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Welcome to Panorama Public, a repository of Skyline documents and supplementary data associated with published manuscripts.  Visitors may freely browse publicly available data, as well as download Skyline documents for further exploration with the Skyline software.   Details on publishing to Panorama Public are available here.  To learn more about Panorama visit panoramaweb.org.

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2020-02-07 Phospho-proteomic Profiling Dataset of Chemical Perturbations in Multiple Biological BackgroundsHomo sapiensQ Exactive HFDataset with its publication pendingYes28PXD017458
2020-02-07 Global Chromatin Profiling Dataset of Chemical Perturbations in Multiple Biological BackgroundsHomo sapiensQ Exactive PlusDataset with its publication pendingYes28PXD017459
2020-01-29 LipidCreator: A workbench to probe the lipidomic landscapeHomo sapiensQ Exactive HF,QTRAP 6500Yes4 
2020-01-24 Parallel reaction monitoring assay development for multiple sclerosis biomarkers in cerebrospinal fluid.Homo sapiens, Rattus norvegicusQ Exactive HFYes8PXD017281
2020-01-22 Data independent acquisition-based proteomics reveals a multi-scale picture of gene expression in Escherichia coliEscherichia coliTripleTOF 5600Yes1PXD017258
2019-12-19 Signaling proteins of a chemosensory pathway from sperm of Arbacia punctulataArbacia punctulataTSQ VantageAbsolute proteomic quantification reveals desig...Yes2PXD015502
2019-12-11 CRK2-mediated control of ROS production by phosphorylation of the RBOHD C-terminus in ArabidopsisArabidopsis thalianaQ Exactive PlusNo4PXD013525
2019-11-19 Mass spectrometry of in-gel digests reveals differences in amino acid sequences of high-molecular-weight glutenin subunits in spelt and emmer compared to common wheatTriticum aestivum, Triticum spelta, Triticum dicoccoidesQTRAP 6500+Geisslitz S, America AH, Scherf KA. Mass spectr...No2PXD016342
2019-11-14 ACE over expression in myeloid cells increases oxidative metabolism and cellular ATPMus musculusQTRAP 6500+DuoYao Cao, Weston R. Spivia, Luciana C. Veiras...Yes1 
2019-10-29 Characterization and relative quantitation of wheat, rye and barley gluten protein types by LC-MS/MScommon wheat, rye, barleyTripleTOF 6600,QTRAP 6500Lexhaller B, Colgrave ML, Scherf KA. Characteri...No6PXD016065
2019-10-08 Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-Labeled Recombinant Protein Fragments Based SRM AssayHomo sapiens6490 Triple Quadrupole LC/MSHober A, Edfors F, Ryaboshapkina M, Malmqvist J...Yes8PXD013314
2019-10-02 Min protein in vitro protein expression kineticsEscherichia coli6460 Triple Quadrupole LC/MSGodino E, López JN, Foschepoth D, Cleij C, Doer...No2PXD015686
2019-09-28 Comprehensive Detection of Isopeptides between Human Tissue Transglutaminase and Gluten PeptidesTriticum, humanQ Exactive HFLexhaller B, Ludwig C, Scherf KA. Comprehensive...No4 
2019-09-14 Antibody-free multiplex measurement of 23 human cytokines in primary cell culture secretome using targeted multiple reaction monitoring mass spectrometryHomo sapiens6490 Triple Quadrupole LC/MSKrueger A, Stoll T, Shah AK, Sinha R, Frazer IH...Yes26PXD015448
2019-09-05 Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypesHomo sapiensLTQ Orbitrap VelosAshwood C, Waas M, Weerasekera R, Gundry RL. Re...No5 
2019-08-22 Skyline for Small Molecules: A Unifying Software Package for Quantitative MetabolomicsHomo sapiens, Mus musculusXevo TQ-S,Triple Quad 5500,Synapt G2 HDMSAdams KJ, Pratt B, Bose N, Dubois LG, St.John-W...Yes6 
2019-08-21 Multiplexed MRM concentration measurements of >200 endogenous proteins in dried blood spots for biomarker discovery and validationHomo sapiens6490 Triple Quadrupole LC/MSEshghi A, Pistawka AJ, Liu J, Chen M, Sinclair ...Yes13PXD015118
2019-08-19 Urinary PRM analysis of early type 1 diabetesHomo sapiensQ Exactive HF-XVan JAD, Clotet-Freixas S, Zhou J, Batruch I, S...Yes1PXD012389
2019-08-14 Structural control of regioselectivity in an unusual bacterial acyl-CoA dehydrogenaseEscherichia coli6460 Triple Quadrupole LC/MSBlake-Hedges JM, Pereira JH, Cruz-Morales P, Th...No3 
2019-08-09 Are These Cardiomyocytes? Protocol Development Reveals Impact of Sample Preparation on the Accuracy of Identifying Cardiomyocytes by Flow CytometryHomo sapiensOrbitrap Fusion LumosWaas M, Weerasekera R, Kropp EM, Romero-Tejeda ...Yes1PXD014971
2019-08-09 Peptide signature for the fast detection of bacterial species in Urinary Tract infections using LC-MSEscherichia coli K-12, Klebsiella pneumoniae subsp. pneumoniae ATCC 700721, Enterococcus faecalis V583, Streptococcus agalactiae 2603V/ROrbitrap Fusion ETD,Q Exactive HF-XRoux-Dalvai F, Gotti C, Leclercq M, Helie M-C, ...No4PXD014970
2019-08-02 Absolute Quantification of Schistosoma mansoni Esophageal Gland ProductsSchistosoma mansoniXevo TQ-SNeves LX, Wilson RA, Brownridge P, Harman VM, H...Yes1PXD014899
2019-07-29 Prion MRM assay development and clinical studyHomo sapiens, Mus musculus, Rattus norvegicus, Macaca cynomolgusTSQ Quantiva,Q ExactiveMinikel EV, Kuhn E, Cocco AR, Vallabh SM, Harti...Yes16PXD014781
2019-07-26 Matrix-matched calibration curvesSaccharomyces cerevisiae, Homo sapiensQ Exactive HF,Orbitrap Fusion Lumos,TSQ QuantivaNo5PXD014815
2019-07-15 Unique-region phosphorylation targets LynA for rapid degradation, tuning its expression and signaling in myeloid cellsMus musculusOrbitrap FusionBrian BF, Jolicoeur AS, Guerrero CR, Nunez MG, ...No6PXD014621
2019-07-10 Light-dependent dynamics of phosphorylation of the thylakoid structural protein CURT1BArabidopsis thalianaTSQ VantageTrotta A, Bajwa AA, Mancini I, Paakkarinen V, P...No7PXD014562
2019-07-04 Analysis of endogenous peptides released from osteoarthritic cartilage unravels novel pathogenic markersHomo sapiensQTRAP 5500Fernandez-Puente P, González-Rodríguez L, Calam...Yes1 
2019-07-03 A targeted strategy for developing proteomic biomarkers: a case study of epithelial ovarian cancerHomo sapiensTSQ Vantage,QTRAP 5500,4000 QTRAPHuttenhain R, Choi M, de la Fuente L, Oehl K, C...No3PXD014474
2019-06-28 ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infectionHuman immunodeficiency virus 1, Homo sapiensTSQ QuantivaHüttenhain R, Xu J, Burton LA, Gordon DE, Hultq...No4 
2019-06-18 A proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationshipsListeria monocytogenesQ ExactiveNo2PXD014294
2019-06-16 Targeted MRM assay Complement System in Health and Infectious DiseaseHomo sapiensXevo TQ-SWillems E, Alkema W, Keizer-Garritsen J, Supper...Yes1PXD014264
2019-06-13 Cell cycle validationMus musculus, Sus scrofa, Xenopus laevis, Xenopus tropicalisQ Exactive HFFederspiel JD, Tandon P, Wilczewski CM, Wasson ...No3 
2019-06-07 An automated ‘cells-to-peptides’ sample preparation workflow for high-throughput, quantitative proteomic assays of microbesEscherichia coli, Saccharomyces cerevisiae, Pseudomonas putida KT2440, Rhodosporidium toruloides6460 Triple Quadrupole LC/MSChen Y, Guenther JM, Gin JW, Chan LJG, Costello...No8PXD014182
2019-05-31 Screening a Resource of Recombinant Protein Fragments for Targeted ProteomicsHomo sapiensQ Exactive HFYes1 
2019-05-29 Light-dependent N-terminal phosphorylation of LHCSR3 and LHCB4 are interlinked in Chlamydomonas reinhardtiiChlamydomonas reinhardtiiQ Exactive PlusScholz M, Gäbelein P, Xue H, Mosebach L, Bergne...No4 
2019-05-14 Rebuilding core abscisic acid signaling pathways of Arabidopsis in yeastSaccharomyces cerevisiae, Arabidopsis thalianaOrbitrap Fusion LumosRuschhaupt M, Mergner J, Mucha S, Papacek M, Do...No1PXD013849
2019-05-09 Novel interconnections of HOG signaling revealed by combined use of two proteomic software packagesSaccharomyces cerevisiaeQ Exactive HFJanschitz M, Romanov N, Varnavides G, Hollenste...No1PXD013789
2019-04-30 Validation of N-terminal Labeling Mass Spectrometry for Characterization of Partially Hydrolyzed Gluten ProteinswheatQ Exactive PlusCao W, Baumert JL, Downs ML. Evaluation of N-te...No7PXD013679
2019-04-12 International Ring Trial of a Broad-Spectrum Targeted Metabolomics and Lipidomics Platform for Serum and Plasma Analysis [System Suitability Files]Homo sapiensQ Exactive HF,Q Exactive Plus,Q ExactiveThompson JW, Adams KJ, Adamski J, Asad Y, Borts...Yes2 
2019-04-10 Endo-Lysosomal Proteins and Ubiquitin CSF Concentrations in Alzheimer’s and Parkinson’s DiseaseHomo sapiensQ ExactiveSjodin S, Brinkmalm G, Ohrfelt A, Parnetti L, P...Yes12PXD013451
2019-04-06 Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptorXanthomonas oryzae pv. oryzae6460 Triple Quadrupole LC/MSLuu DD, Joe A, Chen Y, Parys K, Bahar O, Pruitt...No1PXD013389
2019-04-06 Programmable polyketide biosynthesis platform for production of aromatic compounds in yeastSaccharomyces cerevisiae6460 Triple Quadrupole LC/MSJakociunas T, Klitgaard AK, Kontou EE, Nielsen ...No2PXD013388
2019-04-01 IFI16 pyrin oligomerization mediates antiviral actionsHomo sapiensQ Exactive HFNo1 
2019-03-26 Homeostatic and Interferon-induced gene expression represent different states of promoter-associated transcription factor ISGF3Mus musculusQ Exactive HF-XPlatanitis E, Demiroz D, Schneller A, Fischer K...No1PXD013251
2019-03-08 Standardization of PGC-LC-MS-based glycomics for sample specific glycotypingHomo sapiens, Sus scrofa, Bos taurusVelos PlusStandardization of PGC-LC-MS-based glycomics fo...No15 
2019-03-05 N-terminal amino acid identification using targeted mass spectrometryEscherichia coliQ ExactiveVincent, R. M., Wright, B., & Jaschke, P. R. (2...No2PXD012390
2019-03-01 Targeted Mass Spectrometry of Brain and Pancreatic tissuesHomo sapiensQ Exactive HFYes2PXD012931
2019-02-13 Exploring Non-Canonical Terpene Space With a Heterologous Lepidopteran Mevalonate PathwayEscherichia coli6460 Triple Quadrupole LC/MSEiben CB, de Rond T, Bloszies C, Gin J, Chiniqu...No1PXD012697
2019-02-07 Lysine & Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver DiseaseMus musculusOrbitrap Fusion Lumos,TripleTOF 6600No9PXD012621
2019-01-30 Characterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differencesCrassostrea gigasOrbitrap Fusion Lumos,TSQ VantageVenkataraman YR, Timmins-Schiffman E, Horwith M...No3PXD012569
2019-01-22 Pharmacokinetic analysis of a novel human EGFRvIII:CD3 bispecific antibody in plasma and whole blood using a high-resolution targeted mass spectroscopy approachMus musculus, Homo sapiensQ Exactive HF-XSchaller TH, Foster MW, Thompson JW, Spasojevic...Yes2PXD012472
2019-01-15 Measurement of Nrf2-Regulated Antioxidant Response Proteins as Potential Biomarkers for Radiation Injury AssessmentMus musculusQ ExactiveLiu K, Singer E, Cohn W, Micewicz ED, McBride W...Yes4 
2019-01-11 Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine LearningEscherichia coli6460 Triple Quadrupole LC/MSOpgenorth P, Costello Z, Okada T, Goyal G, Chen...No1PXD012312
2019-01-10 A sensitive and simple targeted proteomics approach to quantify transcription factor and membrane proteins of the unfolded protein response pathway in glioblastoma cellsHomo sapiensQ Exactive HF,Orbitrap Fusion LumosNguyen CDL, Malchow S, Reich S, Steltgens S, Sh...Yes17 
2019-01-09 Juvenile geoduck ctenidia tissue after summer deployment in Puget Sound, WAPacific geoduckTSQ Vantage,Orbitrap Fusion LumosSpencer LH, Horwith M, Lowe AT, Venkataraman YR...No2PXD012294
2019-01-08 Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysatesCorynebacterium glutamicum ATCC 130326460 Triple Quadrupole LC/MSSasaki Yusuke and Eng T and HRA and TJ and CY a...No1PXD012293
2019-01-07 Quantitative assay of targeted proteome in trichome glandular cells using large-scale selected reaction monitoring strategySolanum lycopersicumQTRAP 5500Takemori A, Nakashima T, Ômura H, Tanaka Y, Nak...No2PXD012250
2018-12-21 A dataset describing a suite of novel antibody reagents for the RAS signaling networkHomo sapiensQTRAP 5500,QTRAP 6500Schoenherr RM, Huang D, Voytovich UJ, Ivey RG, ...Yes117PXD012604
2018-12-20 Search for synaptic biomarkers of Alzheimer’s diseaseHomo sapiensQTRAP 5500Lleó A, Núñez-Llaves R, Alcolea D, Chiva C, Bal...Yes4PXD012138
2018-12-13 Isotopologue multi-point calibration for proteomics biomarker quantification in clinical practiceHomo sapiensQTRAP 5500Chiva C, Pastor O, Trilla-Fuertes L, Gámez-Pozo...Yes4PXD012035
2018-12-05 Multiplex assay for quantification of acute phase proteins and immunoglobulin A in dried blood spotsHomo sapiens6495B Triple Quadrupole LC/MS,6495A Triple Quadrupole LC/MSVidova, V., Stuchlikova, E., Vrbova, M., Almasi...Yes12PXD011944
2018-11-30 Improving Precursor Selectivity in Data Independent Acquisition Using Overlapping WindowsSaccharomyces cerevisiae, Bos taurusQ ExactiveAmodei D, Egertson J, MacLean BX, Johnson R, Me...Yes11PXD011910
2018-10-12 Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolismPseudomonas putida KT24406460 Triple Quadrupole LC/MSThompson MG, Blake-Hedges JM, Cruz-Morales P, B...No1PXD011350
2018-10-11 A rapid methods development workflow for high-throughput quantitative proteomic applicationsSaccharomyces cerevisiae, Pseudomonas putida KT2440, Escherichia coli6460 Triple Quadrupole LC/MSChen Y, Vu J, Thompson MG, Sharpless WA, Chan L...No17 
2018-10-10 ATI in Ancient WheatsTriticumTSQ Vantage,LTQ Orbitrap VelosYes7 
2018-10-10 In vitro phosphorylation of ASY1 by CDKA;1Arabidopsis thalianaQ Exactive PlusYang C, Sofroni K, Wijnker E, Hamamura Y, Carst...No1PXD011335
2018-10-05 Single-point CalibrationSaccharomyces cerevisiaeQ Exactive HF,TSQ AltisPino LK, Searle BC, Huang EL, Noble WS, Hoofnag...No2PXD011297
2018-10-04 Plasmalogen Quantification during Human Cytomegalovirus InfectionHuman, Human CytomegalovirusLTQ Orbitrap XLInfection-Induced Peroxisome Biogenesis Is a Me...No3 
2018-09-17 Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cellsHomo sapiensTSQ VantageYes3 
2018-08-30 Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiaeSaccharomyces cerevisiaeQ Exactive PlusKelliher CM, Foster MW, Motta FC, Deckard A, So...Yes4PXD010937
2018-08-29 Data-independent acquisition mass spectrometry to quantify protein levels in FFPE tumor biopsies for molecular diagnosticsHomo sapiensQ Exactive HFKim YJ, Sweet SMM, Egertson JD, Sedgewick AJ, W...No1PXD010934
2018-08-22 Detection of Six Commercially Processed Soy ingredients in an Incurred Food Matrix Using Parallel Reaction MonitoringGlycine maxQ Exactive PlusChen S, Yang C, Downs ML. Detection of Six Comm...No4PXD010843
2018-08-22 Enhanced validation of antibodies for research applicationsHomo sapiensQ Exactive HFEdfors F, Hober A, Linderbäck K, Maddalo G, Azi...Yes2 
2018-08-17 Discrimination of Isomers of Released N- and O-Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MSSus scrofa, Bos taurus, Homo sapiensVelos Plus,HCTultraAshwood C, Lin CH, Thaysen-Andersen M, Packer N...No7 
2018-08-06 Mechanical force induces rapid phosphorylation dependent signaling in Xenopus embryosXenopus laevisQ Exactive HFNo6 
2018-08-01 Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible SuccinylationMus musculusTripleTOF 5600submission to cellNo1PXD010205
2018-07-12 Mass spectrometry-based absolute quantification of 20S proteasome status for controlled ex-vivo expansion of Human Adipose-derived Mesenchymal Stromal/Stem CellsHomo sapiensQTRAP 5500, QTRAP 6500Menneteau T, Fabre B, Garrigues L, Stella A, Zi...No24 
2018-07-05 Identification of novel protein lysine acetyltransferases in Escherichia coliEscherichia coliTripleTOF 6600D.G. Christensen, J.G. Meyer, J.T. Baumgartner,...No2 
2018-07-05 Streptococcus pyogenes evades adaptive immunity through specific modification of host IgG glycosylationhuman and mouseTSQ VantageNaegeli, A., Bratanis, E., Karlsson, C., Shanno...No8 
2018-06-11 targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteinsEscherichia coli6460 Triple Quadrupole LC/MSBatth, Tanveer S., et al. "A targeted proteomic...No45 
2018-06-11 A Kinetic-Based Approach to Understanding Heterologous Mevalonate Pathway Function in E. ColiEscherichia coli6460 Triple Quadrupole LC/MSWeaver, Lane J., et al. "A kinetic‐based approa...No1 
2018-06-11 Metabolic engineering of Escherichia coli for limonene and perillyl alcohol productionEscherichia coliAB Sciex 5500Alonso-Gutierrez, Jorge, et al. "Metabolic engi...No1 
2018-06-11 Viscous control of cellular respiration by membrane lipid compositionEscherichia coli6460 Triple Quadrupole LC/MSBudin I, de Rond T, Chen Y, Chan LJ, Petzold CJ...No1 
2018-06-11 Modular Engineering of L-Tyrosine Production in Escherichia coliEscherichia coliAB Sciex 4000 Q-trapJuminaga, Darmawi, et al. "Modular engineering ...No1 
2018-05-25 Quality Assessment and Interference Detection in Targeted Mass Spectrometry Data using Machine LearningHumanQTRAP 5500Toghi Eshghi S, Auger P, Mathews WR. Quality as...Yes3 
2018-05-22 HR-SRM-baseds analysis of mouse/human SGLT2 in kidney and heart tissue.Mus musculus/Homo sapiensTripleTOF5600+Mustroph et al., ESC Heart Failure, in revision...No1 
2018-04-19 Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics MeasurementsE. coliQ exactive HFTaumer C, Griesbaum L, Kovacevic A, Soufi B, Na...No5 
2018-04-17 Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cellsHomo sapiensTSQ VantageNo12 
2018-03-27 Combining discovery and targeted proteomics reveals a prognostic signature in oral cancerHomo sapiensWaters Xevo TQ-XSYes2 
2018-03-22 Targeted Quantification of the Peroxisome Proteome during Human Cytomegalovirus InfectionHuman, Human CytomegalovirusQ-Exactive HFInfection-Induced Peroxisome Biogenesis Is a Me...No1 
2018-03-22 Identification of functional TEX101 interactome through proteomic profiling of human spermatozoa homozygous for a missense variant rs35033974Homo sapiensQ ExactiveTM Plus Hybrid Quadrupole-Orbitrap and TSQ QuantivaTM triple quadrupole mass spectrometerSchiza, C., Korbakis, D., Jarvi, K., Diamandis,...Yes5 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - PROBE-NET cohort datasetHumanAgilent 6490 QQQShah AK, Hartel G, Brown I, Winterford C, Na R,...Yes4 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - Ochsner cohort datasetHumanAgilent 6490 QQQShah AK, Hartel G, Brown I, Winterford C, Na R,...Yes4 
2018-03-15 PknG physiological substratesMycobacterium bovis BCGQExactiveKehilwe C Nakedi, Bridget Calder, Mousumi Barne...No1 
2018-03-08 Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions. Journal of The American Society for Mass SpectrometryBos taurus, Saccharomyces cerevisiae6560 Q-TOF LC/MSMacLean BX, Pratt BS, Egertson JD, MacCoss MJ, ...Yes5PXD010650
2018-03-05 Discovery of a testis-specific complex TEX101-DPEP3 and selection of its disrupting antibodiesHomo sapiensTSQ Quantiva triple quadrupole (Thermo Scientific)Schiza, C., Korbakis, D., Panteleli, E., Jarvi,...Yes4 
2018-01-31 Monitoring molecular contaminants and interferences in proteomic data sets  Rardin MJ. Rapid assessment of contaminants and...No1 
2018-01-26 Mass spectrometry identification and quantitation of proteins from small pools of developing auditory and vestibular cellsMouseQ Exactive HFNo3 
2018-01-23 Global, site-resolved, quantitative analysis of the yeast redoxomeSaccharomyces cerevisiaeOrbitrap EliteUlrike Topf, Ida Suppanz, Lukasz Samluk, Lidia ...No5 
2018-01-22 Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)Bos taurusTSQ Quantum,TSQ Vantage,4000 QTRAP,QTRAP 5500,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ-XSAbbatiello SE, Mani DR, Schilling B, Maclean B,...No15PXD010535