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2022-12-01 Dynamic Data Independent Acquisition Mass Spectrometry with Real-Time Retrospective AlignmentHomo sapiensOrbitrap Fusion LumosPublication pendingNo2PXD038508
2022-11-17 Effects of alpha-crystallin gene knockout on zebrafish lens developmentDanio rerioQ Exactive HFNo1PXD030918
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
2022-07-29 Sampling the proteome by emerging single-molecule and mass-spectrometry based methodsHomo sapiensOrbitrap EclipsePublication pendingNo1PXD035637
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
2022-06-24 A novel overlapping gene peu-1 affects the translation of zyxin in C. elegans.Caenorhabditis elegansQ Exactive HF-XYes1PXD034878
2022-06-15 A Peptide-Centric Quantitative Proteomics Dataset for the Phenotypic Assessment of Alzheimer’s DiseaseHomo sapiensOrbitrap Fusion LumosPublication pendingNo27PXD034525
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
2022-05-25 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 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 LumosSubmitted.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 HFPublication pendingNo17PXD025879
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
2022-01-05 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
2021-12-13 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
2021-11-30 MRM quantification of circulating CFP-10 in TB patientsMycobacterium tuberculosisTSQ AltisShu Q, Liu S, Alonzi T, LaCourse SM, Singh DK, ...Yes10PXD021150
2021-11-25 Evaluation of volumetric absorptive microsampling and mass spectrometry data-independent acquisition in hemoglobin related clinical markersHomo sapiensQ Exactive HF-XLima DA, Schuch RA, Salgueiro JS, Pintão MCT, C...No1PXD029918
2021-11-22 Uncovering Xenobiotics in the Dark Metabolome using Ion Mobility Spectrometry, Mass Defect Analysis and Machine Learning 6560 Q-TOF LC/MSFoster M, Rainey M, Watson C, Dodds JN, Kirkwoo...No1 
2021-11-17 Absolute quantification of influenza virus proteinsInfluenza A virus (A/Puerto Rico/8/1934(H1N1))timsTOF ProKüchler J, Püttker S, Lahmann P, Genzel Y, Kupk...Yes8PXD029784
2021-11-16 A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomicsHomo sapiens, Escherichia coli, Saccharomyces cerevisiaeTripleTOF 5600,TripleTOF 6600,timsTOF Pro,Q Exactive HF-X,SYNAPT G2-Si,Synapt MSVan Puyvelde B, Daled S, Willems S, Gabriels R,...No6 
2021-11-10 Skyline Batch: An Intuitive User Interface for Batch Processing with SkylineSaccharomyces cerevisiaeTripleTOF 5600Marsh AN, Sharma V, Mani SK, Vitek O, MacCoss M...No4PXD029665
2021-11-10 Skyline Batch: An Intuitive User Interface for Batch Processing with SkylineHomo sapiensQ ExactiveMarsh AN, Sharma V, Mani SK, Vitek O, MacCoss M...Yes2PXD029663
2021-10-20 Gill proteome networks explain salinity tolerance of Oreochromis mossambicusOreochromis mossambicusimpact IIpublication pendingNo4PXD029254
2021-10-14 Quantification of Soy-Derived Ingredients in Model Bread and Frankfurter Matrices with an Optimized LC-MS/MS External Standard Calibration WorkflowGlycine maxQ Exactive PlusKrager J, Baumert JL, Downs M. Quantification o...Yes2PXD029137
2021-10-13 RGI-GOLVEN signalling promotes FLS2 abundance to regulate plant immunityArabidopsis thalianaQ Exactive HF-XNo2PXD023855
2021-10-08 Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury SeverityHomo sapiens6560 Q-TOF LC/MSKirkwood KI, Christopher MW, Burgess JL, Littau...No6 
2021-10-07 Selected reaction monitoring based analysis of proteins in liver tissue of Labeo rohitaLabeo rohitaTSQ AltisPublication pendingYes2PXD028997
2021-10-07 Monitoring of histidine methylated Rpl3pSaccharomyces cerevisiaeOrbitrap Fusion LumosNo1 
2021-10-05 Rapid and Sensitive Detection of SARS-CoV-2 Infection Using Quantitative Peptide Enrichment AnalysisHomo sapiens, SARS-CoV-2Xevo TQ-XSHober A, Tran-Minh KH, Foley D, McDonald T, Vis...Yes1PXD026366
2021-10-05 MS quantification of circulating CFP-10, p24 and VP40Human immunodeficiency virus 1, EBOV, SUDV, Mycobacterium tuberculosisTSQ Altis,Orbitrap Fusion LumosShu Q, Kenny T, Fan J, Lyon CJ, Cazares LH, Hu ...Yes12PXD021149
2021-10-01 Quantification of organelle membrane contact site protein abundances during infection with human virusesHomo sapiens, HHV-5, HSV-1, HCoV-OC43, Influenza A virus (A/Puerto Rico/8/1934(H1N1))Q Exactive HFPublication pendingNo4PXD023761
2021-10-01 Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approachHomo sapiensXevo TQ-SMarques TM, van Rumund A, Kersten I, Bruinsma I...Yes1PXD028888
2021-09-27 Diagnosing pleural effusions using mass spectrometry-based multiplexed targeted proteomics quantitating mid- to high-abundance markers of cancer, infection/inflammation and tuberculosisHomo sapiensXevo TQ MSRobak, A., Kistowski, M., Wojtas, G. et al. Dia...No1 
2021-09-21 Highly multiplexed quantitative phosphosite assay for biology and preclinical studiesHomo sapiensTSQ QuantivaKeshishian H, McDonald ER 3rd, Mundt F, Melanso...Yes9PXD026939
2021-09-18 Next-generation Serology by Mass Spectrometry:Readout of the SARS-CoV-2 Antibody RepertoireHomo sapiensQ Exactive HFMelani RD, Des Soye BJ, Kafader JO, Forte E, Ho...No1PXD028627
2021-09-13 SARS-CoV2 Immunocomplex by LC-MS/MS on vaccinated cohortHomo sapiensXevo TQ-SPublication pendingNo3PXD028450
2021-09-06 HDL proteomics on CPROBE samplesHomo sapiensOrbitrap FusionShao B, Mathew AV, Thornock C, Pennathur S; Mic...No2PXD028216
2021-09-03 Organ wise targeted mass spectrometric analysis of proteins in Labeo rohita using SRM/MRM approachLabeo rohitaTSQ AltisNissa MU, Pinto N, Mukherjee A, Reddy PJ, Ghosh...Yes1PXD028017
2021-09-03 Ocular proteomic and transcriptomic changes with aging in response to lensectomy in a rabbit model of lensectomy with intraocular lens insertionNew Zealand rabbitOrbitrap Fusion LumosNo1PXD028205
2021-09-02 Triage of >1300 candidate biomarkers in plasma using internal standard-triggered parallel reaction monitoring mass spectrometryHomo sapiensOrbitrap EclipsePublication pendingYes16 
2021-08-31 Mitochondrial inorganic polyphosphate (polyP) is a contributor towards maintaining cellular bioenergetics in SH-SY5Y cells: a proteomics and metabolomics approachHomo sapiensOrbitrap Fusion LumosGuitart-Mampel M, Urquiza P, Carnevale Neto F, ...No2PXD028185
2021-08-30 2020_Human BAK125 kit _Room TemperatureHomo sapiens6495B Triple Quadrupole LC/MS,Xevo TQ-XSGaither C, Popp R, Borchers SP, Skarphedinsson ...Yes13PXD028179
2021-08-24 Plasma Protein Biomarker Model for Screening Alzheimer Disease Using Multiple Reaction Monitoring-Mass SpectrometryHomo sapiens6490 Triple Quadrupole LC/MSKim Y, Kim J, Son M, Lee J, Yeo I, Choi KY, Kim...Yes1 
2021-08-20 A hierarchical transcriptional network controls appressorium-mediated plant infection by the rice blast fungus Magnaporthe oryzaeMagnaporthe oryzaeOrbitrap Eclipse,Orbitrap FusionOsés-Ruiz M, Cruz-Mireles N, Martin-Urdiroz M, ...No1PXD028052
2021-08-17 Simultaneous quantitative profiling of clinically relevant immune markers in neonatal stool swabs to reveal inflammationHomo sapiens6495B Triple Quadrupole LC/MSVidova V, Benesova E, Klanova J, Thon V, Spacil...Yes13PXD027988
2021-08-17 A comparative study of synthetic winged peptides for absolute protein quantificationHomo sapiens6495B Triple Quadrupole LC/MSBenesova E, Vidova V, Spacil Z. A comparative s...Yes9PXD027985
2021-08-17 Multisite proteome provides insights into the biology and prognostic markers for head and neck cancerHomo sapiensXevo TQ-XS,ACQUITY UPLCBusso-Lopes AF, Neves LX, Câmara GA, Granato DC...Yes2PXD027984
2021-08-16 Targeted MS based multi-omic analysis of blood plasma from COVID-19 patients to predict survivalHomo sapiens6495B Triple Quadrupole LC/MSRichard VR, Gaither C, Popp R, Chaplygina D, Br...Yes1PXD027959
2021-08-16 Whole blood peptide assay stability by MRM-MSHomo sapiens6495B Triple Quadrupole LC/MSGaither C, Popp R, Zahedi RP, Borchers CH. Mult...Yes1PXD027957
2021-08-16 Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS) 6560 Q-TOF LC/MSYes2 
2021-08-13 Plasma proteomic analysis to identify potential biomarkers of histologic chorioamnionitis in women with preterm premature rupture of membranesHomo sapiens6495A Triple Quadrupole LC/MSLee JE, Dan K, Kim HJ, Kim YM, Park KH. Plasma ...Yes2 
2021-08-02 Linking post-translational modifications and protein turnover by site-resolved protein turnover (SPOT) profilingHomo sapiensQ Exactive HF-X,Orbitrap Fusion LumosZecha J, Gabriel W, Spallek R, Chang YC, Mergne...No7PXD023234
2021-08-02 Targeted MRM assay Complement System AMD cohortHomo sapiensXevo TQ-SAcar IE, Willems E, Kersten E, Keizer-Garritsen...Yes1PXD027689
2021-07-31 Targeted mass spectrometry enables multiplexed quantification of immunomodulatory proteins in clinical biospecimensHomo sapiensQTRAP 5500Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM...No3PXD029167
2021-07-27 Profiling Tryptophan Catabolites of Human Gut Microbiota and Acute-Phase Protein Levels in Neonatal Dried Blood SpecimensHomo sapiens6495B Triple Quadrupole LC/MSAust AC, Benesova E, Vidova V, Coufalikova K, S...Yes5PXD027606
2021-07-23 Quantification of the ratio between the two PsbO protein isoforms in the thylakoids lumen of Arabidopsis thalianaArabidopsis thalianaTSQ VantageGollan PJ, Trotta A, Bajwa AA, Mancini I, Aro E...No1PXD027514
2021-07-20 Age-Related Disruption of the Proteome and Acetylome in Mouse Hearts Correlates with Differential Loss of Function that is Attenuated by SS-31 and NMNMus musculusQ Exactive HF-XWhitson JA, Johnson R, Wang L, Bammler TK, Imai...No3PXD027458
2021-07-19 The metabolome as a biomarker of aging in Drosophila melanogasterDrosophila melanogasterTSQ VantageZhao X, Golic FT, Harrison BR, Manoj M, Hoffman...No2 
2021-07-19 DDR2 pharmacodynamic profilingHomo sapiensQTRAP 5500Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Ke...Yes4 
2021-07-16 Loss of DNAJC3 impairs cholesterol metabolism and mitochondrial functionHomo sapiensOrbitrap Fusion LumosJennings MJ, Hathazi D, Nguyen CDL, Munro B, Mü...Yes1PXD027372
2021-07-10 Comparison of allergen quantification strategies for egg, milk, and peanut in food using targeted LC-MS/MS QTRAP 6500Xiong W, Parker CH, Boo CC, Fiedler KL. Compari...No6 
2021-07-09 Optimized liquid and gas phase fractionations increase HLA-peptidome coverage for primary cell and tissue samplesHomo sapiensTSQ QuantisKlaeger S, Apffel A, Clauser KR, Sarkizova S, O...Yes1PXD027165
2021-07-01 Synthetic biology meets proteomics: Construction of à la carte QconCATs for absolute protein quantificationEscherichia coliQTRAP 5500Johnson J, Harman VM, Franco C, Emmott E, Rockl...No1PXD027047
2021-06-21 Targeted Detection of SARS-CoV-2 Protein Variants by Mass SpectrometryHomo sapiensOrbitrap Exploris 480Maus A, Renuse S, Kemp J, Madugundu AK, Vanderb...Yes2 
2021-06-21 Targeted validation of significantly altered semen proteins in COVID-19 patientsHomo sapiensTSQ AltisGhosh S, Parikh S, Nissa MU, Acharjee A, Singh ...Yes2PXD026849
2021-06-21 Validation of proteins showing significant dysregulation from shotgun proteomics experiments in longitudinal plasma samples of COVID-19 patientsHomo sapiensTSQ AltisSuvarna K, Salkar A, Palanivel V, Bankar R, Ban...Yes1PXD026848
2021-06-17 Multiple reaction monitoring (MRM) based data for targeted validation of proteins in Labeo rohitaLabeo rohitaTSQ AltisPublication pendingNo1PXD026757
2021-06-10 The global Proteome and Ubiquitinome of bacterial and viral co-infected Bronchial Epithelial CellsHomo sapiens, Streptococcus pyogenes, Influenza A virus (A/Germany-BY/74/2009(H1N1)), Staphylococcus aureusQ ExactiveSura T, Surabhi S, Maaß S, Hammerschmidt S, Sie...No1PXD026625
2021-06-10 Targeted validation of interaction between ErbB4 JM-a isoform and β1 integrinHomo sapiensOrbitrap Fusion LumosPublication pendingNo1PXD026617
2021-06-07 GFAP and MBP peptides in Traumatic Brain InjuryHomo sapiensTSQ AltisSarkis GA, Lees-Gayed N, Banoub J, Abbatielo SE...Yes1PXD026550
2021-05-25 Analytical Comparison of absolute quantification strategies to investigate the Insulin signaling pathway in fat cellsMus musculusQ Exactive HFLi T, Hentschel A, Ahrends R. Analytical compar...Yes5PXD026204
2021-05-06 Mapping interactome networks of FOSL1 and FOSL2 in human Th17 cellsHomo sapiensQ Exactive HFShetty A, Bhosale SD, Tripathi SK, Buchacher T,...Yes2PXD025840
2021-05-03 C.auto_3gas_absquant: Spike-in SIL-protein stock absolute quantificationClostridium autoethanogenumQ Exactive HF-XPublication pendingNo1PXD025760
2021-05-03 C.auto_3gas_absquant: Label-free proteome-wide absolute quantificationClostridium autoethanogenumQ Exactive HF-XNo1 
2021-05-03 C.auto_3gas_absquant: Anchor protein absolute quantificationClostridium autoethanogenumQ Exactive HF-XYes1