Proteomics

Article	Citations
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Standard abbreviations	79
Front Cover	72
	68
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	61
Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	59
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Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	50
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	50
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	48
LC‐MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain‐Tetanus Toxoid Conjugate Vaccine Against SARS‐CoV‐2	46
Eye proteome of Drosophila melanogaster	46
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	46
SIMPLEX Enriches Hydrophobic and Lipidated Proteins in Membrane Proteomics Experiments	42
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	39
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	39
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	39
Single Extracellular Vesicles and Omics	38
Proteomic Profiling of Primary Hippocampal Neurons Reveals Noncanonical GFAP Expression and Metabolic Adaptations in Glia‐Free Culture	35
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	33
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	32
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Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	32

Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	31
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	31
Front Cover	31
Contents: Proteomics 19–20'22	27
Standard abbreviations	27
Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	26
Contents: Proteomics 5'24	25
Analyzing domain features of small proteins using a machine‐learning method	25
Editorial Board: Proteomics 21–22'23	25
Review of predicting protein stability changes upon variations	24
Front Cover	24
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	23
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	23
Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles	23
Urinary Peptidomic Profiling In Post‐Acute Sequelae of SARS‐CoV‐2 Infection: A Case‐Control Study	23
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	23
Omics insights into the responses to dietary selenium	23
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	23
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	22
Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	22
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus	22
Global profiling of protein lactylation in Caenorhabditis elegans	21
Exoproteome Remodeling by the BraI/R Quorum Sensing Circuit and Interspecies Competition in Paraburkholderia	21
Plasma Proteomics Across Three Generations of Mass Spectrometry Instruments: Lessons for Biofluid Method Optimisation	21
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	20
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Standard abbreviations	20
Standard abbreviations	20
Editorial Board: Proteomics 5'24	20
Standard abbreviations	20
Standard abbreviations	20
Front Cover	20
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	20
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	19
Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	19
Issue Information: Proteomics 23'25	19
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	18
Structural Syntax of the Vaccinia Virus Entry‐Fusion Complex	18
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	17
Standard abbreviations	17
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	17
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	17
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	17
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	17
Front Cover	16
Metaproteomic Analysis to Assess the Impact of Storage Media on Human Gut Microbiome in Fecal Samples	16
Contents: Proteomics 13–14'23	16
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Front Cover	16

Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	16
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SLB‐msSIM: A Spectral Library‐Based Multiplex Segmented SIM Platform for Single‐Cell Proteomic Analysis	16
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	16
Standard abbreviations	16
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	15
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Contents: Proteomics 7'25	15
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	15
Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	15
Contents: Proteomics 9'23	15
Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput	15
Stage‐Resolved Proteomic and Structural Insights Into Apocarotenoid Biosynthesis During Saffron ( Crocus sativus ) Flower Development	15
Immune capture and protein profiling of small extracellular vesicles from human plasma	14
Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma	14
Contents: Proteomics 15–16'22	14
Data‐Driven Proteomics for Post‐Translational Modification Discovery	14
Contents: Proteomics 8'24	14
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	14
Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	14
Proteomics Advances in Immunology and Infection Research	14
Front Cover	14
The cuticle proteome of a planktonic crustacean	14
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	14
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	14
The utility of proteases in proteomics, from sequence profiling to structure and function analysis	14
Standard abbreviations	14
Front Cover	14
Contents: Proteomics 17'24	14
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	14
Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients	13
A Survey of Annotated smORF‐Encoded Polypeptides in Bacteria Interacting With Eukaryotic Hosts	13
Editorial Board: Proteomics 19–20'22	13
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	13
Standard abbreviations	13
Targeted Quantitation of Phosphotyrosine‐Containing Proteins in T‐Cell Receptor Signaling Using a SureQuant‐Based Mass Spectrometry Approach	13
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	12
Immunoproteome profiling of Listeria monocytogenes under mild acid and salt stress conditions	12
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	12
Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	12
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	12
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics	12
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	12
Progress of Deep Learning Prediction of CD8+ T‐Cell Epitopes	12
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	12
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	12
Issue Information: Proteomics 14'25	12
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	12
Data Processing and Analysis in Positional Proteomics	12
Assessing Discrepancies in miRNA Profiles of Mouse Blood‐Derived Extracellular Vesicles: A Systematic Review of Sequencing Data	12
Standard abbreviations	12
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	11
Proteomic Profiling Using a Proximity Extension Assay Panel on Serum Samples Stored at −25°C Over Several Decades	11
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	11
Standard abbreviations	11
Front Cover	11
Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	11
Optimization of Microfluidic Geometry for Extracellular Vesicle Capture Using an Automated Parallel Pattern Search	11
Quantitative Proteomics Reveals the Adaptive Mechanisms of Aeromonas hydrophila Under Cobalt Stress	11
Molecular methods to study protein trafficking between organs	11
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Contents: Proteomics 8'25	11
Standard abbreviations	11
Improving SWATH‐MS analysis by deep‐learning	11
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	11
Comparative Analysis of Proteoform Clean‐Up Methods for In‐Depth Top‐Down Proteomics	11
Editorial Board: Proteomics 8'24	11
Towards deciphering glioblastoma intra‐tumoral heterogeneity: The importance of integrating multidimensional models	11
Front Cover	11
Front Cover	11
Standard abbreviations	10
Proteome Analysis of Corynebacterium diphtheriae –Macrophage Interaction	10
Editorial Board: Proteomics 7'24	10
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	10
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Computational tools for inferring transcription factor activity	10
A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	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	10
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	10

Microproteins—Discovery, structure, and function	10
Issue Information: Proteomics 19'25	10
Contents: Proteomics 19'24	10
Transforming peptide hormone prediction: The role of AI in modern proteomics	10
Optimized Sample Handling Minimizes Peptide Adsorption to Plastics to Enable High Sensitivity Evosep Based Chemical Proteomics	9
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	9
Imaging Mass Spectrometry‐Based Assessment of ER, PR, and HER2 Protein Expression in Breast Cancer	9
QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry‐Based Proteomics Datasets	9
iMPI: An Integrative Database for MicroProteins Encoded by Intron Retention in Tumors	9
Issue Information: Proteomics 7'26	9
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	9
Contents: Proteomics 23–24'24	9
Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species	9
Proteoform Identification Using Multiplexed Top‐Down Mass Spectra	9
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	9
Hypoxia Modulates Nanovesicle Phenotype and Angiogenic Function From Human Pluripotent Stem Cells	9
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	9
Editorial Board: Proteomics 7–8'23	9
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Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	9
Issue Information: Proteomics 15'25	8
Standard abbreviations	8
From Discovery to Implementation: Bringing Proteomics to the Clinic	8
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Editorial Board: Proteomics 17'24	8
Spectral entropy as a measure of the metaproteome complexity	8
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Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	8
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Contents: Proteomics 18'24	8
Unspecific Molecular Adsorption (UMA) Sample Preparation Method for Bottom‐up and Whole Protein Analysis: The Foundation	8
Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	8
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	8
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Challenges in computational discovery of bioactive peptides in ’omics data	8
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	8
Front Cover	8
Omics and systems view of innate immune pathways	8
Proteomic Characterization of AS1411 Reveals ATP6AP1 as a Mediator of Triple‐Negative Breast Cancer Progression	8
Issue Information: Proteomics 24'25	7
Genetic and epigenetic control of the plant metabolome	7
MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications	7
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Standard abbreviations	7
Editorial Board: Proteomics 3–4'23	7
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Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	7
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Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	7
Standard abbreviations	7
Contents: Proteomics 16'24	7
Optimizing the PROTREC network‐based missing protein prediction algorithm	7
Standard abbreviations	7
What proteomics has taught us about honey bee ( Apis mellifera ) health and disease	7
Editorial Board: Proteomics 14'24	7
Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	7
Contents: Proteomics 11'23	7
Editorial Board: Proteomics 15'24	7
Proteome‐Scale Mining of Metal‐Associated Proteins of Monkeypox Virus	6
Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology	6
Proteomic Profiling of Myofiber Repair Annexins and Their Role in Duchenne Muscular Dystrophy	6
Charge site manipulation to enhance top‐down fragmentation efficiency	6
An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources	6
Prediction of peptide hormones using an ensemble of machine learning and similarity‐based methods	6
Tissue‐Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency	6
Metaproteomics and Meta‐Omics to Decrypt Microbiome Functionality	6
A Proteomics Resource Investigating Fibrosis: Proof‐of‐Concept for Identifying Novel Drug Candidates	6
See the Unseen: Rapid, Multiparametric Single‐Particle Analysis of Extracellular Vesicles With Nano‐Flow Cytometry	6
Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt‐Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica)	6
Isolation and Characterization of Extracellular Vesicles From Ascochyta rabiei , a Necrotrophic Fungal Chickpea Pathogen	6
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	6
Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects	6
Contents: Proteomics 20'24	6
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Identification of proteoforms by top‐down proteomics using two‐dimensional low/low pH reversed‐phase liquid chromatography‐mass spectrometry	6
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Sensitive Profiling of Mouse Liver Membrane Proteome Dysregulation Following a High‐Fat and Alcohol Diet Treatment	6
Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients	6
AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures	6