Proteomics

Article	Citations
Transcription factors: Bridge between cell signaling and gene regulation	107
Deep Learning in Proteomics	91
N‐Terminomics for the Identification of In Vitro Substrates and Cleavage Site Specificity of the SARS‐CoV‐2 Main Protease	59
Stability and reproducibility of proteomic profiles in epidemiological studies: comparing the Olink and SOMAscan platforms	53
Omics in Systems Biology: Current Progress and Future Outlook	51
Understanding extracellular vesicle and nanoparticle heterogeneity: Novel methods and considerations	46
The impact of AlphaFold Protein Structure Database on the fields of life sciences	45
Mass spectrometry‐based high‐throughput proteomics and its role in biomedical studies and systems biology	45
Proteomic profiling of human uterine extracellular vesicles reveal dynamic regulation of key players of embryo implantation and fertility during menstrual cycle	42
Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame‐encoded peptides	41
Recent advances in isobaric labeling and applications in quantitative proteomics	34
Proteome characterisation of extracellular vesicles isolated from heart	33
Potential of deep representative learning features to interpret the sequence information in proteomics	33
Microproteomic sample preparation	32
A tale of two lipids: Lipid unsaturation commands ferroptosis sensitivity	31
Targeted liquid chromatography‐tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives	30
Dealing with missing values in proteomics data	30
Longitudinal proteomic profiling provides insights into host response and proteome dynamics in COVID‐19 progression	28
Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore	28
Protein‐protein interaction networks as miners of biological discovery	28
A practical guide to interpreting and generating bottom‐up proteomics data visualizations	28
Label‐free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing	27
Urinary Peptides Significantly Associate with COVID‐19 Severity: Pilot Proof‐of‐Principle Data and Design of a Multicentric Diagnostic Study	26
Clinical applications of mass spectrometry‐based proteomics in cancer: Where are we?	26
Protein–DNA/RNA interactions: Machine intelligence tools and approaches in the era of artificial intelligence and big data	23

Computational Analysis of Phosphoproteomics Data in Multi‐Omics Cancer Studies	23
Proteome reprogramming of endometrial epithelial cells by human trophectodermal small extracellular vesicles reveals key insights into embryo implantation	22
Targeting peptide‐mediated interactions in omics	22
Advances in quantitative high‐throughput phosphoproteomics with sample multiplexing	22
Size‐exclusion chromatography allows the isolation of EVs from the filamentous fungal plant pathogen Fusarium oxysporum f. sp. vasinfectum (Fov)	21
Mass spectrometry‐based proteomic platforms for better understanding of SARS‐CoV‐2 induced pathogenesis and potential diagnostic approaches	20
Ion mobility‐resolved phosphoproteomics with dia‐PASEF and short gradients	20
Opportunities for pharmacoproteomics in biomarker discovery	20
Targeted proteomics on its way to discovery	20
Biomarker identification and pathway analysis of rheumatoid arthritis based on metabolomics in combination with ingenuity pathway analysis	20
The clinical and mechanistic roles of bile acids in depression, Alzheimer's disease, and stroke	20
29‐Plex tandem mass tag mass spectrometry enabling accurate quantification by interference correction	19
CD99 and polymeric immunoglobulin receptor peptides deregulation in critical COVID‐19: A potential link to molecular pathophysiology?	19
Metabolomic profile of combined healthy lifestyle behaviours in humans: A systematic review	19
In‐depth proteomic analysis of Plasmodium berghei sporozoites using trapped ion mobility spectrometry with parallel accumulation‐serial fragmentation	19
Site‐specific glycosylation of SARS‐CoV‐2: Big challenges in mass spectrometry analysis	19
Proteomic and metabolomic investigation of serum lactate dehydrogenase elevation in COVID‐19 patients	18
Proteomics in the COVID‐19 Battlefield: First Semester Check‐Up	18
An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue	18
Elucidation of the protein composition of mouse seminal vesicle fluid	17
Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit	17
First comprehensive proteomics analysis of lysine crotonylation in leaves of peanut (Arachis hypogaea L.)	17
Automation of single‐cell proteomic sample preparation	16
A Microfluidic Chip for Efficient Circulating Tumor Cells Enrichment, Screening, and Single‐Cell RNA Sequencing	16
Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells	16
Pannexin‐1 channel regulates nuclear content packaging into apoptotic bodies and their size	15
Global profiling of protein lysine lactylation and potential target modified protein analysis in hepatocellular carcinoma	15
Proteomic profiling in extracellular vesicles for cancer detection and monitoring	15
Recent advances in demystifying O‐glycosylation in health and disease	15
Human peripheral blood mononuclear cells: A review of recent proteomic applications	14
The mechanism of Pseudomonas aeruginosa outer membrane vesicle biogenesis determines their protein composition	14
Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT‐based multiplexing	14
Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles	14
Proteomics and glycoproteomics of beer and wine	13
Fingolimod effects on the brain are mediated through biochemical modulation of bioenergetics, autophagy, and neuroinflammatory networks	13
Drug hapten‐specific T‐cell activation: Current status and unanswered questions	13
Ubiquitinomics: History, methods, and applications in basic research and drug discovery	13
A simple organic solvent precipitation method to improve detection of low molecular weight proteins	13
Leveraging transformers‐based language models in proteome bioinformatics	13
HLA class II immunopeptidomics reveals that co‐inherited HLA‐allotypes within an extended haplotype can improve proteome coverage for immunosurveillance	12
Toward proteome‐wide exploration of proteins in dried blood spots using liquid chromatography‐coupled mass spectrometry	12
Global profiling of lysine lactylation in human lungs	12
Benchmarking accuracy and precision of intensity‐based absolute quantification of protein abundances in Saccharomyces cerevisiae	12
Mapping shifts in nanopore signal to changes in protein and protein‐DNA conformation	12
Single polypeptide detection using a translocon EXP2 nanopore	12
Proteomic analysis of koala (phascolarctos cinereus) spermatozoa and prostatic bodies	12
Protein Interaction Network Biology in Neuroscience	12
Human myeloma cell‐ and plasma‐derived extracellular vesicles contribute to functional regulation of stromal cells	12
Impact of chemically defined culture media formulations on extracellular vesicle production by amniotic epithelial cells	12
Proteomic profiling of the oncogenic septin 9 reveals isoform‐specific interactions in breast cancer cells	12

Optimizing data‐independent acquisition (DIA) spectral library workflows for plasma proteomics studies	12
Identification of spliced peptides in pancreatic islets uncovers errors leading to false assignments	12
DDASSQ: An open‐source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform	11
prPred‐DRLF: Plant R protein predictor using deep representation learning features	11
An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis	11
A novel role for milk fat globule‐EGF factor 8 protein (MFGE8) in the mediation of mouse sperm–extracellular vesicle interactions	11
Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis	11
Recent developments in data acquisition, treatment and analysis with ion mobility‐mass spectrometry for lipidomics	11
A prostate cancer tissue specific spectral library for targeted proteomic analysis	10
Proteomic Characterization of the Pseudomonas sp. Strain phDV1 Response to Monocyclic Aromatic Compounds	10
Thiol redox proteomics: Characterization of thiol‐based post‐translational modifications	10
Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography	10
Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study	10
O‐GlcNAcylation promotes fatty acid synthase activity under nutritional stress as a pro‐survival mechanism in cancer cells	10
Structure of prion β‐oligomers as determined by short‐distance crosslinking constraint‐guided discrete molecular dynamics simulations	10
A Time‐Resolved Cryo‐EM Study of Saccharomyces cerevisiae 80S Ribosome Protein Composition in Response to a Change in Carbon Source	10
Portable mass spectrometry system: instrumentation, applications, and path to ‘omics analysis	10
Neuronal Differentiation of LUHMES Cells Induces Substantial Changes of the Proteome	10
Mass spectrometry detection of monkeypox virus: Comprehensive coverage for ranking the most responsive peptide markers	10
Evaluation of four phosphopeptide enrichment strategies for mass spectrometry‐based proteomic analysis	10
In‐depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells	10
High‐throughput, in‐depth and estimated absolute quantification of plasma proteome using data‐independent acquisition/mass spectrometry (“HIAP‐DIA”)	9
Data‐independent acquisition proteomics methods for analyzing post‐translational modifications	9
Large‐scale top‐down proteomics of the Arabidopsis thaliana leaf and chloroplast proteomes	9
Proteomic profiling of impaired excitation–contraction coupling and abnormal calcium handling in muscular dystrophy	9
Proteome and secretome analysis of pancreatic cancer cells	9
Identifying a urinary peptidomics profile for hypertension in young adults: The African‐PREDICT study	9
CLN6 deficiency causes selective changes in the lysosomal protein composition	9
Using Deep Learning to Extrapolate Protein Expression Measurements	9
Dynamic Profiling of Protein Mole Synthesis Rates during C2C12 Myoblast Differentiation	8
Proteomics‐driven identification of short open reading frame‐encoded peptides	8
Microproteins—Discovery, structure, and function	8
Recent advances of data‐independent acquisition mass spectrometry‐based proteomics	8
Database search engines and target database features impinge upon the identification of post‐translationally cis‐spliced peptides in HLA class I immunopeptidomes	8
Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype	8
The Brain Protein Atlas: A conglomerate of proteomics datasets of human neural tissue	8
Covalent Modification of Proteins by Plant‐Derived Natural Products: Proteomic Approaches and Biological Impacts	8
Direct‐MS analysis of antibody‐antigen complexes	8
The utility of proteases in proteomics, from sequence profiling to structure and function analysis	8
Proteomics‐based interrogation of the kinome and its implications for precision oncology	7
Capillary electrophoresis‐mass spectrometry for protein analyses under native conditions: Current progress and perspectives	7
A peptidoform based proteomic strategy for studying functions of post‐translational modifications	7
An innovative standard for LC‐MS‐based HCP profiling and accurate quantity assessment: Application to batch consistency in viral vaccine samples	7
Multifunctionality and intrinsic disorder of royal jelly proteome	7
Computational systems approach towards phosphoproteomics and their downstream regulation	7
An emerging field: Post‐translational modification in microbiome	7
Comparative Secretomics Gives Access to High Confident Secretome Data: Evaluation of Different Methods for the Determination of Bona Fide Secreted Proteins	7
Parallel‐reaction monitoring revealed altered expression of a number of epitranscriptomic reader, writer, and eraser proteins accompanied with colorectal cancer metastasis	7
Data‐independent acquisition and quantification of extracellular matrix from human lung in chronic inflammation‐associated carcinomas	7
Combination of size‐exclusion chromatography and ion exchange adsorption for improving the proteomic analysis of plasma‐derived extracellular vesicles	7
Resourcing, annotating, and analysing synthetic peptides of SARS‐CoV‐2 for immunopeptidomics and other immunological studies	7
Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry	7
Proteomics‐based scoring of cellular response to stimuli for improved characterization of signaling pathway activity	7
Current noise of a protein‐selective biological nanopore	7
Cracking chromatin with proteomics: From chromatome to histone modifications	7
Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF	7
JUMPptm: Integrated software for sensitive identification of post‐translational modifications and its application in Alzheimer's disease study	6
Insights into the vision of the hadal snailfish Pseudoliparis swirei through proteomic analysis of the eye	6
Co‐culturing multicellular tumor models: Modeling the tumor microenvironment and analysis techniques	6
BLI‐MS: Combining biolayer interferometry and mass spectrometry	6
Food allergen detection by mass spectrometry: From common to novel protein ingredients	6
In‐depth analysis of the Sirtuin 5‐regulated mouse brain malonylome and succinylome using library‐free data‐independent acquisitions	6
Global profiling of lysine succinylation in human lungs	6
The utilization of the search engine, Bolt, to decrease search time and increase peptide identifications in hydroxyl radical protein footprinting‐based workflows	6
Omics insights into extracellular vesicles in embryo implantation and their therapeutic utility	6
Proteomic analysis of the meristematic root zone in contrasting genotypes reveals new insights in drought tolerance in rice	6
A random forest model for predicting exosomal proteins using evolutionary information and motifs	6
Enrichment and fragmentation approaches for enhanced detection and characterization of endogenous glycosylated neuropeptides	6
Machine learning‐based peptide‐spectrum match rescoring opens up the immunopeptidome	6
Effects of 4‐Br‐A23187 on Bacillus subtilis cells and unilamellar vesicles reveal it to be a potent copper ionophore	6
Proteomics evaluation of five economical commercial abundant protein depletion kits for enrichment of diseases‐specific biomarkers from blood serum	6
Know thy immune self and non‐self: Proteomics informs on the expanse of self and non‐self, and how and where they arise	6
Quantitative phosphoproteomics reveals novel roles of cAMP in plants	6
Small proteins in bacteria – Big challenges in prediction and identification	6
Proteomics as a tool to decipher plant responses in arbuscular mycorrhizal interactions: a meta‐analysis	6
Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD	6
Single‐molecule, hybridization‐based strategies for short nucleic acids detection and recognition with nanopores	6
Rapid and in‐depth proteomic profiling of small extracellular vesicles for ultralow samples	6
Assessing interference in isobaric tag‐based sample multiplexing using an 18‐plex interference standard	6
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT	6

ProSight Annotator: Complete control and customization of protein entries in UniProt XML files	6
Sometimes faster can be better: Microneedling IPG strips enables higher throughput for integrative top‐down proteomics	5
Protein‐enabled detection of ibuprofen and sulfamethoxazole using solid‐state nanopores	5
Progress in methodologies and quality‐control strategies in protein cross‐linking mass spectrometry	5
Molecular histoproteomy by MALDI mass spectrometry imaging to uncover markers of the impact of Nosema on Apis mellifera	5
Quantitative Proteomic Analysis of Global Protein Acetylation in PRRSV‐Infected Pulmonary Alveolar Macrophages	5
Quantitative proteomic analyses reveal the dynamics of protein and amino acid accumulation during soybean seed development	5
Proteomic and phosphoproteomic landscape of salivary extracellular vesicles to assess OSCC therapeutical outcomes	5
Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future	5
A transformer architecture for retention time prediction in liquid chromatography mass spectrometry‐based proteomics	5
Enabling cryo‐EM density interpretation from yeast native cell extracts by proteomics data and AlphaFold structures	5
Comprehensive serum N‐glycan profiling identifies a biomarker panel for early diagnosis of non‐small‐cell lung cancer	5
On possible trypsin‐induced biases in peptides analysis with aerolysin nanopore	5
Advanced mass spectrometry workflows for accurate quantification of trace‐level host cell proteins in drug products: Benefits of FAIMS separation and gas‐phase fractionation DIA	5
In‐depth discovery of protein lactylation in hepatocellular carcinoma	5
Tail‐Robust Quantile Normalization	5
Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens	5
DNA‐Barcoded Fluorescence Microscopy for Spatial Omics	5
The use of pharmacological chaperones in rare diseases caused by reduced protein stability	5
Exploring the role of m6A modification in cancer	5
Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non‐inducing cancer cells	5
Comprehensive review of MS‐based studies on N‐glycoproteome and N‐glycome of extracellular vesicles	5
Systematic analysis of the ubiquitome in mouse testis	5
Advances in ionisation techniques for mass spectrometry‐based omics research	5
Combining label‐free and label‐based accurate quantifications with SWATH‐MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects	5
In‐depth proteome of perilymph in guinea pig model	5
Extracellular vesicles in the transfusion medicine field: The potential of proteomics	5
Transglutaminase‐2, RNA‐binding proteins and mitochondrial proteins selectively traffic to MDCK cell‐derived microvesicles following H‐Ras‐induced epithelial–mesenchymal transition	5
Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry	5
Mapping the interaction between eukaryotic initiation factor 4A (eIF4A) and the inhibitor hippuristanol using carbene footprinting and mass spectrometry	5
Quantitative proteomic analysis reveals altered enzyme expression profile in Zea mays roots during the early stages of colonization by Herbaspirillum seropedicae	5
Global analysis of lysine acetylome reveals the potential role of CCL18 in non‐small cell lung cancer	5
Advances in proteomic phenotyping of microglia in neurodegeneration	5
Direct identification of HLA‐presented CD8 T cell epitopes from transmitted founder HIV‐1 variants	5
A qualitative and quantitative analysis of the human gingival crevicular fluid proteome and metaproteome	5
Assessing the activation/inhibition of tyrosine kinase‐related pathways with a newly developed platform	5
Mouse model of Alzheimer's disease demonstrates differential effects of early disease pathology on various brain regions	5
Probing protein nanopores with poly(ethylene glycol)s	5
Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants	5
Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells	5
Distinct Metabolic Features of Pathogenic Escherichia coli and Shigella spp. Determined by Label‐Free Quantitative Proteomics	5
Integration of proteomics in the molecular tumor board	5
Proteomics reveals the potential mechanism of Mrps35 controlling Listeria monocytogenes intracellular proliferation in macrophages	5
Phosphoproteomic studies of alamandine signaling in CHO‐MrgD and human pancreatic carcinoma cells: An antiproliferative effect is unveiled	5
The utility of molecularly imprinted polymers for mass spectrometric protein and proteomics analysis	4
Target‐decoy false discovery rate estimation using Crema	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
Glycoblotting enables seamless and straightforward workflow for MALDI‐TOF/MS‐based sulphoglycomics of N‐ and O‐glycans	4
Capillary zone electrophoresis‐high field asymmetric ion mobility spectrometry‐tandem mass spectrometry for top‐down characterization of histone proteoforms	4
Isobaric Tag‐Based Protein Profiling across Eight Human Cell Lines Using High‐Field Asymmetric Ion Mobility Spectrometry and Real‐Time Database Searching	4
Comparative Proteomic Analysis Reveals Complex Responses to Bordetella bronchiseptica Infections in the Spleen of Rabbits	4
ORS‐Pred: An optimized reduced scheme‐based identifier for antioxidant proteins	4
A comprehensive revisit of the machine‐learning tools developed for the identification of enhancers in the human genome	4
iBench: A ground truth approach for advanced validation of mass spectrometry identification method	4
Advances in mass spectrometry‐based footprinting of membrane proteins	4
Impact of Asp/Glu‐ADP‐ribosylation on protein‐protein interaction and protein function	4
Tissue‐based absolute quantification using large‐scale TMT and LFQ experiments	4
Insights from tissue “omics” analysis on intestinal remodeling in celiac disease	4
A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation	4
Skeletal muscle proteome expression differentiates severity of cancer cachexia in mice and identifies loss of fragile X mental retardation syndrome‐related protein 1	4
Phosphoproteomic Effects of Acute Depletion of PP2A Regulatory Subunit Cdc55	4
Improving SWATH‐MS analysis by deep‐learning	4
Molecular characterization of triple negative breast cancer formaldehyde‐fixed paraffin‐embedded samples by data‐independent acquisition proteomics	4
Solvent‐induced proteome profiling for proteomic quantitation and target discovery of small molecular drugs	4
A field guide to the proteomics of post‐translational modifications in DNA repair	4
Bovine milk‐derived extracellular vesicles enhance doxorubicin sensitivity in triple negative breast cancer cells by targeting metabolism and STAT signalling	4
Membrane to cytosol redistribution of αII‐spectrin drives extracellular vesicle biogenesis in malignant breast cells	4
LEVELNET to visualize, explore, and compare protein–protein interaction networks	4
The Choice of HLA‐Associated Peptide Enrichment and Purification Strategy Affects Peptide Yields and Creates a Bias in Detected Sequence Repertoire	4
Antidepressant treatment effects on hippocampal protein turnover: Molecular and spatial insights from mass spectrometry	4
Integration of data‐independent acquisition (DIA) with co‐fractionation mass spectrometry (CF‐MS) to enhance interactome mapping capabilities	4
Exploring the significance of lipids in Alzheimer's disease and the potential of extracellular vesicles	4
Integrated changes in thermal stability and proteome abundance during altered nutrient states in Escherichia coli and human cells	4
Bioinformatic analysis of the SPs and NFTs proteomes unravel putative biomarker candidates for Alzheimer's disease	4
Systems Biology and Multi‐Omics	4
SWATH‐MS and MRM: Quantification of Ras‐related proteins in HIV‐1 infected and methamphetamine‐exposed human monocyte‐derived macrophages (hMDM)	4
Computational tools for inferring transcription factor activity	4
Investigating Byssogenesis with Proteomic Analysis of Byssus, Foot, and Mantle in Mytilus Mussels by LC‐MS/MS	4
Proteomics reveals MRPL4 as a high‐risk factor and a potential diagnostic biomarker for prostate cancer	4
Differentially expressed glycoproteins in pre‐ and post‐digital rectal examination urine samples for detecting aggressive prostate cancer	4
Proteomic analysis of Giardia lamblia and Trichomonas vaginalis flagella reveal unique post‐translational modifications in tubulin that provide clues to regulation of their motilities	4
RapiGest precipitation depends on peptide concentration	4
Improving the proteome coverage of Daphnia magna ‐ implications for future ecotoxicoproteomics studies	4