Proteomics

Article	Citations
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LC‐MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain‐Tetanus Toxoid Conjugate Vaccine Against SARS‐CoV‐2	53
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	52
Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	51
Front Cover	49
Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three‐dimensional culture	45
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation	42
Standard abbreviations	42
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	40
Front Cover	40
Editorial Board: Proteomics 10'22	39
Contents: Proteomics 9'22	35
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	35
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	35
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	33
Eye proteome of Drosophila melanogaster	32
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	32
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	31
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	30
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	30
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	29
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	28

SIMPLEX Enriches Hydrophobic and Lipidated Proteins in Membrane Proteomics Experiments	27
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	26
Omics insights into the responses to dietary selenium	25
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis inOreochromis mossambicus	25
Review of predicting protein stability changes upon variations	24
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	24
Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	24
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	24
Standard abbreviations	24
Editorial Board: Proteomics 21–22'23	23
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	23
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	22
Contents: Proteomics 5'24	21
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	19
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs	19
Editorial Board: Proteomics 11–12'22	19
Standard abbreviations	19
Editorial Board: Proteomics 8'22	19
Front Cover	18
Front Cover	18
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	17
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Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	17
Analyzing domain features of small proteins using a machine‐learning method	17
Contents: Proteomics 19–20'22	17
Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	17
Standard abbreviations	16
In‐silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases	16
Front Cover	16
Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development	16
An antibody‐free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis	16
Standard abbreviations	15
Front Cover	15
Universal and cross‐cancer prognostic biomarkers for predicting survival risk of cancer patients from expression profile of apoptotic pathway genes	15
Proteomic changes associated with the development of açaí (Euterpe oleracea Mart.) seeds	15
Front Cover	15
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	15
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	15
Global profiling of protein lactylation in Caenorhabditis elegans	14
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	14
Standard abbreviations	13
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	13
Standard abbreviations	13
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	13
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	13
Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry	13
Front Cover	13
Standard abbreviations	13
Editorial Board: Proteomics 5'24	13
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Passages in culture and stimulation conditions influence protein expression of primary fibroblasts	12
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	12
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Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	12
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Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin	12
Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	12
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	12
Standard abbreviations	12
Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma	11
iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	11
Contents: Proteomics 11–12'22	11
Contents: Proteomics 13–14'23	11
Contents: Proteomics 7'25	11
Contents: Proteomics 9'23	11
Metaproteomic Analysis to Assess the Impact of Storage Media on Human Gut Microbiome in Fecal Samples	10
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Standard abbreviations	10
The utility of proteases in proteomics, from sequence profiling to structure and function analysis	10
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	10
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	10
Editorial Board: Proteomics 19–20'22	10
Front Cover	10
Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	10
Front Cover	10
Front Cover	10
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	10
Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	10
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	10
Standard abbreviations	10
Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	10
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	10
The cuticle proteome of a planktonic crustacean	10
A peptidoform based proteomic strategy for studying functions of post‐translational modifications	10
Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	10
Immune capture and protein profiling of small extracellular vesicles from human plasma	10
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	10
Contents: Proteomics 15–16'22	10
Data‐Driven Proteomics for Post‐Translational Modification Discovery	9
Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients	9
Targeted Quantitation of Phosphotyrosine‐Containing Proteins in T‐Cell Receptor Signaling Using a SureQuant‐Based Mass Spectrometry Approach	9
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	9
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	9
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	9
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	9
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	9
A dataset resource for clinically associated phosphosites in hepatocellular carcinoma	9
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	9
Issue Information: Proteomics 14'25	9
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	9
Contents: Proteomics 17–18'21	9
Characterization of HLA‐A*33:03 epitopes via immunoprecipitation and LC‐MS/MS	9
Standard abbreviations	9
A Survey of Annotated smORF‐Encoded Polypeptides in Bacteria Interacting With Eukaryotic Hosts	9
Immunoproteome profiling of Listeria monocytogenes under mild acid and salt stress conditions	9
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics	9
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	9
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	9
Contents: Proteomics 17'24	9
Contents: Proteomics 8'24	9
Front Cover	9
Computational systems approach towards phosphoproteomics and their downstream regulation	8
Microproteins—Discovery, structure, and function	8
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	8
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	8
Editorial Board: Proteomics 8'24	8
Back Cover: Protein‐enabled detection of ibuprofen and sulfamethoxazole using solid‐state nanopores	8
Front Cover	8
Towards deciphering glioblastoma intra‐tumoral heterogeneity: The importance of integrating multidimensional models	8
Editorial Board: Proteomics 20'21	8
Computational tools for inferring transcription factor activity	8
Standard abbreviations	8
Proteome Analysis of Corynebacterium diphtheriae–Macrophage Interaction	8
Standard abbreviations	8
Editorial Board: Proteomics 9'22	8
A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	8
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Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	8
Standard abbreviations	8

Front Cover	8
Front Cover	8
Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	8
Contents: Proteomics 19'24	7
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	7
Improving SWATH‐MS analysis by deep‐learning	7
Contents: Proteomics 8'25	7
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	7
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DREAMweb: An online tool for graph‐based modeling of NMR protein structure	7
Transforming peptide hormone prediction: The role of AI in modern proteomics	7
Molecular methods to study protein trafficking between organs	7
Potential of deep representative learning features to interpret the sequence information in proteomics	7
Contents: Proteomics 23–24'24	7
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	7
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	7
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	7
Standard abbreviations	7
Automation of single‐cell proteomic sample preparation	7
Proteoform Identification Using Multiplexed Top‐Down Mass Spectra	7
Editorial Board: Proteomics 7'24	7
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	7
Editorial Board: Proteomics 5–6'22	7
Editorial Board: Proteomics 7–8'23	7
Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens	6
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Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	6
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Standard abbreviations	6
From Discovery to Implementation: Bringing Proteomics to the Clinic	6
Editorial Board: Proteomics 17'24	6
Issue Information: Proteomics 15'25	6
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Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	6
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	6
Challenges in computational discovery of bioactive peptides in ’omics data	6
Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	6
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Genetic and epigenetic control of the plant metabolome	6
Quantitative Top–Down Proteomics Reveals Significant Differences in Histone Proteoforms Between Metastatic and Nonmetastatic Colorectal Cancer Cells	6
Front Cover	6
Contents: Proteomics 18'24	6
What proteomics has taught us about honey bee (Apis mellifera) health and disease	6
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	6
Human peripheral blood mononuclear cells: A review of recent proteomic applications	6
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	6
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Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	6
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Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	6
Spectral entropy as a measure of the metaproteome complexity	6
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An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus	6
Omics and systems view of innate immune pathways	6
Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics	6
Novel histone modifications in microglia derived from a mouse model of chronic pain	5
Editorial Board: Proteomics 14'24	5
Editorial Board: Proteomics 15'24	5
Editorial Board: Proteomics 20'24	5
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	5
Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients	5
Contents: Proteomics 20'24	5
Standard abbreviations	5
Optimizing the PROTREC network‐based missing protein prediction algorithm	5
AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures	5
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	5
Contents: Proteomics 16'24	5
Charge site manipulation to enhance top‐down fragmentation efficiency	5
Metaproteomics and Meta‐Omics to Decrypt Microbiome Functionality	5
Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects	5
MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications	5
Standard abbreviations	5
Standard abbreviations	5
Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	5
An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources	5
Tissue‐Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency	5
Prediction of peptide hormones using an ensemble of machine learning and similarity‐based methods	5
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Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	5
Contents: Proteomics 11'23	5
Editorial Board: Proteomics 3–4'23	5
Editorial Board: Proteomics 15'23	4
Front Cover	4
Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells	4
Identification of proteoforms by top‐down proteomics using two‐dimensional low/low pH reversed‐phase liquid chromatography‐mass spectrometry	4
Contents: Proteomics 2'23	4
TopDownApp: An open and modular platform for analysis and visualisation of top‐down proteomics data	4
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Front Cover	4
Front Cover	4
A crustacean neuropeptide spectral library for data‐independent acquisition (DIA) mass spectrometry applications	4
Secretome analysis of human schwann cells derived from malignant peripheral nerve sheath tumor	4