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2024-05-15 GlyCombo enables rapid, complete glycan composition identification across diverse glycomic sample typesHomo sapiensLTQ Orbitrap XL,LTQ Orbitrap Velos,Orbitrap Fusion Lumos,Velos Plus,LTQ XL,amaZon SpeedGlyCombo enables rapid, complete glycan composi...No12 
2024-04-30 Defective pgsA contributes to increased membrane fluidity and cell wall thickening in S. aureus with high-level daptomycin resistanceStaphylococcus aureusSynapt XSNo9 
2024-04-09 A framework for quality control in quantitative proteomicsHomo sapiens, Mus musculus, Saccharomyces cerevisiae, Bos taurusOrbitrap Eclipse,Orbitrap Fusion Lumos,Orbitrap FusionKristine A Tsantilas, Gennifer E Merrihew, Juli...No9PXD051318
2024-03-10 Effect of burn wound treatment with fish skin on mouse skin proteomeMus musculusimpact IIGarrity C, Garcia-Rovetta C, Rivas I, Delatorre...No1PXD050514
2024-02-22 Brain Creatine Kinase as a biomarker for Alzheimer’s diseaseHomo sapiensQ Exactive HFPublication pendingYes1PXD050060
2024-02-18 AD-BXD Mouse PreFrontal Cortex ProteomicsMus musculusOrbitrap Fusion,Orbitrap Fusion LumosNo50PXD045403
2024-01-30 IO3 immunoMRM panel experimental dataHomo sapiensQTRAP 5500Publication pendingYes5PXD049020
2024-01-26 Analysis of N-Glycosylation for SARS-CoV-2 expressed receptor-binding domain VOCs and membrane protein with LC-MS.Severe acute respiratory syndrome coronavirus 2SYNAPT G2-SiSchwarze M, Volke D, Rojas Echeverri JC, Schick...No1PXD048930
2024-01-26 Fecal Microbiota Transplant_Bile AcidHomo sapiens6560 Q-TOF LC/MSMetagenomic, metabolomic, and lipidomic shifts ...No2 
2024-01-15 Plasma proteomics identify biomarkers predicting Parkinson's disease up to 7 years before symptom onsetHomo sapiensXevo TQ MS,ACQUITY UPLCPlasma proteomics identify biomarkers predictin...No3PXD041419
2023-12-22 Targeted Proteomics Reveals Quantitative Differences in Low Abundance Glycosyltransferases of Patients with Congenital Disorders of GlycosylationHomo sapiensQTRAP 5500,nanoACQUITY UPLC,TSQ VantageSakson R, Beedgen L, Bernhard P, Alp KM, Lübbeh...Yes6PXD048072
2023-12-20 Development of a Mass Spectrometry-Based Method for Quantification of Total Cashew Protein in Roasting OilAnacardium occidentaleQ Exactive,Q Exactive PlusChen S, Downs ML. Development of a Mass Spectro...Yes9PXD047985
2023-12-15 Modeling the simultaneous dynamics of proteins in blood plasma and the cerebrospinal fluid in human in vivoHomo sapienstimsTOF Pro 2Publication pendingNo8PXD047851
2023-12-02 Evaluation of Solid Phase Adsorption Toxin Tracking (SPATTs) for passive monitoring of Per- and Polyfluoroalkyl Substances (PFAS) using Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) 6560 Q-TOF LC/MSExpected in the near future.No3 
2023-11-30 Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomicsHomo sapiensOrbitrap EclipsePublication pendingYes1PXD047419
2023-11-27 Peptide centric detection of cross-linked peptides using PASEF, MeroX, and SkylineBos taurustimsTOF ProRojas Echeverri JC, Hause F, Iacobucci C, Ihlin...No4PXD047307
2023-11-16 PRM quantification of interferon-induced proteins upon Type I IFN-beta, Type II IFN-gamma, and LPS stimulation of differentiated THP-1 cellsHomo sapiensQ Exactive HFNo1 
2023-11-01 Assessment of Kinome-wide Rewiring Upon Picornavirus InfectionHomo sapiensTSQ AltisVeth TS, Nouwen LV, Zwaagstra M, Lyoo H, Wieren...Yes2PXD046598
2023-10-30 Metabolic, Neurotoxic and Immunotoxic Effects of PFAAs and their
Mixtures on the Proteome of Plasma and Head Kidney from Rainbow
Trout
Oncorhynchus mykiss6545 Q-TOF LC/MSPollard S, De Silva AO, Simmons DBD. Metabolic,...No2PXD046517
2023-10-30 TFAM Tg Mice skeletal muscle_iMPAQTMus musculusQTRAP 6500Igami K, Kittaka H, Yagi M, Gotoh K, Matsushima...No1 
2023-10-30 METLIN-CCS: an ion mobility spectrometry
collision cross-section database
  Baker ES, Hoang C, Uritboonthai W, Heyman HM, P...No1 
2023-10-19 Acoustic Ejection Mass Spectrometry Empowers Ultra-Fast Peptide Biomarker Quantification... A Paradigm shiftHomo sapiens, SARS-CoV-2Triple Quad 6500+Publication pendingNo29PXD046249
2023-10-02 In-Gel Digest to identify Aspergillus fumigatus protein antigens in severe equine asthma (SEA)Aspergillus fumigatusSYNAPT G2-SiJentsch MC, Lübke S, Schrödl W, Volke D, Krizsa...No3PXD045869
2023-09-21 In-Gel digest and filter-aided sample preparation to identify Dermatophagoides - and yeast protein antigens in severe equine asthma.Saccharomyces cerevisiae, Dermatophagoides pteronyssinusSYNAPT G2-SiSchnabel CL, Jentsch MC, Lübke S, Kaiser-Thom S...No3PXD045568
2023-09-21 Cognitive Functions, Neurotransmitter Alterations, and Hippocampal Microstructural Changes in Mice Caused by Feeding on Western DietMus musculusQ ExactiveCustodio RJ, Hobloss Z, Myllys M, Hassan R, Gon...No3 
2023-09-17 AD-BXD Mouse Hippocampus ProteomicsMus musculusOrbitrap Fusion LumosNo49PXD045425
2023-09-11 Serum proteome signatures associated with ileal and colonic ulcers in Crohn's diseaseHomo sapiensXevo TQ-SN. Pierre, V.A. Huynh-Thu, D. Baiwir, et al., S...No2PXD045278
2023-09-09 Skeletal Muscle TFEB Signaling Promotes Central Nervous System Function and Reduces Neuroinflammation during Aging and Neurodegenerative DiseaseMus musculusOrbitrap Fusion LumosMatthews I, Birnbaum A, Gromova A, Huang AW, Li...No1PXD045241
2023-09-03 Proteomic characterization of extracellular matrix (ECM) produced by human fibroblast activation protein (FAP)-positive pericyte-like cells and glioma cellsHomo sapiensTripleTOF 5600+Vymola P, Garcia-Borja E, Cervenka J, Balaziova...No1PXD045057
2023-09-01 Assessing Per- and Polyfluoroalkyl Substances (PFAS) in Fish Fillet Using Non-Targeted Analyses 6560 Q-TOF LC/MSYes1 
2023-08-25 The phosphorylation landscape of infection-related development by the rice blast fungusMagnaporthe oryzaeOrbitrap FusionCruz-Mireles N, Osés-Ruiz M, Derbyshire P, Jégo...No1PXD044865
2023-08-08 Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis.Arabidopsis thalianaQ Exactive HF-X,Orbitrap Fusion LumosNo6PXD044142
2023-08-08 Validation of a proteomic signature of lung cancer risk from bronchial specimens of risk-stratified individualsHomo sapiensTSQ Altis,TSQ VantageCancers 2023, 15(18), 4504; https://doi.org/10....Yes5 
2023-07-23 Quantitative Measurement of Secretory Protein Mistargeting by Proximity Labeling and Parallel Reaction MonitoringHomo sapiensLTQ Orbitrap Velos Pro,LTQ Orbitrap VelosNo2PXD044008
2023-07-20 Breeding from 1891 to 2010 did not increase the content of amylase/trypsin-inhibitors in wheat (Triticum aestivum L.)Triticum aestivumTSQ VantageGeisslitz S, Pronin D, Neerukonda M, Curella V,...Yes25PXD043968
2023-07-20 Label-free Parallel Reaction Monitoring (PRM) analysis of selected novel potential targets of IFNg stimulation in Hela cells.Homo sapiensQ Exactive HFBorteçen T, Müller T, Krijgsveld J. An integrat...No1PXD043967
2023-07-14 A novel overlapping gene azyx-1 affects the translation of zyxin in C. elegansCaenorhabditis elegansQ Exactive HF-XPublication pendingYes2PXD034878
2023-07-06 Gut Microbiome IMS-MS ExperimentsHomo sapiens, Mus musculus6560 Q-TOF LC/MSNo2 
2023-07-05 Development and analytical validation of a multiplexed targeted mass spectrometry assay to detect ovarian cancer protein biomarkers in seraHomo sapiensQ Exactive PlusRyu J, Boylan KLM, Twigg CAI, Evans R, Skubitz ...Yes8 
2023-07-02 Comparing peptide identifications by FAIMS versus quadrupole gas phase fractionationHomo sapiensOrbitrap EclipsePublication pendingNo4PXD043458
2023-06-22 Targeted Proteomics Quantitation of NRF2 and Predictive Biomarkers in HNSCCHomo sapiensOrbitrap EclipseNo4 
2023-06-21 Sensitive detection of HIV-1 and Mycobacterium tuberculosis peptides in blood for rapid diagnosis of co-infected individuals by immuno-affinity liquid chromatography tandem mass spectrometryHomo sapiensTSQ AltisLi L, Lyon CJ, LaCourse SM, Zheng W, Stern J, E...Yes24PXD043191
2023-06-16 Deep quantitative proteomics of North American Pacific coast star tunicateBotryllus schlosseriimpact IIKültz D, Gardell AM, DeTomaso A, Stoney G, Rink...No1PXD043046
2023-06-13 Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteomeHomo sapiensOrbitrap EclipsePublication pendingNo5PXD042947
2023-06-07 In-vitro differential redox-labeling of NTRCChlamydomonas reinhardtiiQ Exactive PlusNo1PXD042813
2023-06-04 Environmental Conditions Elicit a Slow but Enduring Response of Histone Post-Translational Modifications in Mozambique TilapiaOreochromis mossambicusimpact IINo2PXD042718
2023-06-02 Evaluating the Performance of the Astral Mass Analyzer for Quantitative Proteomics Using Data Independent AcquisitionHomo sapiensOrbitrap Fusion Lumos,Orbitrap AstralHeil LR, Damoc E, Arrey TN, Pashkova A, Denisov...No15PXD042704
2023-05-23 Assessing the role of trypsin in quantitative plasma- and single-cell
proteomics towards clinical application
Homo sapiensTSQ Altis,Orbitrap Eclipse,Q Exactive HFWoessmann J, Petrosius V, Üresin N, Kotol D, Ar...Yes2PXD042450
2023-05-17 S-Adenosylmethionine Negatively Regulates the Mitochondrial Respiratory Chain Repressor MCJ in the LiverMus musculusOrbitrap Fusion LumosNo1PXD042309
2023-04-01 Tapioca – A Novel Platform for Prediction Of Protein-Protein Interaction Dynamics Identifies NUCKS1 as a Broad-Spectrum Herpesvirus Proviral FactorHomo sapiens, Human herpesvirus 8 strain GK18Q Exactive HFPublication pendingNo1PXD041269
2023-03-30 PRM data for "Functional analysis of a common BAG3 allele associated with protection from heart failure"Homo sapiensQ Exactive PlusFunctional analysis of a common BAG3 allele ass...No1PXD041228
2023-03-12 Global response of Octopus berrima to ocean warmingOctopus berrimaimpact IIPublication pendingNo1PXD040795
2023-03-09 Proteogenomic analysis of chemo-refractory high grade serous ovarian cancerHomo sapiensQTRAP 6500Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, H...Yes4PXD040742
2023-03-07 Targeted Proteomics of Lung Squamous Cell CarcinomasHomo sapiensTSQ AltisPutty Reddy S, Alontaga AY, Welsh EA, Haura EB,...Yes1PXD040680
2023-03-05 PRM quantification of MCS proteins and viral proteins in HCMV virus microenvironmentHomo sapiens, HHV-5Q Exactive HFSong B, Sheng X, Justice JL, Lum KK, Metzger PJ...No2PXD038466
2023-03-02 Development and validation of a matrix independent calibration strategy for targeted mass spectrometry-based quantification of milk protein allergens from complex food matricesBos taurusQ Exactive PlusRamachandran, B. and M.L. Downs, Development an...No15PXD040564
2023-03-02 Salinity-responsive histone PTMs identified in Mozambique tilapia tissuesOreochromis mossambicusimpact IIPublication pendingNo18PXD040557
2023-03-01 A strategy to characterize the global histone PTM landscape within tissues of non-model organismsOreochromis mossambicusimpact IIMojica EA, Kültz D. A Strategy to Characterize ...No9PXD040536
2023-02-27 Metrologically traceable quantification of three apolipoprotein E isoforms in cerebrospinal fluidHomo sapiensXevo TQ-SHuynh HH, Kuch K, Orquillas A, Forrest K, Barah...No27PXD038803
2023-02-17 Correlative study using immuno-MRM in the Cancer Immunotherapy Trials Network (CITN-10) phase 2 clinical trial of pembrolizumab for the treatment of refractory or relapsed Mycosis fungoides (MF) and Sezary syndrome (SS)Homo sapiensQTRAP 5500Whiteaker JR, Zhao L, Schoenherr RM, Huang D, L...No2 
2023-02-06 PeakDecoder enables machine learning-1 based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurementsPseudomonas putida KT2440TSQ AltisNature CommunicationsYes1 
2023-01-18 Degradation kinetics of lignocellulolytic enzymes in a biogas reactor by quanti-tative mass spectrometryLentinula edodestimsTOF ProKüchler, J.; Willenbücher, K.; Reiß, E.; Nuß, L...No3 
2022-12-20 Elucidating Fibroblast Growth Factor-induced kinome dynamics using targeted mass spectrometry and dynamic modelingHomo sapiensTSQ AltisVeth TS, Francavilla C, Heck AJR, Altelaar M. E...Yes6PXD039005
2022-12-12 Synergistic targeting of DNA-PK and KIT signaling pathways in KIT mutant acute myeloid leukemiaMus musculusOrbitrap Exploris 480Murray HC, Miller K, Brzozowski JS, Kahl RGS, S...No6PXD030214
2022-12-07 Relative complement deficiency predicts development of islet autoimmunity and type 1 diabetesHomo sapiensTSQ AltisWebb-Robertson BM, Nakayasu ES, Dong F, Waugh K...Yes12 
2022-12-04 HIC1 interacts with FOXP3 multi protein complex: a novel mechanism to regulate human regulatory T cell differentiation and functionHomo sapiensTSQ VantageAndrabi SBA, Batkulwar K, Bhosale SD, Moulder R...Yes1PXD038532
2022-12-01 Dynamic Data Independent Acquisition Mass Spectrometry with Real-Time Retrospective AlignmentHomo sapiensOrbitrap Fusion LumosHeil LR, Remes PM, Canterbury JD, Yip P, Barsho...No2PXD038508
2022-11-30 Monitoring extended stable isotope-labeled synthetic peptides as a quality control for protease digestion in targeted, multiplexed mass spectrometry-based assaysHomo sapiensQTRAP 6500,QTRAP 5500Yes5PXD038465
2022-11-25 Dynamic monitoring of myeloma minimal residual disease with targeted mass spectrometryHomo sapiensOrbitrap Exploris 120Noori S, Wijnands C, Langerhorst P, Bonifay V, ...No47PXD038370
2022-11-17 Effects of alpha-crystallin gene knockout on zebrafish lens developmentDanio rerioQ Exactive HFNo1PXD030918
2022-11-10 Orthogonal proteomics methods warrants development of Duchenne Muscular Dystrophy biomarkersHomo sapiensQ Exactive HFJohansson C, Hunt H, Signorelli M, Edfors F, Ho...Yes2PXD038089
2022-11-02 Quantitative proteomics and phosphoproteomics of urinary extracellular vesicles define putative diagnostic biosignatures for Parkinson’s diseaseHomo sapiensQ Exactive HF-XHadisurya, M., Li, L., Kuwaranancharoen, K. et ...No1PXD032175
2022-10-28 Sirtuin 5 Reduces Malonylation in Non-mitochondrial Metabolic Pathways in Diabetic Kidney DiseaseMus musculusQ ExactiveBaek J, Sas K, He C, Nair V, Giblin W, Inoki A,...Yes1PXD037819
2022-10-27 Characterizing the origin of blood plasma proteins from organ tissues in rainbow trout (Oncorhynchus mykiss) using a comparative non-targeted proteomics approachOncorhynchus mykiss6545 Q-TOF LC/MS,1200 series LC/MSD SLTannouri N, Simmons DBD. Characterizing the ori...No24PXD037782
2022-10-06 Analysis of the effect of ClpC1 directed antibiotics on ClpC1, ClpC2 and ClpC3 protein levels.Mycolicibacterium smegmatisQ Exactive HF-X,Orbitrap Exploris 480Hoi DM, Junker S, Junk L, Schwechel K, Fischel ...Yes3PXD037198
2022-09-27 Serum APOC1 levels are decreased in young autoantibody positive children who rapidly progress to type 1 diabetesHomo sapiensTSQ VantageHirvonen MK, Lietzén N, Moulder R, Bhosale SD, ...Yes6PXD033946
2022-09-24 Differential isotope labelling by amino acids (DILAC) reveals metabolic cross-feeding and phenotypic heterogeneity in a clonal cell populationSaccharomyces cerevisiaeTripleTOF 6600Stephan Kamrad, Clara Correia-Melo, Lukasz Szyr...No7PXD036959
2022-09-15 The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 and is targeted by a bacterial type-III effectorArabidopsis thalianaOrbitrap Fusionaccepted for publication in EMBONo1PXD036761
2022-09-05 Activity-dependent regulation of SLK phosphorylationMus musculusQ ExactivePublication pendingNo2PXD036547
2022-09-05 Reduction of MRM protein target list using correlation analysisBos taurus6495A Triple Quadrupole LC/MSEbhardt HA, Ponchon P, Theodosiadis K, Fuerer C...No1PXD036543
2022-08-25 Multisite proteome provides insights into the biology and prognostic markers for head and neck cancerHomo sapiensOrbitrap Exploris 240Busso-Lopes AF, Neves LX, Câmara GA, Granato DC...No1PXD036311
2022-08-23 Absolute and relative quantitation of ATI in modified wheatTriticum aestivum subsp. aestivum, Triticum turgidum subsp. durumTSQ Vantage,Q Exactive PlusGeisslitz S, Islam S, Buck L, Grunwald-Gruber C...Yes3 
2022-08-16 Dynamic acylome reveals metabolite driven modifications in Syntrophomonas wolfeiSyntrophomonas wolfeiOrbitrap Exploris 480No1PXD036088
2022-08-10 Validation of known and novel AKT, S6K and RSK targets by targeted MSMus musculusQ Exactive PlusFricke AL, Mühlhäuser WWD, Reimann L, Zimmerman...Yes1PXD035962
2022-07-29 Sampling the proteome by emerging single-molecule and mass-spectrometry based methodsHomo sapiensOrbitrap EclipseMacCoss MJ, Alfaro JA, Faivre DA, Wu CC, Wanunu...No1PXD035637
2022-07-08 Kinase activity profiling in breast cancer samplesHomo sapiensTSQ AltisYes1PXD035186
2022-07-07 MRM based validation of target antigen expression in Pituitary Adenoma patientsHomo sapiensTSQ AltisEvaluation of autoantibody signatures in Pituit...No1PXD035165
2022-06-27 NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotencyHomo sapiensTripleTOF 5600+,TripleTOF 5600No1PXD021497
2022-06-26 Longitudinal evaluation of biomarkers in wound fluids of venous leg ulcers treated with a protease-modulating wound dressingHomo sapiensOrbitrap Exploris 480Mikosiński J, Kalogeropoulos K, Bundgaard L, La...Yes4PXD025748
2022-06-25 Tandem Mass Tag-Based Quantitative Proteomic Profiling Identifies Novel Serum Biomarkers of Drug-Induced Liver Injury in HumansHomo sapiensOrbitrap Exploris 480Ravindra KC, Vaidya VS, Wang Z, Federspiel JD, ...No3PXD034882
2022-06-20 Mass spectrometry-driven discovery of neuropeptides mediating nictation behavior of nematodesCaenorhabditis elegansQ Exactive HF-XCockx B, Van Bael S, Boelen R, Vandewyer E, Yan...No2 
2022-06-15 A Peptide-Centric Quantitative Proteomics Dataset for the Phenotypic Assessment of Alzheimer’s DiseaseHomo sapiensOrbitrap Fusion LumosMerrihew GE, Park J, Plubell D, Searle BC, Keen...No27PXD034525
2022-06-13 Sortase A-cleavable CD1d identifies sphingomyelins as major class of CD1d-associated lipidsHomo sapiensQ Exactive HFSortase A-cleavable CD1d identifies sphingomyel...Yes1PXD034495
2022-06-08 Retrospective longitudinal monitoring of multiple myeloma patients by mass spectrometry using archived serum protein electrophoresis gels and de novo sequence analysisHomo sapiensQ Exactive HFNoori S, Zajec M, Russcher H, Tintu AN, Broijl ...No10PXD034406
2022-06-02 Multiple phosphorylation combinatorially regulates IFI16 antiviral immune signalingHomo sapiensQ Exactive HFNo2 
2022-05-25 Rapid assessment of lipidomics sample purity and quantity using attenuated total reflectance Fourier-transform infrared spectroscopyHomo sapiens6470A Triple Quadrupole LC/MSRobinson, H.; Molendijk, J.; Shah, A.K.; Rahman...No1 
2022-05-09 SARS-CoV-2 PRM-MS Assay with Clinical Patient SamplesHomo sapiensQ Exactive HFGajbhiye A, Nalbant A, Heunis T, Sidgwick F, Po...No1PXD033790
2022-05-03 Addressing the Protease Bias in Quantitative ProteomicsHomo sapiensTSQ AltisWoessmann J, Kotol D, Hober A, Uhlén M, Edfors ...Yes12PXD033574
2022-04-28 A proteomics investigation of cigarette smoke exposed Wistar rats revealed improved anti-inflammatory effects of the cysteamine nanoemulsions delivered via inhalationRattus norvegicusTSQ AltisSharma G, Pund S, Govindan R, Nissa MU, Biswas ...No1PXD033559
2022-04-28 Iron-Regulated Assembly of the Cytosolic Iron-Sulfur Cluster Biogenesis MachineryHomo sapiensOrbitrap Fusion LumosFan X, Barshop WD, Vashisht AA, Pandey V, Leal ...No3PXD033557