Proteomics

Papers
(The TQCC of Proteomics is 4. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-01-01 to 2025-01-01.)
ArticleCitations
Proteomic profiling of ovarian clear cell carcinomas identifies prognostic biomarkers for chemotherapy127
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved60
BLI‐MS: Combining biolayer interferometry and mass spectrometry54
Editorial Board: Proteomics 11–12'2151
Front Cover50
46
Front Cover42
Standard abbreviations41
37
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics36
TermineR: Extracting information on endogenous proteolytic processing from shotgun proteomics data34
Front Cover33
Standard abbreviations33
Contents: Proteomics 19'2432
DREAMweb: An online tool for graph‐based modeling of NMR protein structure32
Front Cover29
Standard abbreviations29
Contents: Proteomics 9'2228
Standard abbreviations28
27
Editorial Board: Proteomics 10'2227
26
24
Contents: Proteomics 10'2323
23
Whole lung proteome of an acute epithelial injury mouse model in comparison to spatially resolved proteomes23
Proteomic and electron microscopy study of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells in three‐dimensional culture22
22
Identification of multiple proteins whose interaction with mannitol dehydrogenase is induced by salicylic acid: Implications for unconventional secretion22
Front Cover20
Spectral averaging with outlier rejection algorithms to increase identifications in top‐down proteomics20
20
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype20
On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation19
19
Comparing and integrating TMT‐SPS‐MS3 and label‐free quantitative approaches for proteomics scrutiny in recalcitrant Mango (Mangifera indica L.) peel tissue during postharvest period19
Editorial Board: Proteomics 5–6'2219
Proteomics analysis reveals the correlation of programmed ROS‐autophagy loop and dysregulated G1/S checkpoint with imatinib resistance in chronic myeloid leukemia cells19
Front Cover: Nanopore sensing of γ‐cyclodextrin induced host‐guest interaction to reverse the binding of perfluorooctanoic acid to human serum albumin19
Assign‐MALDI – A free software for assignment of MALDI‐TOF MS spectra of glycans derivatized using common and novel labeling strategies18
Combining label‐free and label‐based accurate quantifications with SWATH‐MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects18
17
Multi‐omics analysis reveals expression complexity and functional diversity of mouse kinome17
16
Standard abbreviations16
Top‐down proteomics and proteoforms – special issue16
Extracellular vesicles from non‐neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells15
Advances in ionisation techniques for mass spectrometry‐based omics research15
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants15
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF15
Contents: Proteomics 15'2114
Editorial Board: Proteomics 17–18'2114
Peptide probes containing a non‐hydrolyzable phosphotyrosine‐mimetic residue for enrichment of protein tyrosine phosphatases14
Contents: Proteomics 13–14'2114
Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD13
Application of sample displacement batch chromatography for fractionation of proteoforms13
Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT‐based multiplexing13
On the excessive use of coefficient of variation as a metric of quantitation quality in proteomics13
Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore13
13
Mechanism of action of pseudopteroxazole and pseudopterosin G: Diterpenes from marine origin12
Standard abbreviations12
Comprehensive insight on protein modification by V‐type agent: A chemical proteomic approach employing bioorthogonal reaction12
Front Cover12
Standard abbreviations12
Eye proteome of Drosophila melanogaster12
Probing protein nanopores with poly(ethylene glycol)s12
Sperm‐borne proteins improve rabbit cloning efficiency via regulating embryonic cleavage and epigenetics12
Contents: Proteomics 19'2312
Front Cover12
Enrichment and fragmentation approaches for enhanced detection and characterization of endogenous glycosylated neuropeptides12
Editorial Board: Proteomics 21'2212
Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys12
Editorial Board: Proteomics 15–16'2211
11
Standard abbreviations11
Editorial Board: Proteomics 11'2311
11
Characterization of diverse lysine acylations in Bacillus thuringiensis: Substrate profiling and functional exploration10
Editorial Board: Proteomics 7–8'2310
Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown10
10
Structural biology: The transformational era10
Standard abbreviations10
Editorial Board: Proteomics 3–4'2110
Contents: Proteomics 7–8'2310
State‐of‐the‐art computational methods to predict protein–protein interactions with high accuracy and coverage10
First comprehensive proteomics analysis of lysine crotonylation in leaves of peanut (Arachis hypogaea L.)10
Solvent‐induced proteome profiling for proteomic quantitation and target discovery of small molecular drugs9
Editorial Board: Proteomics 23–24'239
Editorial Board: Proteomics 7'249
Computational approaches to identify sites of phosphorylation9
Standard abbreviations9
Integrated tandem affinity protein purification using the polyhistidine plus extra 4 amino acids (HiP4) tag system9
Contents: Proteomics 3–4'219
An AI‐generated proteome‐scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi8
Characterization of outer membrane vesicles released by clinical isolates of Neisseria gonorrhoeae8
Contents: Proteomics 23–24'248
Systematic analysis of the ubiquitome in mouse testis8
Human myeloma cell‐ and plasma‐derived extracellular vesicles contribute to functional regulation of stromal cells8
HLA class II immunopeptidomics reveals that co‐inherited HLA‐allotypes within an extended haplotype can improve proteome coverage for immunosurveillance8
Recent advances in demystifying O‐glycosylation in health and disease8
Proteomics special issue: Precision immunology and oncology8
SWATH‐MS and MRM: Quantification of Ras‐related proteins in HIV‐1 infected and methamphetamine‐exposed human monocyte‐derived macrophages (hMDM)8
Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification8
Standard abbreviations7
The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments7
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation7
People with obesity exhibit losses in muscle proteostasis that are partly improved by exercise training7
Specialised skin cancer spectral library for use in data‐independent mass spectrometry7
Development of a Proteomic Workflow for the Identification of Heparan Sulphate Proteoglycan‐Binding Substrates of ADAM177
Computational Methods for Data Integration and Imputation of Missing Values in Omics Datasets7
Co‐culturing multicellular tumor models: Modeling the tumor microenvironment and analysis techniques7
Proteomics‐driven identification of short open reading frame‐encoded peptides7
Systems Biology and Multi‐Omics7
Structure of prion β‐oligomers as determined by short‐distance crosslinking constraint‐guided discrete molecular dynamics simulations7
Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics7
Identification of spliced peptides in pancreatic islets uncovers errors leading to false assignments7
Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top‐down proteomics7
Unveiling the molecular complexity of intestinal ischemia–reperfusion injury through omics technologies7
Multi‐omic analyses and network biology in cardiovascular disease7
Multifunctionality and intrinsic disorder of royal jelly proteome6
Insights into the sulfur metabolism of Chlorobaculum tepidum by label‐free quantitative proteomics6
Glycoblotting enables seamless and straightforward workflow for MALDI‐TOF/MS‐based sulphoglycomics of N‐ and O‐glycans6
Combination of size‐exclusion chromatography and ion exchange adsorption for improving the proteomic analysis of plasma‐derived extracellular vesicles6
Human peripheral blood mononuclear cells: A review of recent proteomic applications6
Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future6
Investigation of the Urinary Peptidome to Unravel Collagen Degradation in Health and Kidney Disease6
Single‐cell proteomics by mass spectrometry: Advances and implications in cancer research6
Benchmarking accuracy and precision of intensity‐based absolute quantification of protein abundances in Saccharomyces cerevisiae6
Effects of dopamine D2 receptor antagonists on retinal pigment epithelial/choroid complex metabolism in form‐deprived myopic guinea pigs6
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 controls6
Diabetic retinopathy from the vitreous proteome perspective: The INSC94Y transgenic pig model study6
Proteomic and phosphoproteomic landscape of salivary extracellular vesicles to assess OSCC therapeutical outcomes6
6
Contents: Proteomics 18'246
RETRACTED: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination6
(Prote)omics for Superior Management of Kidney and Cardiovascular Disease—A Thought‐Provoking Impulse From Nephrology6
In‐depth proteomic analysis of Plasmodium berghei sporozoites using trapped ion mobility spectrometry with parallel accumulation‐serial fragmentation6
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles6
An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue6
Comprehensive kinomic study via a chemical proteomic approach reveals kinome reprogramming in hepatocellular carcinoma tissues6
Transforming peptide hormone prediction: The role of AI in modern proteomics6
Recent advances in isobaric labeling and applications in quantitative proteomics6
Cracking chromatin with proteomics: From chromatome to histone modifications6
Data acquisition approaches for single cell proteomics6
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma6
Recent Advances in Labeling‐Based Quantitative Glycomics: From High‐Throughput Quantification to Structural Elucidation6
Large‐scale top‐down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes5
Serum starvation induces sexual dimorphisms in secreted proteins of human umbilical vein endothelial cells (HUVECs) from twin pairs5
Standard abbreviations5
Editorial Board: Proteomics 17'245
A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation5
Identification and quantification of degradome components in human synovial fluid reveals an increased proteolytic activity in knee osteoarthritis patients vs controls5
Integrated changes in thermal stability and proteome abundance during altered nutrient states in Escherichia coli and human cells5
Skeletal muscle proteome expression differentiates severity of cancer cachexia in mice and identifies loss of fragile X mental retardation syndrome‐related protein 15
Editorial Board: Proteomics 7'225
Editorial Board: Proteomics 21–22'235
A novel role for milk fat globule‐EGF factor 8 protein (MFGE8) in the mediation of mouse sperm–extracellular vesicle interactions5
Omics and systems view of innate immune pathways5
Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles5
Regulation of the microsomal proteome by salicylic acid and deficiency of phosphatidylinositol‐4‐kinases β1 and β2 in Arabidopsis thaliana5
Direct‐MS analysis of antibody‐antigen complexes5
Editorial Board: Proteomics 6'215
Proteomics is advancing the understanding of stallion sperm biology5
5
Proteome characterisation of extracellular vesicles isolated from heart5
Standard abbreviations5
Hepatocyte nuclear factor 4α multiple isoforms, their functions, and their interactomes5
Transcriptome–proteome compendium of the Antarctic krill (Euphausia superba): Metabolic potential and repertoire of hydrolytic enzymes5
Editorial Board: Proteomics 23‐24'225
Four sides to the story: A proteomic comparison of liquid‐phase and matrix‐bound extracellular vesicles in 2D and 3D cell cultures5
Extracellular vesicles—An omics view5
Genetic and epigenetic control of the plant metabolome5
Front Cover5
5
Model fusion for predicting unconventional proteins secreted by exosomes using deep learning5
5
Contents: Proteomics 16'235
Prediction of Anti‐Freezing Proteins From Their Evolutionary Profile5
Proteome reprogramming of endometrial epithelial cells by human trophectodermal small extracellular vesicles reveals key insights into embryo implantation5
Assessing the activation/inhibition of tyrosine kinase‐related pathways with a newly developed platform5
Editorial Board: Proteomics 8'225
Omics insights into the responses to dietary selenium5
An N‐glycopeptide MS/MS data analysis workflow leveraging two complementary glycoproteomic software tools for more confident identification and assignments5
Contents: Proteomics 5'215
Front Cover5
Multi‐omics analysis to characterize molecular adaptation of Entamoeba histolytica during serum stress4
4
Contents: Proteomics 11–12'214
Editorial Board: Proteomics 5'234
Standard abbreviations4
Intratympanic steroid treatment can reduce ROS and immune response in human perilymph investigated by in‐depth proteome analysis4
What proteomics has taught us about honey bee (Apis mellifera) health and disease4
4
Contents: Proteomics 19'214
Quantitative proteomic analyses reveal the impact of nitrogen starvation on the proteome of the model diatom Phaeodactylum tricornutum4
Global analysis of lysine acetylome reveals the potential role of CCL18 in non‐small cell lung cancer4
Editorial Board: Proteomics 19'234
Contents: Proteomics 16'214
Front Cover4
Contents: Proteomics 22'224
Contents: Proteomics 1'214
Front Cover4
Quantitative proteomics reveals arsenic attenuates stem‐loop binding protein stability via a chaperone complex containing heat shock proteins and ERp444
Contents: Proteomics 18'224
Database search engines and target database features impinge upon the identification of post‐translationally cis‐spliced peptides in HLA class I immunopeptidomes4
iTRAQ‐based proteomic analysis reveals proteins associated with cold stress response in two different populations of Manila clam (Ruditapes philippinarum)4
An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus4
Contents: Proteomics 8'224
Proteomic analyses reveal that immune integrins are major targets for regulation by Membrane‐Associated Ring‐CH (MARCH) proteins MARCH2, 3, 4 and 94
Editorial Board: Proteomics 11–12'224
Front Cover4
Front Cover4
Contents: Proteomics 19–20'224
Editorial Board: Proteomics 1'214
4
Contents: Proteomics 21–22'234
Editorial Board: Proteomics 9'234
Editorial Board: Proteomics 19'244
Standard abbreviations4
Editorial Board: Proteomics 16'214
Front Cover4
Highlights on the current state of proteomic detection and characterization with nanopore sensors4
Global analysis of lysine acetylation in the brain cortex of K18‐hACE2 mice infected with SARS‐CoV‐24
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