Proteomics

Article	Citations
Proteomic profiling of ovarian clear cell carcinomas identifies prognostic biomarkers for chemotherapy	143
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved	70
BLI‐MS: Combining biolayer interferometry and mass spectrometry	66
Editorial Board: Proteomics 11–12'21	60
Front Cover	56
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Front Cover	47
Standard abbreviations	43
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Recent Advances in Labeling‐Based Quantitative Glycomics: From High‐Throughput Quantification to Structural Elucidation	38
Computational Methods for Data Integration and Imputation of Missing Values in Omics Datasets	36
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification	36
Contents: Proteomics 4'25	34
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	33
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data	33
DREAMweb: An online tool for graph‐based modeling of NMR protein structure	32
Front Cover	32
Contents: Proteomics 19'24	32
Standard abbreviations	32
Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment	31
(Prote)omics for Superior Management of Kidney and Cardiovascular Disease—A Thought‐Provoking Impulse From Nephrology	31
Standard abbreviations	30
Characterization of diverse lysine acylations in Bacillus thuringiensis: Substrate profiling and functional exploration	29
Front Cover	27
Contents: Proteomics 9'22	27

Standard abbreviations	27
Editorial Board: Proteomics 10'22	23
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Whole lung proteome of an acute epithelial injury mouse model in comparison to spatially resolved proteomes	21
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Contents: Proteomics 10'23	20
Editorial Board: Proteomics 3'25	20
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Front Cover	20
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RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination	20
Identification of multiple proteins whose interaction with mannitol dehydrogenase is induced by salicylic acid: Implications for unconventional secretion	20
Transforming peptide hormone prediction: The role of AI in modern proteomics	20
Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three‐dimensional culture	19
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Spectral averaging with outlier rejection algorithms to increase identifications in top‐down proteomics	18
Front Cover	17
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin	16
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	16
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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	16
Editorial Board: Proteomics 5–6'22	16
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation	15
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies	15
Proteomics analysis reveals the correlation of programmed ROS‐autophagy loop and dysregulated G1/S checkpoint with imatinib resistance in chronic myeloid leukemia cells	15
Multi‐omics analysis reveals expression complexity and functional diversity of mouse kinome	14
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Proteomic and phosphoproteomic landscape of salivary extracellular vesicles to assess OSCC therapeutical outcomes	14
Standard abbreviations	14
Top‐down proteomics and proteoforms – special issue	13
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	13
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Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells	13
Peptide probes containing a non‐hydrolyzable phosphotyrosine‐mimetic residue for enrichment of protein tyrosine phosphatases	12
On the excessive use of coefficient of variation as a metric of quantitation quality in proteomics	12
Computational approaches to identify sites of phosphorylation	12
Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT‐based multiplexing	12
Contents: Proteomics 15'21	12
Editorial Board: Proteomics 17–18'21	12
Solvent‐induced proteome profiling for proteomic quantitation and target discovery of small molecular drugs	12
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	12
Contents: Proteomics 13–14'21	12
Integrated tandem affinity protein purification using the polyhistidine plus extra 4 amino acids (HiP4) tag system	12
Application of sample displacement batch chromatography for fractionation of proteoforms	12
Eye proteome of Drosophila melanogaster	11
Mechanism of action of pseudopteroxazole and pseudopterosin G: Diterpenes from marine origin	11
Sperm‐borne proteins improve rabbit cloning efficiency via regulating embryonic cleavage and epigenetics	11
Front Cover	11
Comprehensive insight on protein modification by V‐type agent: A chemical proteomic approach employing bioorthogonal reaction	11

Enrichment and fragmentation approaches for enhanced detection and characterization of endogenous glycosylated neuropeptides	11
Probing protein nanopores with poly(ethylene glycol)s	11
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Standard abbreviations	11
Contents: Proteomics 19'23	11
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Editorial Board: Proteomics 11'23	10
Editorial Board: Proteomics 21'22	10
Standard abbreviations	10
Contents: Proteomics 7–8'23	10
Front Cover	10
Standard abbreviations	10
Editorial Board: Proteomics 15–16'22	10
Editorial Board: Proteomics 7–8'23	10
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys	10
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi	9
Specialised skin cancer spectral library for use in data‐independent mass spectrometry	9
Structural biology: The transformational era	9
Editorial Board: Proteomics 23–24'23	9
Recent advances in demystifying O‐glycosylation in health and disease	9
Systematic analysis of the ubiquitome in mouse testis	9
Multi‐omic analyses and network biology in cardiovascular disease	9
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown	9
Effects of dopamine D2 receptor antagonists on retinal pigment epithelial/choroid complex metabolism in form‐deprived myopic guinea pigs	9
Standard abbreviations	9
Contents: Proteomics 5–6'25	9
HLA class II immunopeptidomics reveals that co‐inherited HLA‐allotypes within an extended haplotype can improve proteome coverage for immunosurveillance	9
Standard abbreviations	9
Editorial Board: Proteomics 7'24	9
Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics	8
Contents: Proteomics 23–24'24	8
Unveiling the molecular complexity of intestinal ischemia–reperfusion injury through omics technologies	8
Glycoblotting enables seamless and straightforward workflow for MALDI‐TOF/MS‐based sulphoglycomics of N‐ and O‐glycans	8
An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue	8
Proteomics special issue: Precision immunology and oncology	8
Standard abbreviations	8
Development of a Proteomic Workflow for the Identification of Heparan Sulphate Proteoglycan‐Binding Substrates of ADAM17	8
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study	8
Single‐cell proteomics by mass spectrometry: Advances and implications in cancer research	8
SWATH‐MS and MRM: Quantification of Ras‐related proteins in HIV‐1 infected and methamphetamine‐exposed human monocyte‐derived macrophages (hMDM)	8
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments	8
Combination of size‐exclusion chromatography and ion exchange adsorption for improving the proteomic analysis of plasma‐derived extracellular vesicles	8
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People with obesity exhibit losses in muscle proteostasis that are partly improved by exercise training	8
Investigation of the Urinary Peptidome to Unravel Collagen Degradation in Health and Kidney Disease	7
Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future	7
Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD	7
Comprehensive kinomic study via a chemical proteomic approach reveals kinome reprogramming in hepatocellular carcinoma tissues	7
Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore	7
Data acquisition approaches for single cell proteomics	7
Human peripheral blood mononuclear cells: A review of recent proteomic applications	7
Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study	7
Insights into the sulfur metabolism of Chlorobaculum tepidum by label‐free quantitative proteomics	7
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	7
Benchmarking accuracy and precision of intensity‐based absolute quantification of protein abundances in Saccharomyces cerevisiae	7
Direct‐MS analysis of antibody‐antigen complexes	6
Characterization of outer membrane vesicles released by clinical isolates of Neisseria gonorrhoeae	6
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	6
Recent advances in isobaric labeling and applications in quantitative proteomics	6
Cracking chromatin with proteomics: From chromatome to histone modifications	6
Editorial Board: Proteomics 16'21	6
An N‐glycopeptide MS/MS data analysis workflow leveraging two complementary glycoproteomic software tools for more confident identification and assignments	6
Omics insights into the responses to dietary selenium	6
A top‐down proteomic approach reveals a salivary protein profile able to classify Parkinson's disease with respect to Alzheimer's disease patients and to healthy controls	6
Advances in ionisation techniques for mass spectrometry‐based omics research	6
Proteomics‐driven identification of short open reading frame‐encoded peptides	6
State‐of‐the‐art computational methods to predict protein–protein interactions with high accuracy and coverage	6
Identification of Key Genes in Fetal Gut Development at Single‐Cell Level by Exploiting Machine Learning Techniques	6
Contents: Proteomics 8'22	6
Contents: Proteomics 16'21	6
Editorial Board: Proteomics 21–22'23	6
Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top‐down proteomics	6
Structure of prion β‐oligomers as determined by short‐distance crosslinking constraint‐guided discrete molecular dynamics simulations	6
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs	6
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation	6
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Deep phosphotyrosine characterisation of primary murine T cells using broad spectrum optimisation of selective triggering	6
Front Cover	6
Assessing the activation/inhibition of tyrosine kinase‐related pathways with a newly developed platform	6

Standard abbreviations	6
Parallel Analyses by Mass Spectrometry (MS) and Reverse Phase Protein Array (RPPA) Reveal Complementary Proteomic Profiles in Triple‐Negative Breast Cancer (TNBC) Patient Tissues and Cell Cultures	5
Direct identification of HLA‐presented CD8 T cell epitopes from transmitted founder HIV‐1 variants	5
Contents: Proteomics 16'23	5
Contents: Proteomics 21–22'23	5
Editorial Board: Proteomics 23‐24'22	5
Development and Validation of a Capillary Electrophoresis Coupled to Mass Spectrometry Pipeline for Comparable Assessment of the Plasma Peptidome	5
Editorial Board: Proteomics 7'22	5
Editorial Board: Proteomics 24–1'2	5
Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis inOreochromis mossambicus	5
Analyzing domain features of small proteins using a machine‐learning method	5
Identifying dynamical persistent biomarker structures for rare events using modern integrative machine learning approach	5
Characterization of Trivalently Crosslinked C‐Terminal Telopeptide of Type I Collagen (CTX) Species in Human Plasma and Serum Using High‐Resolution Mass Spectrometry	5
Database search engines and target database features impinge upon the identification of post‐translationally cis‐spliced peptides in HLA class I immunopeptidomes	5
Intratympanic steroid treatment can reduce ROS and immune response in human perilymph investigated by in‐depth proteome analysis	5
Contents: Proteomics 18'24	5
Global analysis of lysine acetylation in the brain cortex of K18‐hACE2 mice infected with SARS‐CoV‐2	5
Editorial Board: Proteomics 19'23	5
Front Cover	5
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles	5
Editorial Board: Proteomics 16'24	5
Pannexin‐1 channel regulates nuclear content packaging into apoptotic bodies and their size	5
Integrated changes in thermal stability and proteome abundance during altered nutrient states in Escherichia coli and human cells	5
Editorial Board: Proteomics 8'22	5
Front Cover	5
An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus	5
Analysis of small EV proteomes reveals unique functional protein networks regulated by VAP‐A	5
Quantitative proteomic analyses reveal the impact of nitrogen starvation on the proteome of the model diatom Phaeodactylum tricornutum	5
Spectral entropy as a measure of the metaproteome complexity	5
Contents: Proteomics 22'22	4
Contents: Proteomics 18'22	4
Editorial Board: Proteomics 11–12'22	4
Standard abbreviations	4
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Standard abbreviations	4
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Review of predicting protein stability changes upon variations	4
Large‐scale top‐down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes	4
Beyond the model organism—Mechanistic analysis of protein post‐translational modifications is ready for all challengers	4
Contents: Proteomics 7#x02013;8'21	4
Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice	4
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Front Cover	4
Contents: Proteomics 19–20'22	4
iTRAQ‐based proteomic analysis reveals proteins associated with cold stress response in two different populations of Manila clam (Ruditapes philippinarum)	4
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Skeletal muscle proteome expression differentiates severity of cancer cachexia in mice and identifies loss of fragile X mental retardation syndrome‐related protein 1	4
Front Cover	4
Front Cover	4
Changes in the astronaut serum proteome during prolonged spaceflight	4
What proteomics has taught us about honey bee (Apis mellifera) health and disease	4
Front Cover	4
Proteins and metabolites fingerprints of gestational diabetes mellitus forming protein–metabolite interactomes are its potential biomarkers	4
Standard abbreviations	4
Analytical comparison of absolute quantification strategies to investigate the insulin signaling pathway in fat cells	4
Multi‐omics analysis to characterize molecular adaptation of Entamoeba histolytica during serum stress	4
Editorial Board: Proteomics 9'23	4
Contents: Proteomics 11–12'21	4
Exact p‐value calculation for XCorr scoring of high‐resolution MS/MS data	4
Contents: Proteomics 19'21	4
Standard abbreviations	4
Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes	4
CD99 and polymeric immunoglobulin receptor peptides deregulation in critical COVID‐19: A potential link to molecular pathophysiology?	4
From flesh to bones: Multi‐omics approaches in forensic science	4
Proteomic analyses reveal that immune integrins are major targets for regulation by Membrane‐Associated Ring‐CH (MARCH) proteins MARCH2, 3, 4 and 9	4
Contents: Proteomics 5'24	4
Editorial Board: Proteomics 5'23	4
Analysis of N‐ and O‐linked site‐specific glycosylation by ion mobility mass spectrometry: State of the art and future directions	4
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Single‐cell transcriptomic survey of cell diversity and functional changes in yak hearts at different altitude	4