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2024-06-10 Swift Universal Glycan Acquisition (SUGA) Enables Quantitative Glycan Profiling Across Diverse Sample TypesBos taurus, Chinese hamster, Homo sapiensOrbitrap Fusion LumosNo1 
2024-06-04 Linear Ion Trap Global to Targeted Proteomics: A workflow for targeted proteomics assay development using a versatile linear ion trapMus musculusStellarA workflow for targeted proteomics assay develo...No6PXD052847
2024-05-30 Characterization of Stellar MSHomo sapiens, Gallus gallus, Escherichia coliStellarRemes PM, Jacob CC, Heil LR, Shulman N, MacLean...Yes17PXD052734
2024-05-30 Tutorials on How to Use PRM Conductor, a Skyline External Tool  Remes, P. M.; Jacob, C. C.; Heil, L. R.; Shulma...No21 
2024-05-21 Coho ovarian tissue response to gonadotropinsOncorhynchus kisutchTSQ AltisNo1PXD052463
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
2024-03-12 Targeted MS assay to evaluate Cereblon neosubstrate changes in rabbit embryos following maternal administration of IMiDsOryctolagus cuniculusOrbitrap EclipsePublication pendingNo6PXD050568
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 
2024-01-24 Loss of POGLUT2 and 3 eliminates O-glucose at predicted sites but does not alter other modifications on EGFsMus musculusQ Exactive PlusNeupane S, Williamson DB, Roth RA, Halabi CM, H...No5PXD043827
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
2023-11-25 Serum proteomics of mother-infant dyads carrying HLA-conferred type 1 diabetes riskHomo sapiensTSQ VantageBhosale SD, Moulder R, Suomi T, et al (2024) Se...Yes1PXD047235
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 
2023-08-27 Antimicrobial peptides of the apidaecin family inhibit the bacterial ribosome by multimodal mechanisms involving three different sites on the large ribosomal subunitEscherichia coliSYNAPT G2-SiLauer SM, Reepmeyer M, Berendes O, Klepacki D, ...No3PXD044892
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 
2023-02-02 MED6-189: An effective Antimalarial Kalihinol Analog Targets Plasmodium falciparum Apicoplast and Membrane BiogenesisPlasmodium falciparumXevo G2-XS QTof,Xevo TQ MSNatureNo4 
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
2022-11-30 Control of intracellular pH and bicarbonate by CO2 diffusion into human spermHomo sapiensOrbitrap Exploris 480Grahn E, Kaufmann SV, Askarova M, Ninov M, Welp...Yes16 
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