods	6
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Standard abbreviations	6
A Proteomics Resource Investigating Fibrosis: Proof‐of‐Concept for Identifying Novel Drug Candidates	6
Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology	6
Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects	6
Tissue‐Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency	6
Proteomic Profiling of Myofiber Repair Annexins and Their Role in Duchenne Muscular Dystrophy	6
Front Cover	6
See the Unseen: Rapid, Multiparametric Single‐Particle Analysis of Extracellular Vesicles With Nano‐Flow Cytometry	6
AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures	6
Issue Information: Proteomics 24'25	6
Contents: Proteomics 2'23	5
Proteomics Insights Into Lysosome Biogenesis and Maturation	5
Multi‐Omics and Extracellular Vesicles	5
Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt‐Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica)	5
Front Cover	5
Identification of proteoforms by top‐down proteomics using two‐dimensional low/low pH reversed‐phase liquid chromatography‐mass spectrometry	5
Protein‐protein interaction networks as miners of biological discovery	5
Issue Information: Proteomics 2–3'26	5
Front Cover	5
Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases‐specific biomarkers from blood serum	5
Editorial Board: Proteomics 15'23	5
A crustacean neuropeptide spectral library for data‐independent acquisition (DIA) mass spectrometry applications	5