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2024-02-18 AD-BXD Mouse PreFrontal Cortex ProteomicsMus musculusOrbitrap Fusion,Orbitrap Fusion LumosNo50PXD045403
2024-01-26 Fecal Microbiota Transplant_Bile AcidHomo sapiens6560 Q-TOF LC/MSMetagenomic, metabolomic, and lipidomic shifts ...No2 
2024-01-15 Targeted proteomics of plasma from de novo Parkinson's diseaseHomo sapiensXevo TQ MS,ACQUITY UPLCProteomics and machine learning identify a dist...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
2023-12-02 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 
2023-10-30 METLIN-CCS: an ion mobility spectrometry
collision cross-section database
  Baker ES, Hoang C, Uritboonthai W, Heyman HM, P...No1 
2023-10-02 In-Gel Digest to identify Aspergillus fumigatus protein antigens in severe equine asthma (SEA)Aspergillus fumigatusSYNAPT G2-SiJentsch M-C, Lübke S, Schrödl W, Volke D, Kriz...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
2023-09-09 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
2023-09-01 Assessing Per- and Polyfluoroalkyl Substances (PFAS) in Fish Fillet Using Non-Targeted Analyses 6560 Q-TOF LC/MSYes1 
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 
2023-07-02 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 IIPublication pendingNo1PXD043046
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
2023-03-09 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 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 IIPublication pendingNo9PXD040536
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
2022-12-04 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
2022-07-07 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
2022-04-21 Targeted proteomics (parallel reaction monitoring) to quantify starch-biosynthetic proteins in yeastSaccharomyces cerevisiae, Arabidopsis thalianaQ ExactivePublication pendingYes2PXD033364
2022-04-14 An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemiaHomo sapiensTripleTOF 6600,TripleTOF 5600No1PXD031500
2022-04-07 Elevation of fatty acid desaturase 2 in esophageal adenocarcinoma increases polyunsaturated lipids and may exacerbate bile acid-induced genotoxicityHomo sapiens6470A Triple Quadrupole LC/MSMolendijk J, Kolka CM, Cairns H, Brosda S, Moha...No2 
2022-03-29 Mouse apolipoproteome study - hyperlipidemic mouse modelsMus musculusTSQ AltisSteffensen LB, Larsen JH, Hansen DR, Tha TML, L...Yes8PXD032868
2022-03-24 The addition of FAIMS Increases Targeted Proteomics Sensitivity from FFPE Tumor BiopsiesHomo sapiensOrbitrap Fusion LumosSweet S, Chain D, Yu W, Martin P, Rebelatto M, ...Yes5PXD027134
2022-03-09 Prediction and experimental validation of a new salinity-responsive cis-regulatory element (CRE) in tilapiaOreochromis mossambicusimpact IIKim C, Wang X, Kültz D. Prediction and Experime...No1PXD032181
2022-02-23 HDL Proteomics in Coronary Artery Calcification in Type 1 Diabetes (CACTI) StudyHomo sapiensOrbitrap Fusion LumosShao B, Snell-Bergeon JK, Pyle LL, Thomas KE, d...No6PXD031854
2022-02-23 IFI16-mediated suppression of HSV-1 protein expressionHomo sapiens, Human herpesvirus 1Q Exactive HFPublication pendingNo1PXD031850
2022-02-16 Absolute Protein Quantitation of the Mouse Macrophage Toll-Like Receptor and Chemotaxis PathwaysMus musculusQ Exactive HFManes NP, Calzola JM, Kaplan PR, Fraser IDC, Ge...Yes1PXD031697
2022-02-14 Skin cancer-associated S. aureus downregulates DNA repair mechanisms, and promotes oxidative stress and DNA damage in human keratinocytesStaphylococcus capitis, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus6470A Triple Quadrupole LC/MSKrueger A, Mohamed A, Kolka CM, Stoll T, Zaugg ...No1PXD031676
2022-02-03 PrP concentration in the central nervous system: regional variability, genotypic effects, and pharmacodynamic impactHomo sapiens, Rattus norvegicusTSQ QuantivaMortberg MA, Zhao HT, Reidenbach AG, Gentile JE...Yes2PXD031432
2022-02-03 A scalable, targeted mass spectrometry-based assay for monitoring the progression of herpesvirus infectionsHuman betaherpesvirus 5, Herpes simplex virus 1, Kaposi's sarcoma-associated herpesvirus, Homo sapiensQ Exactive HFKennedy MA, Tyl MD, Betsinger CN, Federspiel JD...No17PXD025879
2022-02-03 Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum.Plasmodium falciparumXevo TQ-XS,Xevo G2-XS TofHollin T, Abel S, Falla A, Pasaje CFA, Bhatia A...No6 
2022-02-02 Cov²MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid proteinSARS-CoV-2Xevo TQ-XS,TripleTOF 6600No36PXD031401
2022-01-31 Imetelstat Is a Potent Inducer of Ferroptosis That Effectively Diminishes Acute Myeloid Leukemia Burden and Delays Relapse Following Pro-Oxidant TherapyHomo sapiens6470A Triple Quadrupole LC/MSBruedigam C, Porter AH, Song A, Vroeg In de Wei...No2 
2022-01-18 The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5Homo sapiensTSQ QuantivaMaven et al., The multi-lineage transcription f...Yes1PXD031059
2022-01-10 One-Pot Isotope Dilution PRM for Quantitative Protein Heterogeneity in Red Blood CellsHomo sapiensOrbitrap Fusion ETD,Orbitrap Exploris 480,6495B Triple Quadrupole LC/MSEshghi A, Xie X, Hardie D, Chen MX, Izaguirre F...Yes14PXD030875
2022-01-05 FastCAT accelerates absolute quantification of proteins by using multiple short non-purified chimeric standardsHomo sapiensQ Exactive HFpublication pendingYes1PXD030762
2021-12-22 OE240 PFAS Method Validation Orbitrap Exploris 240TBDNo1 
2021-12-15 Improving peptide fragment ion detection using travelling wave ion mobility spectrometry with signal enhancement MSE (seMSE)Escherichia coli, Bos taurus, Saccharomyces cerevisiae, Oryctolagus cuniculusSYNAPT G2-SiRojas Echeverri JC, Volke D, Milkovska-Stamenov...No3PXD030431
2021-12-15 Proteomic Blueprint of the Pituitary anterior and posterior lobes for better understanding of the physiology of pituitary gland.Homo sapiensOrbitrap FusionBanerjee A, Biswas D, Barpanda A, Halder A, Sib...No1PXD029991
2021-12-13 Proteomic Analysis of Oil-Roasted Cashew Using a Customized Allergen-Focused Protein DatabaseAnacardium occidentaleQ Exactive PlusChen S, Downs ML. Proteomic Analysis of Oil-Roa...No1PXD030375
2021-12-09 Preserving the phosphoproteome of clinical biopsies using a quick freeze collection deviceMus musculusQTRAP 5500Publication pendingYes3PXD030367
2021-12-09 Check of selected NTR peptide spectra by comparison with synthetic peptidesHomo sapiensOrbitrap Fusion LumosBogaert A, Fijalkowska D, Staes A, Van de Steen...No1PXD030285
2021-12-08 Relative quantification of acetylated histone peptides in HAP1 cells after treatment with MS-275Homo sapiensQ Exactive HF-XPublication pendingNo1PXD030272