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CreatedShareTitleOrganismInstrumentSpike InPublicationRunsPX ID
2019-08-09 Are These Cardiomyocytes? Protocol Development Reveals Impact of Sample Preparation on the Accuracy of Identifying Cardiomyocytes by Flow CytometryHomo sapiensOrbitrap Fusion LumosYesWaas M, Weerasekera R, Kropp EM, Romero-Tejeda ...1PXD014971
2019-07-31 LipidCreator: A workbench to probe the lipidomic landscape Q Exactive HF,QTRAP 6500Yes3 
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 FusionNoBrian BF, Jolicoeur AS, Guerrero CR, Nunez MG, ...6PXD014621
2019-07-04 Analysis of endogenous peptides released from osteoarthritic cartilage unravels novel pathogenic markersHomo sapiensQTRAP 5500YesFernandez-Puente P, González-Rodríguez L, Calam...1 
2019-07-03 A targeted strategy for developing proteomic biomarkers: a case study of epithelial ovarian cancerHomo sapiensTSQ Vantage,QTRAP 5500,4000 QTRAPNoHuttenhain R, Choi M, de la Fuente L, Oehl K, C...3PXD014474
2019-06-28 ARIH2 is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infectionHuman immunodeficiency virus 1, Homo sapiensTSQ QuantivaNoHüttenhain R, Xu J, Burton LA, Gordon DE, Hultq...4 
2019-06-16 Targeted MRM assay Complement System in Health and Infectious DiseaseHomo sapiensXevo TQ-SYesWillems E, Alkema W, Keizer-Garritsen J, Supper...1PXD014264
2019-06-13 Cell cycle validationMus musculus, Sus scrofa, Xenopus laevis, Xenopus tropicalisQ Exactive HFNo3 
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 PlusNoScholz M, Gäbelein P, Xue H, Mosebach L, Bergne...4 
2019-05-14 Rebuilding core abscisic acid signaling pathways of Arabidopsis in yeastSaccharomyces cerevisiae, Arabidopsis thalianaOrbitrap Fusion LumosNoRuschhaupt M, Mergner J, Mucha S, Papacek M, Do...1PXD013849
2019-05-09 Novel interconnections of HOG signaling revealed by combined use of two proteomic software packagesSaccharomyces cerevisiaeQ Exactive HFNoJanschitz M, Romanov N, Varnavides G, Hollenste...1PXD013789
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/MSNoLuu DD, Joe A, Chen Y, Parys K, Bahar O, Pruitt...1PXD013389
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-XNoPlatanitis E, Demiroz D, Schneller A, Fischer K...1PXD013251
2019-03-08 Standardization of PGC-LC-MS-based glycomics for sample specific glycotypingHomo sapiens, Sus scrofa, Bos taurusVelos PlusNoStandardization of PGC-LC-MS-based glycomics fo...15 
2019-03-05 N-terminal amino acid identification using targeted mass spectrometryEscherichia coliQ ExactiveNoVincent, R. M., Wright, B., & Jaschke, P. R. (2...2PXD012390
2019-03-01 Targeted Mass Spectrometry of Brain and Pancreatic tissuesHomo sapiensQ Exactive HFYes2PXD012931
2019-01-30 Characterization of Pacific oyster (Crassostrea gigas) proteomic response to natural environmental differencesCrassostrea gigasOrbitrap Fusion Lumos,TSQ VantageNoVenkataraman YR, Timmins-Schiffman E, Horwith M...3PXD012569
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-XYesSchaller TH, Foster MW, Thompson JW, Spasojevic...2PXD012472
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/MSNoOpgenorth P, Costello Z, Okada T, Goyal G, Chen...1PXD012312
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 LumosYesNguyen CDL, Malchow S, Reich S, Steltgens S, Sh...17 
2019-01-09 Juvenile geoduck ctenidia tissue after summer deployment in Puget Sound, WAPacific geoduckTSQ Vantage,Orbitrap Fusion LumosNoSpencer LH, Horwith M, Lowe AT, Venkataraman YR...2PXD012294
2019-01-08 Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysatesCorynebacterium glutamicum ATCC 130326460 Triple Quadrupole LC/MSNoSasaki Yusuke and Eng T and HRA and TJ and CY a...1PXD012293
2019-01-07 Quantitative assay of targeted proteome in trichome glandular cells using large-scale selected reaction monitoring strategySolanum lycopersicumQTRAP 5500NoTakemori A, Nakashima T, Ômura H, Tanaka Y, Nak...2PXD012250
2018-12-21 A dataset describing a suite of novel antibody reagents for the RAS signaling networkHomo sapiensQTRAP 5500,QTRAP 6500Yes117PXD012604
2018-12-20 Search for synaptic biomarkers of Alzheimer’s diseaseHomo sapiensQTRAP 5500YesLleó A, Núñez-Llaves R, Alcolea D, Chiva C, Bal...4PXD012138
2018-12-13 Isotopologue multi-point calibration for proteomics biomarker quantification in clinical practiceHomo sapiensQTRAP 5500YesChiva C, Pastor O, Trilla-Fuertes L, Gámez-Pozo...4PXD012035
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/MSYesVidova, V., Stuchlikova, E., Vrbova, M., Almasi...12PXD011944
2018-11-30 Improving Precursor Selectivity in Data Independent Acquisition Using Overlapping WindowsSaccharomyces cerevisiae, Bos taurusQ ExactiveYesAmodei D, Egertson J, MacLean BX, Johnson R, Me...11PXD011910
2018-10-12 Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolismPseudomonas putida KT24406460 Triple Quadrupole LC/MSNoThompson MG, Blake-Hedges JM, Cruz-Morales P, B...1PXD011350
2018-10-11 A rapid methods development workflow for high-throughput quantitative proteomic applicationsSaccharomyces cerevisiae, Pseudomonas putida KT2440, Escherichia coli6460 Triple Quadrupole LC/MSNoChen Y, Vu J, Thompson MG, Sharpless WA, Chan L...17 
2018-10-10 ATI in Ancient WheatsTriticumTSQ Vantage,LTQ Orbitrap VelosYes7 
2018-10-05 Single-point CalibrationSaccharomyces cerevisiaeQ Exactive HF,TSQ AltisNoPino LK, Searle BC, Huang EL, Noble WS, Hoofnag...2PXD011297
2018-10-04 Plasmalogen Quantification during Human Cytomegalovirus InfectionHuman, Human CytomegalovirusLTQ Orbitrap XLNoInfection-Induced Peroxisome Biogenesis Is a Me...3 
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 PlusYesKelliher CM, Foster MW, Motta FC, Deckard A, So...4PXD010937
2018-08-22 Detection of Six Commercially Processed Soy ingredients in an Incurred Food Matrix Using Parallel Reaction MonitoringGlycine maxQ Exactive PlusNoChen S, Yang C, Downs ML. Detection of Six Comm...4PXD010843
2018-08-22 Enhanced validation of antibodies for research applicationsHomo sapiensQ Exactive HFYesEdfors F, Hober A, Linderbäck K, Maddalo G, Azi...2 
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,HCTultraNoAshwood C, Lin CH, Thaysen-Andersen M, Packer N...7 
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 5600Nosubmission to cell1PXD010205
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 6500NoMenneteau T, Fabre B, Garrigues L, Stella A, Zi...24 
2018-07-05 Identification of novel protein lysine acetyltransferases in Escherichia coliEscherichia coliTripleTOF 6600NoD.G. Christensen, J.G. Meyer, J.T. Baumgartner,...2 
2018-07-05 Streptococcus pyogenes evades adaptive immunity through specific modification of host IgG glycosylationhuman and mouseTSQ VantageNoNaegeli, A., Bratanis, E., Karlsson, C., Shanno...8 
2018-06-11 targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteinsEscherichia coli6460 Triple Quadrupole LC/MSNoBatth, Tanveer S., et al. "A targeted proteomic...45 
2018-06-11 A Kinetic-Based Approach to Understanding Heterologous Mevalonate Pathway Function in E. ColiEscherichia coli6460 Triple Quadrupole LC/MSNoWeaver, Lane J., et al. "A kinetic‐based approa...1 
2018-06-11 Metabolic engineering of Escherichia coli for limonene and perillyl alcohol productionEscherichia coliAB Sciex 5500NoAlonso-Gutierrez, Jorge, et al. "Metabolic engi...1 
2018-06-11 Viscous control of cellular respiration by membrane lipid compositionEscherichia coli6460 Triple Quadrupole LC/MSNoBudin I, de Rond T, Chen Y, Chan LJ, Petzold CJ...1 
2018-06-11 Modular Engineering of L-Tyrosine Production in Escherichia coliEscherichia coliAB Sciex 4000 Q-trapNoJuminaga, Darmawi, et al. "Modular engineering ...1 
2018-05-25 Quality Assessment and Interference Detection in Targeted Mass Spectrometry Data using Machine LearningHumanQTRAP 5500YesToghi Eshghi S, Auger P, Mathews WR. Quality as...3 
2018-05-22 HR-SRM-baseds analysis of mouse/human SGLT2 in kidney and heart tissue.Mus musculus/Homo sapiensTripleTOF5600+NoMustroph et al., ESC Heart Failure, in revision...1 
2018-04-19 Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics MeasurementsE. coliQ exactive HFNoTaumer C, Griesbaum L, Kovacevic A, Soufi B, Na...5 
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 HFNoInfection-Induced Peroxisome Biogenesis Is a Me...1 
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 spectrometerYesSchiza, C., Korbakis, D., Jarvi, K., Diamandis,...5 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - PROBE-NET cohort datasetHumanAgilent 6490 QQQYesShah AK, Hartel G, Brown I, Winterford C, Na R,...4 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - Ochsner cohort datasetHumanAgilent 6490 QQQYesShah AK, Hartel G, Brown I, Winterford C, Na R,...4 
2018-03-15 PknG physiological substratesMycobacterium bovis BCGQExactiveNoKehilwe C Nakedi, Bridget Calder, Mousumi Barne...1 
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/MSYesMacLean BX, Pratt BS, Egertson JD, MacCoss MJ, ...5PXD010650
2018-03-05 Discovery of a testis-specific complex TEX101-DPEP3 and selection of its disrupting antibodiesHomo sapiensTSQ Quantiva triple quadrupole (Thermo Scientific)YesSchiza, C., Korbakis, D., Panteleli, E., Jarvi,...4 
2018-01-31 Monitoring molecular contaminants and interferences in proteomic data sets  NoMatthew J. Rardin1 
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 EliteNoUlrike Topf, Ida Suppanz, Lukasz Samluk, Lidia ...5 
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-XSNoAbbatiello SE, Mani DR, Schilling B, Maclean B,...15PXD010535
2018-01-03 Targeted Proteomics of HDL in People With Type 2 DiabetesHumanTSQ VantageNo2 
2017-12-18 Curated DIA assay for consistent ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus)Gasterosteus aculeatusImpactHD UHR-QTOFNoJ. Li, B.B. Levitan, S. Gomez-Jimenez and D. Kü...4 
2017-11-29 Measurement by a Novel LC-MS/MS Methodology of Vitamin D–Binding ProteinHumanQ Exactive Plus, Thermo FischerYesHenderson CM, Lutsey PL, Misialek JR, Laha TJ, ...1 
2017-11-20 Quantification of Site-Specific Protein Lysine Acetylation and Succinylation Stoichiometry using Data-Independent Acquisitions (DIA) Mass Spectrometry --Protocol ExampleBovineTripleTOF 5600NoLei Wei, Jesse G. Meyer, Birgit Schilling "Quan...1 
2017-11-02 Nitric oxide prevents Aft1 activation and metabolic remodeling in Frataxin-deficient yeastSaccharomyces cerevisiaeAgilent 6420 Triple Quadrupole SpectrometerYesAlsina D, Ros J, Tamarit J. Redox Biology. Vo...1 
2017-11-02 SpkG kinase phosphorylates the ferredoxin 5 protein in Synechocystis 6803Synechocystis 6803TSQ VantageNoFEBS Lett, in submission1 
2017-10-25 Targeted proteomics in triple negative breast cancer on FFPE samplesHomo sapiensOrbitrap Fusion LumosYes1.Gámez-Pozo, A. et al. Prediction of adjuvant ...2 
2017-10-17 DDR panel radiation responseHomo sapiens6500 QTRAPNoWhiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, S...3 
2017-10-09 MEERCAT: MULTIPLEXED EFFICIENT CELL FREE EXPRESSION OF RECOMBINANT QconCATS FOR LARGE SCALE ABSOLUTE PROTEOME QUANTIFICATION SCIEX QT5500Yes6 
2017-09-27 The conservation of sirtuin lipoamidase activity in bacteria as a regulator of metabolic enzyme complexesE. coliQ-Exactive, Orbitrap VelosNoRowland EA, Greco TM, Snowden CK, McCabe AL, Si...5 
2017-09-21 Streptococcus pyogenes infection and the human proteome with a special focus on the IgG-cleaving enzyme IdeSHuman, Streptococcus pyogenesTSQ Vantage, TSQ QuantivaNoChristofer A. Q. Karlsson, Sofia Järnum, Lena W...2 
2017-09-21 Cellular signaling underlying GSIS in pancreatic β-cellsRatThermo QE-HFNoKang T, Jensen P, Huang H, Lund Christensen G, ...1 
2017-07-05 A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brainMouseOrbitrap Elite, TSQ QuantivaNoScott P. Goulding, Karen K. Szumlinski, Candice...3 
2017-06-21 MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experimentsHomo sapiens, BovineTriple QuadrupolesNoDogu, E, Mohammad-Taheri, S, Abbatiello, SE et ...8 
2017-06-14 An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomicsBartonella henselae strain Houston-1 (Bhen)Orbitrap Fusion Mass Spectrometer (Thermo Fisher Scientific)NoUlrich Omasits, Adithi R. Varadarajan, Michael ...2 
2017-05-18 Quantification of Mutant SPOP Proteins in Prostate CancerHomo sapiensTSQ Vantage, Waters NanoACQUITY UPLCYes16 
2017-05-03 Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancerHomo sapiensTSQ Vantage, Waters NanoACQUITY UPLCNo70 
2017-05-03 PSB33 sustains Photosystem II D1 protein under fluctuating light conditionsArabidopsis thaliana Col-0TSQ vantage Thermo ScientificNo1 
2017-04-20 Proteomics analysis identifies orthologs of human chitinase-like proteins as inducers of tube-morphogenesis defects in DrosophilaDrosophila melanogasterThermo TSQ Vantage 2NoSandra G. Zimmerman, Gennifer E. Merrihew, Mich...2 
2017-04-17 Proteomic assay development for reproductive maturation state determination in Geoduck: towards a non-invasive proteomic assay for improving aquaculturePanopea generosaThermo VantageNoEmma B. Timmins-Schiffman, Grace A Crandall, Br...2 
2017-04-13 Multiplexed MRM-based Protein Quantitation Using Two Different Stable Isotope Labeled Peptides for Calibration  NoAndré LeBlanc, Sarah A. Michaud, Andrew J. Perc...16 
2017-03-03 Spatially and temporally resolved protein interaction networks in living cells.HumanTSQ QuantivaNoB. T. Lobingier, R. Hüttenhain, K. Eichel, A. Y...2 
2017-02-17 Inactivation of iron-sulfur cluster biogenesis regulator SufR in Synechocystis sp. PCC 6803 induces unique iron-dependent protein-level responsesSynechocystis sp. PCC 6803TSQ VantageNoLinda Vuorijoki, Arjun Tiwari, Pauli Kallio, Ev...1 
2017-02-13 Stoichiometric surface density modelStreptococcus pyogenesThermo TSQ QuantivaYesKristoffer Sjöholm, Ola Kilsgård, Johan Teleman...2 
2017-01-25 Quantitative mass spectrometry analysis of PD-L1 protein expression, N-glycosylation and expression stoichiometry with PD-1 and PD-L2 in human melanomaHomo sapiensQ Exactive PlusYesMorales-Betanzos CA, Lee H, Gonzalez-Ericsson P...5 
2017-01-10 An optimized chromatographic strategy for multiplexing in parallel reaction monitoring mass spectrometry: Insights from quantitation of activated kinasesHomo sapiensThermo Orbitrap Q Exactive PlusNoUrisman A, Levin RS, Gordan JD, Webber JT, Hern...2 
2016-12-01 Photosynthesis-related phosphopeptides in Synechocystis 6803Synechocystis sp. PCC 6803TSQ VantageYesMartina Angeleri, Dorota Muth-Pawlak, Eva-Mari ...3 
2016-11-16 Impact of cystinosin glycosylation on protein stability by differential dynamic SILACHumanQexactive plusNoNathalie Nevo, Lucie Thomas, Cerina Chhuon, Zuz...6 
2016-11-15 Time-resolved proteomics vs. ribosome profiling reveals translation dynamics under stressHomo SapiensQTRAP 5500 (SCIEX)NoTzu-Yu Liu, Hector H. Huang, Diamond Wheeler, ...9 
2016-10-31 Plastin 1 widens stereocilia by transforming actin filament packing from hexagonal to liquidMouseOrbitrap FusionYesKrey JF, Krystofiak ES, Dumont RA, Vijayakumar ...3 
2016-10-26 Osmolality/ salinity responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fishOreochromis mossambicusImpactHD UHR-QTOFNoWang X. and Kültz D2 
2016-10-20 PECAN - A Library Free Peptide Detection Tool for DIA DataHuman, YeastQ-Exactive, Q-Exactive HF, TSQ-Vantage, TSQ-QuantivaNo5 
2016-10-18 Robust Label-Free, Quantitative Profiling of Circulating Plasma Microparticle Associated ProteinsHumanQExactiveNoBraga-Lagache S, Buchs N, Iacovache MI, Zuber B...2