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	56
Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three‐dimensional culture	51
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation	51
Standard abbreviations	50
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	47
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	41
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	41
Front Cover	40
Editorial Board: Proteomics 10'22	40
Contents: Proteomics 9'22	39
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	38
Eye proteome of Drosophila melanogaster	35
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	33
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	33
Establishment of a Protocol for CE‐MS Based Peptidome Analysis of Human Saliva	32
Front Cover	32
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	32
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	29
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	27
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	27
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	26

Review of predicting protein stability changes upon variations	26
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	26
Direct‐MS analysis of antibody‐antigen complexes	26
Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	24
Editorial Board: Proteomics 21–22'23	24
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	24
Standard abbreviations	24
Contents: Proteomics 5'24	23
RETRACTION: Evaluation of Proteome Dynamics: Implications for Statistical Confidence in Mass Spectrometric Determination	23
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	23
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs	23
Filling the gaps in peptide maps with a platform assay for top‐down characterization of purified protein samples	23
Standard abbreviations	22
Editorial Board: Proteomics 8'22	21
Editorial Board: Proteomics 11–12'22	20
Front Cover	19
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls	19
Contents: Proteomics 19–20'22	19
Front Cover	19
Analyzing domain features of small proteins using a machine‐learning method	18
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis inOreochromis mossambicus	18
Identification of the native Torpedo californica nicotinic acetylcholine receptor's glycan composition after a multi‐step sequential purification method using MALDI‐ToF MS	18
Omics insights into the responses to dietary selenium	17
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	17
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Quantitative proteomics reveals PPAR signaling pathway regulates the cardiomyocyte activity of neonatal mouse heart	17
Proteomic profiling of paired human liver homogenate and tissue derived extracellular vesicles	16
An antibody‐free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis	16
Proteomic changes associated with the development of açaí (Euterpe oleracea Mart.) seeds	16
Standard abbreviations	16
Passages in culture and stimulation conditions influence protein expression of primary fibroblasts	16
Front Cover	16
Front Cover	16
In‐silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases	16
Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development	16
Standard abbreviations	15
Standard abbreviations	15
Global profiling of protein lactylation in Caenorhabditis elegans	15
Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells	15
Pharmaco‐phosphoproteomic analysis of cancer‐associated KIT mutations D816V and V560G	15
Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cell lines	15
Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing	14
Universal and cross‐cancer prognostic biomarkers for predicting survival risk of cancer patients from expression profile of apoptotic pathway genes	14
Editorial Board: Proteomics 5'24	14
Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway	13
Front Cover	13
Standard abbreviations	13
Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry	13
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase‐9 inhibition in chondrogenic cells	13
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	13

Comparative Proteomics of Salinity Stress Responses in Fish and Aquatic Invertebrates	13
Front Cover	13
Standard abbreviations	13
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Immune capture and protein profiling of small extracellular vesicles from human plasma	12
Contents: Proteomics 9'23	12
Contents: Proteomics 13–14'23	12
Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	12
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iDVEIP: A computer‐aided approach for the prediction of viral entry inhibitory peptides	12
Front Cover	12
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	11
Insights into the vision of the hadal snailfish Pseudoliparis swirei through proteomic analysis of the eye	11
Front Cover	11
Triple extraction method enables high quality mass spectrometry‐based proteomics and phospho‐proteomics for eventual multi‐omics integration studies	11
Quantitative proteome remodeling characterization of two human reference pluripotent stem cell lines during neurogenesis and cardiomyogenesis	11
Contents: Proteomics 7'25	11
Voltage‐activated complexation of α‐synuclein with three diverse β‐barrel channels: VDAC, MspA, and α‐hemolysin	11
Standard abbreviations	11
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	11
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	11
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	10
Editorial Board: Proteomics 15'21	10
Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma	10
A peptidoform based proteomic strategy for studying functions of post‐translational modifications	10
VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins	10
Issue Information: Proteomics 14'25	10
Contents: Proteomics 17'24	10
Contents: Proteomics 17–18'21	10
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	10
Standard abbreviations	10
Decoding Microbial Plastic Colonisation: Multi‐Omic Insights Into the Fast‐Evolving Dynamics of Early‐Stage Biofilms	10
Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	10
Characterization of HLA‐A*33:03 epitopes via immunoprecipitation and LC‐MS/MS	10
A dataset resource for clinically associated phosphosites in hepatocellular carcinoma	10
The cuticle proteome of a planktonic crustacean	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
Contents: Proteomics 11–12'22	10
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Extracellular vesicle proteins as breast cancer biomarkers: Mass spectrometry‐based analysis	9
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	9
Contents: Proteomics 15–16'22	9
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	9
Front Cover	9
Monitoring Changes in the Levels of Newly Synthesized Proteins in Response to Nutlin‐3 Treatment	9
Proteome‐wide abundance profiling of yeast deletion strains for GET pathway members using sample multiplexing	9
Data‐Driven Proteomics for Post‐Translational Modification Discovery	9
Front Cover	9
Standard abbreviations	9
Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients	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
Top‐down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms	9
Editorial Board: Proteomics 19–20'22	9
Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin	9
Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential	9
Contents: Proteomics 8'24	9
Towards deciphering glioblastoma intra‐tumoral heterogeneity: The importance of integrating multidimensional models	8
Computational systems approach towards phosphoproteomics and their downstream regulation	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
Review and Practical Guide for Getting Started With Single‐Cell Proteomics	8
Automation of single‐cell proteomic sample preparation	8
Editorial Board: Proteomics 9'22	8
Front Cover	8
Front Cover	8
Standard abbreviations	8
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	8
GeLC‐FAIMS‐MS workflow for in‐depth middle‐down proteomics	8
One amino acid drives the lipid droplet targeting sequence of a new noncoding RNA‐encoded protein to mitochondrion	8
Editorial Board: Proteomics 20'21	8
Proteome Analysis of Corynebacterium diphtheriae–Macrophage Interaction	8
Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	8
Back Cover: Protein‐enabled detection of ibuprofen and sulfamethoxazole using solid‐state nanopores	8
Standard abbreviations	8
Computational tools for inferring transcription factor activity	8
Assessing the precision of a detergent‐assisted cartridge precipitation workflow for non‐targeted quantitative proteomics	8

A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin	8
Contents: Proteomics 8'25	8
Standard abbreviations	8
Front Cover	8
Toward proteome‐wide exploration of proteins in dried blood spots using liquid chromatography‐coupled mass spectrometry	8
Single‐molecule, hybridization‐based strategies for short nucleic acids detection and recognition with nanopores	8
Potential of deep representative learning features to interpret the sequence information in proteomics	8
Editorial Board: Proteomics 8'24	8
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	7
Editorial Board: Proteomics 7–8'23	7
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	7
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	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
Contents: Proteomics 19'24	7
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	7
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	7
Specialised skin cancer spectral library for use in data‐independent mass spectrometry	7
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	7
Improving SWATH‐MS analysis by deep‐learning	7
Molecular methods to study protein trafficking between organs	7
DREAMweb: An online tool for graph‐based modeling of NMR protein structure	7
Editorial Board: Proteomics 5–6'22	7
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	7
Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics	7
Transforming peptide hormone prediction: The role of AI in modern proteomics	7
Contents: Proteomics 23–24'24	7
Microproteins—Discovery, structure, and function	7
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Human peripheral blood mononuclear cells: A review of recent proteomic applications	7
Standard abbreviations	7
Editorial Board: Proteomics 17'24	6
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Editorial Board: Proteomics 7'24	6
From Discovery to Implementation: Bringing Proteomics to the Clinic	6
Contents: Proteomics 16'21	6
What proteomics has taught us about honey bee (Apis mellifera) health and disease	6
Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)	6
Challenges in computational discovery of bioactive peptides in ’omics data	6
Contents: Proteomics 18'24	6
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Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	6
Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens	6
Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics	6
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Standard abbreviations	6
Spectral entropy as a measure of the metaproteome complexity	6
Front Cover	6
An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus	6
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	6
Proteoform Identification Using Multiplexed Top‐Down Mass Spectra	6
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Omics and systems view of innate immune pathways	6
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
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	6
Optimizing the PROTREC network‐based missing protein prediction algorithm	5
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies	5
An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources	5
Standard abbreviations	5
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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	5
Novel histone modifications in microglia derived from a mouse model of chronic pain	5
Contents: Proteomics 20'21	5
Secretome analysis of human schwann cells derived from malignant peripheral nerve sheath tumor	5
Identification of a rare [Gγ(Aγδβ)0] ‐thalassemia using tandem mass spectrometry	5
Contents: Proteomics 16'24	5
Standard abbreviations	5
Prediction of peptide hormones using an ensemble of machine learning and similarity‐based methods	5
Contents: Proteomics 20'24	5
Standard abbreviations	5
Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects	5
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AlphaCutter: Efficient removal of non‐globular regions from predicted protein structures	5
Identification of proteoforms by top‐down proteomics using two‐dimensional low/low pH reversed‐phase liquid chromatography‐mass spectrometry	5
Editorial Board: Proteomics 20'24	5
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Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	5
Association of Urinary Collagen Type III Degradation Product With Kidney Function and Fibrosis in Chronic Kidney Disease Patients	5
Standard abbreviations	5
Contents: Proteomics 11'23	5
Editorial Board: Proteomics 14'24	5
Editorial Board: Proteomics 3–4'23	5
Front Cover: Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	5
Editorial Board: Proteomics 15'24	5
MassSpecPreppy—An end‐to‐end solution for automated protein concentration determination and flexible sample digestion for proteomics applications	5
Tissue‐Specific Regulation of Fatty Acid Metabolism in a Mouse Model of Isolated Complex I Deficiency	5
Editorial Board: Proteomics 19'21	5
Charge site manipulation to enhance top‐down fragmentation efficiency	5
Proteome profiling of vascular sap regarding Eucalyptus grandis, Eucalyptus urophylla, and Eucalyptus camaldulensis	5