Proteomics

Article	Citations
	116
	106
	81
Standard abbreviations	71
	65
Front Cover	65
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	62
Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	58
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	55
	55
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	48
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	44
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	43
Eye proteome of Drosophila melanogaster	42
Proteomic Profiling of Primary Hippocampal Neurons Reveals Noncanonical GFAP Expression and Metabolic Adaptations in Glia‐Free Culture	41
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	41
LC‐MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain‐Tetanus Toxoid Conjugate Vaccine Against SARS‐CoV‐2	38
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	38
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	37
SIMPLEX Enriches Hydrophobic and Lipidated Proteins in Membrane Proteomics Experiments	37
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	37
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	35
Single Extracellular Vesicles and Omics	33
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	33
Omics insights into the responses to dietary selenium	32

Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus	32
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	30
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	30
	30
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	29
Front Cover	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	26
Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	25
Standard abbreviations	25
Contents: Proteomics 5'24	25
Front Cover	24
Editorial Board: Proteomics 21–22'23	24
Editorial Board: Proteomics 11–12'22	24
Analyzing domain features of small proteins using a machine‐learning method	24
Urinary Peptidomic Profiling In Post‐Acute Sequelae of SARS‐CoV‐2 Infection: A Case‐Control Study	23
Review of predicting protein stability changes upon variations	23
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	22
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	22
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	22
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	22
Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	21
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	21
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	21
Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles	21
Standard abbreviations	20
Global profiling of protein lactylation in Caenorhabditis elegans	20
	20
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	20
	19
Standard abbreviations	19
Front Cover	19
Front Cover	19
Standard abbreviations	19
Standard abbreviations	19
Editorial Board: Proteomics 5'24	19
Issue Information: Proteomics 23'25	18
Plasma Proteomics Across Three Generations of Mass Spectrometry Instruments: Lessons for Biofluid Method Optimisation	18
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	18
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	18
Standard abbreviations	17
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	17
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	17
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	17
Proteomic changes associated with the development of açaí ( Euterpe oleracea Mart.) seeds	17
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	17
Proteomics Advances in Immunology and Infection Research	17
Structural Syntax of the Vaccinia Virus Entry‐Fusion Complex	17
	16
Contents: Proteomics 11–12'22	16

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

Proteomic Profiling Using a Proximity Extension Assay Panel on Serum Samples Stored at −25°C Over Several Decades	10
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	10
Editorial Board: Proteomics 7'24	10
Microproteins—Discovery, structure, and function	10
Optimization of Microfluidic Geometry for Extracellular Vesicle Capture Using an Automated Parallel Pattern Search	10
Contents: Proteomics 19'24	9
DREAMweb: An online tool for graph‐based modeling of NMR protein structure	9
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	9
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	9
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	9
Imaging Mass Spectrometry‐Based Assessment of ER, PR, and HER2 Protein Expression in Breast Cancer	9
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	9
Transforming peptide hormone prediction: The role of AI in modern proteomics	9
Contents: Proteomics 23–24'24	9
	9
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	9
Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species	9
Editorial Board: Proteomics 7–8'23	9
Standard abbreviations	9
QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry‐Based Proteomics Datasets	9
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	9
Proteoform Identification Using Multiplexed Top‐Down Mass Spectra	9
	8
	8
Omics and systems view of innate immune pathways	8
Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	8
Unspecific Molecular Adsorption (UMA) Sample Preparation Method for Bottom‐up and Whole Protein Analysis: The Foundation	8
	8
Standard abbreviations	8
Issue Information: Proteomics 15'25	8
Editorial Board: Proteomics 17'24	8
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	8
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	8
What proteomics has taught us about honey bee ( Apis mellifera ) health and disease	8
Genetic and epigenetic control of the plant metabolome	8
Spectral entropy as a measure of the metaproteome complexity	8
Hypoxia Modulates Nanovesicle Phenotype and Angiogenic Function From Human Pluripotent Stem Cells	8
	8
Contents: Proteomics 18'24	8
Front Cover	8
	8
Proteomic Characterization of AS1411 Reveals ATP6AP1 as a Mediator of Triple‐Negative Breast Cancer Progression	8
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	8
Challenges in computational discovery of bioactive peptides in ’omics data	8
Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	8
From Discovery to Implementation: Bringing Proteomics to the Clinic	8
	8
Editorial Board: Proteomics 14'24	7
Standard abbreviations	7
Standard abbreviations	7
Metaproteomics and Meta‐Omics to Decrypt Microbiome Functionality	7
Contents: Proteomics 11'23	7
Editorial Board: Proteomics 15'24	7
Optimizing the PROTREC network‐based missing protein prediction algorithm	7
	7
	7
Editorial Board: Proteomics 3–4'23	7
Contents: Proteomics 20'24	7
Contents: Proteomics 16'24	7
Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	7
	7
Issue Information: Proteomics 24'25	7
	7
Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	7
Standard abbreviations	7
Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt‐Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica)	6
Charge site manipulation to enhance top‐down fragmentation efficiency	6
MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications	6
An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources	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
Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology	6
Issue Information: Proteomics 2–3'26	6
Microglia Display Altered Spatial Morphology and Proteome After Stroke	6
Isolation and Characterization of Extracellular Vesicles From Ascochyta rabiei , a Necrotrophic Fungal Chickpea Pathogen	6
	6
AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures	6
Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients	6
Proteomic Profiling of Myofiber Repair Annexins and Their Role in Duchenne Muscular Dystrophy	6
Multi‐Omics and Extracellular Vesicles	6
	6
Editorial Board: Proteomics 6'23	6
See the Unseen: Rapid, Multiparametric Single‐Particle Analysis of Extracellular Vesicles With Nano‐Flow Cytometry	6
Prediction of peptide hormones using an ensemble of machine learning and similarity‐based methods	6
A Proteomics Resource Investigating Fibrosis: Proof‐of‐Concept for Identifying Novel Drug Candidates	6
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	6
Identification of proteoforms by top‐down proteomics using two‐dimensional low/low pH reversed‐phase liquid chromatography‐mass spectrometry	6
Front Cover	5
Editorial Board: Proteomics 15'23	5
Advancing Understanding of the Protein Composition of Human Seminal Extracellular Vesicles	5
Prediction of Lung Adenocarcinoma Driver Genes Through Protein–Protein Interaction Networks Utilizing GenePlexus	5
Contents: Proteomics 2'23	5
	5
Parallel Analysis of Acidic and Basic Proteoforms in Cell Lysates via Native Cation and Anion Exchange Chromatography—Native Mass Spectrometry	5
Front Cover	5