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2024-10-14 Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomicsHomo sapiens, Saccharomyces cerevisiaeOrbitrap Fusion Lumos,Orbitrap Exploris 480,Orbitrap AstralWen, Bo, Chris Hsu, Wen-Feng Zeng, Michael Riff...No6PXD056793
2024-10-10 Streamlining Workflows in Ion Mobility Data Acquisition, Calibration and Processing: A Cross-Platform Assessment of Drift Tube and Traveling Wave Methodologies 6560 Q-TOF LC/MSYes2 
2024-09-26 High-resolution metaproteomic analysis of an ocean microbiome preceding a Chaetoceros bloommarine metagenomeOrbitrap Fusion LumosNo3PXD052911
2024-09-12 RPLC-IM-MS of S. aureus Branched LipidsStaphylococcus aureusSynapt XSNo2 
2024-08-22 Automated sequential derivatization for Gas Chromatography-[Orbitrap] Mass Spectrometry based metabolite profiling of human blood-based samplesHomo sapiensQ Exactive GC OrbitrapNo3 
2024-08-22 Meta-Analysis and DIA-MS-based Proteomic Investigation of COPD Patients and Asymptomatic Smokers in the Indian populationHomo sapiensOrbitrap FusionSharma G, Gupta DP, Ganguly K, Anand MP, Srivas...No1PXD055103
2024-08-19 Label-free Multiple Reaction Monitoring-Mass Spectrometry for Quantifying Phosphopeptides from Extracellular VesiclesHomo sapiensQTRAP 6500No13 
2024-08-16 A framework for quality control in quantitative proteomicsHomo sapiens, Mus musculus, Saccharomyces cerevisiae, Bos taurusOrbitrap Eclipse,Orbitrap Fusion Lumos,Orbitrap FusionTsantilas KA, Merrihew GE, Robbins JE, Johnson ...No9PXD051318
2024-07-25 Detection and Quantification of Drug-Protein Adducts in Human LiverHomo sapiens, fall armywormOrbitrap Exploris 480,Orbitrap EclipseZelter A, Riffle M, Shteynberg DD, Zhong G, Rid...No4PXD054246
2024-07-11 Absolute abundance of human crystallins in lensHomo sapiens, Mus musculusOrbitrap EclipseHalverson-Kolkind KA, Caputo N, Lampi KJ, Sriva...Yes4PXD053890
2024-06-25 External validation of serum biomarkers predicting short-term and mid/long-term relapse in Crohn’s disease patients stopping infliximabHomo sapiensXevo TQ-SPierre N, Huynh-Thu VA, Baiwir D, Mazzucchelli ...No2PXD051233
2024-06-21 A transformer model for de novo sequencing of data-independent acquisition mass spectrometry dataHomo sapiens, Mus musculusOrbitrap Astral,Q Exactive HF-XJustin Sanders, Bo Wen, Paul Rudnick, Rich John...No2PXD053291
2024-06-18 An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MSHomo sapiens, Mus musculusQ Exactive,Q Exactive HF,Orbitrap FusionLopes M, Lund PJ, Garcia BA. Optimized and Robu...Yes12PXD053212
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 musculusStellarNo6PXD052847
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 
2024-05-29 Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pigmentosaMus musculusQ ExactiveMontaser AB, Gao F, Peters D, Vainionpää K, Zhi...No1PXD052698
2024-05-27 Retinal proteome profiling of inherited retinal degeneration across three different mouse models suggests common drug targets in retinitis pigmentosaMus musculusQ ExactiveMontaser AB, Gao F, Peters D, Vainionpää K, Zhi...No1PXD052598
2024-05-21 Coho ovarian tissue response to gonadotropinsOncorhynchus kisutchTSQ AltisNo1PXD052463
2024-05-17 DIA Proteomics of Coho Salmon Ovaries Across 4 StagesOncorhynchus kisutchOrbitrap Fusion LumosTimmins-Schiffman E, Telish J, Field C, Monson ...No1PXD052361
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 
2024-05-13 A Novel High-Throughput Immunoaffinity LC-MS/MS Assay for P III-NP and other Fragments of Type III Procollagen in Human SerumHomo sapiensXevo TQ-SHuynh HH, Barahona-Carrillo L, Moncrieffe D, Co...No30PXD052245
2024-05-03 Lost in translation? Proteomic evidence for a muted molecular response to thermal stress in a stenothermal Antarctic fish and possible evolutionary mechanismsTrematomus bernacchiiimpact IIDowd WW, Kültz D. Lost in translation? Evidence...No3PXD051983
2024-04-30 Defective pgsA contributes to increased membrane fluidity and cell wall thickening in S. aureus with high-level daptomycin resistanceStaphylococcus aureusSynapt XSNo9 
2024-04-24 optiPRM: A targeted immunopeptidomics LC-MS workflow with ultra-high sensitivity for the detection of mutation-derived tumor neoepitopes from limited input materialHomo sapiensOrbitrap Exploris 480Salek M, Förster JD, Becker JP, Meyer M, Charoe...No7 
2024-03-12 Targeted MS assay to evaluate Cereblon neosubstrate changes in rabbit embryos following maternal administration of IMiDsOryctolagus cuniculusOrbitrap EclipseFederspiel JD, Catlin NR, Nowland WS, Stethem C...No6PXD050568
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 HFZheng T, Kotol D, Sjöberg R, Mitsios N, Uhlén M...Yes1PXD050060
2024-02-18 AD-BXD Mouse PreFrontal Cortex ProteomicsMus musculusOrbitrap Fusion,Orbitrap Fusion LumosNo50PXD045403
2024-02-06 Development of a fit-for-purpose multi-marker panel for early diagnosis of pancreatic ductal adenocarcinomaHomo sapiensQTRAP 5500Kim H, Huh S, Park J, Han Y, Ahn KG, Noh Y, Lee...Yes1 
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
2024-01-19 Mouse Skeletal Muscle SarcopeniaMus musculusOrbitrap EclipseKerr HL, Krumm K, Anderson B, Christiani A, Str...No4PXD048723
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
2024-01-04 Selected reaction monitoring of dysregulated proteins in gut tissue of Labeo rohita infected with Aeromonas hydrophilaLabeo rohitaTSQ AltisYes2PXD048261
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
2023-12-06 Evidence for an RNAi-independent role of DICER-LIKE2 in conferring growth inhibition and basal antiviral resistanceArabidopsis thalianaOrbitrap EclipseNielsen CPS, Arribas-Hernández L, Han L, Reiche...No1PXD046163
2023-12-03 It’s a trap: ClpP substrates caught in actionStaphylococcus aureusOrbitrap FusionAngew. Chem. Int. Ed. 2024, e202409220No1PXD047469
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+Van Puyvelde B, Hunter CL, Zhgamadze M, Savant ...No29PXD046249
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
2023-10-02 HAMSAB modified gut microbiota signature in human type 1 diabetes delays disease after transfer into gnotobiotic miceMus musculus6470A Triple Quadrupole LC/MSNo2 
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
2023-07-08 Multiple reaction monitoring based targeted validation of over-expressed proteins of high-grade gliomasHomo sapiensTSQ AltisVerma A, Patel R, Mahale A, Thorat RV, Rath SL,...Yes2PXD043621
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 IIMojica EA, Petcu KA, Kültz D. Environmental con...No2PXD042718
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 IIHua QQH, Kültz D, Wiltshire K, Doubleday ZA, Gi...No1PXD040795
2023-03-12 Dysregulations in the levels of lactate dehydrogenase and pyruvate kinase upon IL-17A and echinomycin treatments in human primary keratinocytesHomo sapiensTSQ AltisDhamija B, Marathe S, Sawant V, Basu M, Attrish...No1PXD040678
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 IIMojica EA, Fu Y, Kültz D. Salinity-responsive h...No18PXD040557
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 
2023-01-31 Validation of protein expression in kidney tissue of Labeo rohita during Edwardsiella tarda infectionLabeo rohita, Edwardsiella tardaTSQ AltisPinto N, Nissa MU, Yashwanth BS, Sathiyanarayan...No1PXD039749
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