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CreatedShareTitleOrganismInstrumentSpike InPublicationRunsPX ID
2015-02-06 Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasmaHomo sapiensTriple Quadrupole (Agilent, SCIEX, Thermo, Waters)YesS.E. Abbatiello, B. Schilling, D.R. Mani, L.J. ...54 
2015-03-09 Protein acetylation in response to carbon overflow: detecting dynamic acetylation changes by mass spectrometryEscherichia coliTripleTOF 6600,TripleTOF 5600NoBirgit Schilling, David Christensen, Robert Dav...4 
2015-04-28 Mtb ALF-SWATH: Absolute quantification of Anchor proteins using AQUA peptidesMycobacterium TuberculosisTripleTOF 5600YesSchubert et. al; Absolute Proteome Composition ...1 
2015-04-28 Mtb ALF-SWATH: Dilution series of AQUA peptides used for anchor protein quantificationMycobacterium TuberculosisTripleTOF 5600YesSchubert et. al; Absolute Proteome Composition ...1 
2015-04-28 Mtb ALF-SWATH: Manual data analysis of the Top21 proteins (most intense) using SkylineMycobacterium TuberculosisTripleTOF 5600NoSchubert et. al; Absolute Proteome Composition ...1 
2015-04-30 Analytical protein standardsHumanTSQ VantageNoSearle et. al.; Using Data Independent Acquisit...14 
2015-06-09 Characterization of a human pluripotent stem cell-derived model of neuronal development using multiplexed targeted proteomicsHumanTSQ VantageYesDunkley et al. (2015) Characterization of a hum...1 
2015-06-14 Ariadne’s thread: a robust software solution leading to automated absolute and relative quantification of SRM datasynthetic peptides, Drosophila melanogasterTSQ Quantum EMRYesNasso et. al.; Ariadne's Thread: A Robust Softw...3 
2015-06-16 Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded Breast Cancer TissuesHumanTSQ Vantage ThermoYesSteiner et. al, Mol Cell Proteomics. 2015 Oct;1...13 
2015-06-18 MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic ExperimentsMouseTripleTOF 5600NoRardin MJ, Schilling B, Cheng L, MacLean BX, So...8 
2015-07-17 Multiplexed, scheduled high resolution (sMRM-HR) acquisition on a full scan QqTOF instrument with integrated data-dependent and targeted mass spectrometric workflows.B. taurus, S. cerevisiae, E. coliTripleTOF 5600NoMultiplexed, scheduled high resolution sMRM-HR ...4 
2015-08-07 Population-specific plasma proteomes of marine and freshwater three-spined sticklebacksGasterosteus aculeatusImpactHD (Bruker)NoProteomics Volume 15, Issue 23-24, December 201...1 
2015-08-10 Development of a quantitative SRM-based proteomics method to study iron metabolism of Synechocystis sp. PCC 6803Synechocystis sp. PCC 6803TSQ VantageNoDevelopment of a quantitative SRM-based proteom...3 
2015-10-15 Renal proteomes of marine and FW sticklebacksGasterosteus aculeatusImpactHD UHR-QTOFNoJournal of Proteomics. 2015 Sep;14(9):2331-40. ...1 
2015-10-27 Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry.Human, Mouse, YeastTripleTOF, Orbitrap/HCDNoParker SJ, Rost H, Rosenberger G, Collins BC, M...1 
2015-12-07 Assembly dynamics and stoichiometry of the apoptosis signal-regulating kinase (ASK) signalosome in response to electrophile stressHomo sapiensQ Exactive PlusNoJoel D. Federspiel, Simona G. Codreanu, Amy M. ...4 
2015-12-18 A quantitative tagless co-purification method to validate and identify protein-protein interactionsDesulfovibrio vulgaris Hildenborough wild-type ATCC29579AB Sciex 4800 TOF/TOF, AB Sciex 5800 TOF/TOFNoMaxim Shatsky, Ming Dong, Haichuan Liu, Lee Lis...1 
2015-12-21 Proteomic profile of deleted in breast cancer 1 (DBC1) protein-protein interactionsHomo sapiensOrbitrap VelosNoGiguère SS, Guise AJ, Jean Beltran PM, Joshi PM...1 
2016-02-08 Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reportedDesulfovibrio vulgaris Hildenborough wild-type ATCC29579Thermo LTQ Velos Orbitrap, Thermo LTQ XL and Sciex QSTAR XLNoM. Shatsky, S. Allen, B.L. Gold, N.L. Liu, T.R....1 
2016-02-18 Differential light-dependent phosphorylation of Ser and Thr residues regulates plant STN7 kinaseArabidopsis thalianaTSQ vantage Thermo ScientificNo14 
2016-03-07 Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspectiveHomo sapiensTSQ Vantage, QTRAP5500, Q Exactive, Q Exactive HF and tripleTOF5600YesTobias Kockmann, Christian Trachsel, Christian ...12 
2016-03-18 Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissuesHumanSciex 5500 QTRAPYesKennedy JJ, Whiteaker JR, Schoenherr RM, Yan P,...7 
2016-03-23 Annexin A5 is the Most-Abundant Membrane-Associated Protein in Stereocilia but is DispensableMouseOrbitrap Fusion Tribrid mass spectrometerNoKrey JF, Drummond M, Foster S, Porsov E, Vijaya...2 
2016-05-06 Conserved protein abundance pattern of the EGFR-MAPK pathway reveals its regulatory architecturePacific Northwest National LaboratoryTSQ VantageYesTujin Shi, Mario Niepel, Jason E. McDermott, Yu...20 
2016-05-12 In vitro kinase assay of human and mouse FLNc domain 23-24Human, MouseObritrap Velos Elite, QExactive PlusNoLena Reimann, Heike Wiese, Yvonne Leber, Anja N...1 
2016-05-12 In vivo kinase assay of mouse FLNcC2C12 mouse myotubesThermo Scientific Orbitrap Velos EliteNoLena Reimann, Heike Wiese, Yvonne Leber, Anja N...1 
2016-05-20 Development, Validation, and Application of a MRM with SIS Peptide Strategy to Quantify Multiplexed Panels of Proteins in Mouse Plasma and Heart TissuesMus musculusAgilent’s 6490 Triple QuadrupoleYes2 
2016-05-25 Quantifiable peptide tags for targeted proteomics.Homo sapiensTSQ VantageYesGiel Vandemoortele, An Staes, Giulia Gonnelli, ...9 
2016-06-02 PRM analysis of EC uterine aspirateHomo sapiensQExactive PlusYesMartinez-Garcia E, Lesur A, Devis L, Campos AR,...1 
2016-06-08 Robust temporal profiling of GRB2 protein complexes in primary T cells using SWATH mass spectrometryMouse5600 Triple-TOFNoEtienne Caron, Romain Roncagalli, Takeshi Hase,...4 
2016-06-14 Identification and characterization of protein acetylation in Neisseria gonorrhoeaeNeisseria gonorrhoeaeTriple TOF 5600NoPost DMB, Schilling B, Reinders LM, D'Souza AK,...1 
2016-07-13 Gadd45a Promotes Skeletal Muscle Atrophy by Forming a Complex with the Protein Kinase MEKK4MouseTripleTOF 5600NoBullard, S.A., Seo, S., Schilling, B., Dyle, M....1 
2016-07-29 SELECTIVE AND SENSITIVE QUANTIFICATION OF THE CYTOCHROME P450 3A4 PROTEIN IN HUMAN LIVER HOMOGENATES THROUGH MULTIPLE REACTION MONITORING MASS SPECTROMETRYHuman5500QTRAP SciexYesCieślak A, Kelly I, Trottier J, Verreault M, Wu...2 
2016-08-08 Detection of Low Abundance Ocean Bacteria PeptidesRuegeria pomeroyiThermo VantageNo2 
2016-09-21 A general method for targeted quantitative cross-linking mass spectrometryBovine, HumanQ-Exactive Plus, Q-Exactive Plus HFNoJuan D. Chavez, Jimmy K. Eng, Devin K. Schweppe...2 
2016-09-22 Dynamic phosphorylation of apoptosis signal regulating kinase 1 (ASK1) in response to oxidative and electrophilic stress Q Exactive plusNoCarlos Morales Betanzos, Joel D. Federspiel, Am...2 
2016-10-03 ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experimentsYeastThermo Scientific Q ExactiveYesChoi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS...9 
2016-10-07 FLNc Calpain GluC SRM AnalysisHumanQExactive PlusNoLena Reimann, Heike Wiese, Yvonne Leber, Anja N...1 
2016-10-17 Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1 in cyanobacteriaSynechocystis sp. PCC 6803TSQ VantageNoGeorg J, Kostova G, Vuorijoki L, Schön V, Kadow...2 
2016-10-18 Robust Label-Free, Quantitative Profiling of Circulating Plasma Microparticle Associated ProteinsHumanQExactiveNoBraga-Lagache S, Buchs N, Iacovache MI, Zuber B...2 
2016-10-20 PECAN - A Library Free Peptide Detection Tool for DIA DataHuman, YeastQ-Exactive, Q-Exactive HF, TSQ-Vantage, TSQ-QuantivaNo5 
2016-10-26 Osmolality/ salinity responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fishOreochromis mossambicusImpactHD UHR-QTOFNoWang X. and Kültz D2 
2016-10-31 Plastin 1 widens stereocilia by transforming actin filament packing from hexagonal to liquidMouseOrbitrap FusionYesKrey JF, Krystofiak ES, Dumont RA, Vijayakumar ...3 
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 
2016-11-16 Impact of cystinosin glycosylation on protein stability by differential dynamic SILACHumanQexactive plusNoNathalie Nevo, Lucie Thomas, Cerina Chhuon, Zuz...6 
2016-12-01 Photosynthesis-related phosphopeptides in Synechocystis 6803Synechocystis sp. PCC 6803TSQ VantageYesMartina Angeleri, Dorota Muth-Pawlak, Eva-Mari ...3 
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 
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 
2017-02-13 Stoichiometric surface density modelStreptococcus pyogenesThermo TSQ QuantivaYesKristoffer Sjöholm, Ola Kilsgård, Johan Teleman...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 
2017-03-03 Spatially and temporally resolved protein interaction networks in living cells.HumanTSQ QuantivaNoB. T. Lobingier, R. Hüttenhain, K. Eichel, A. Y...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 
2017-04-17 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 
2017-04-20 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 
2017-05-03 PSB33 sustains Photosystem II D1 protein under fluctuating light conditionsArabidopsis thaliana Col-0TSQ vantage Thermo ScientificNo1 
2017-05-03 Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancerHomo sapiensTSQ Vantage, Waters NanoACQUITY UPLCNo70 
2017-05-18 Quantification of Mutant SPOP Proteins in Prostate CancerHomo sapiensTSQ Vantage, Waters NanoACQUITY UPLCYes16 
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 
2017-06-21 MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experimentsHomo sapiens, BovineTriple QuadrupolesNoDogu, E, Mohammad-Taheri, S, Abbatiello, SE et ...8 
2017-07-05 A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brainMouseOrbitrap Elite, TSQ QuantivaNoScott P. Goulding, Karen K. Szumlinski, Candice...3 
2017-09-21 Cellular signaling underlying GSIS in pancreatic β-cellsRatThermo QE-HFNoKang T, Jensen P, Huang H, Lund Christensen G, ...1 
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 
2017-09-27 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 
2017-10-09 MEERCAT: MULTIPLEXED EFFICIENT CELL FREE EXPRESSION OF RECOMBINANT QconCATS FOR LARGE SCALE ABSOLUTE PROTEOME QUANTIFICATION SCIEX QT5500Yes6 
2017-10-17 DDR panel radiation responseHomo sapiens6500 QTRAPNoWhiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, S...3 
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 
2017-11-02 SpkG kinase phosphorylates the ferredoxin 5 protein in Synechocystis 6803Synechocystis 6803TSQ VantageNoFEBS Lett, in submission1 
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 
2017-11-20 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 
2017-11-29 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 
2017-12-18 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 
2018-01-03 Targeted Proteomics of HDL in People With Type 2 DiabetesHumanTSQ VantageNo2 
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
2018-01-23 Global, site-resolved, quantitative analysis of the yeast redoxomeSaccharomyces cerevisiaeOrbitrap EliteNoUlrike Topf, Ida Suppanz, Lukasz Samluk, Lidia ...5 
2018-01-26 Mass spectrometry identification and quantitation of proteins from small pools of developing auditory and vestibular cellsMouseQ Exactive HFNo3 
2018-01-31 Monitoring molecular contaminants and interferences in proteomic data sets  NoMatthew J. Rardin1 
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 
2018-03-08 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
2018-03-15 PknG physiological substratesMycobacterium bovis BCGQExactiveNoKehilwe C Nakedi, Bridget Calder, Mousumi Barne...1 
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 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - PROBE-NET cohort datasetHumanAgilent 6490 QQQYesShah AK, Hartel G, Brown I, Winterford C, Na R,...4 
2018-03-22 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 
2018-03-22 Targeted Quantification of the Peroxisome Proteome during Human Cytomegalovirus InfectionHuman, Human CytomegalovirusQ-Exactive HFNoInfection-Induced Peroxisome Biogenesis Is a Me...1 
2018-03-27 Combining discovery and targeted proteomics reveals a prognostic signature in oral cancerHomo sapiensWaters Xevo TQ-XSYes2 
2018-04-17 Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cellsHomo sapiensTSQ VantageNo12 
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 
2018-05-22 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 
2018-05-25 Quality Assessment and Interference Detection in Targeted Mass Spectrometry Data using Machine LearningHumanQTRAP 5500YesToghi Eshghi S, Auger P, Mathews WR. Quality as...3 
2018-06-11 Modular Engineering of L-Tyrosine Production in Escherichia coliEscherichia coliAB Sciex 4000 Q-trapNoJuminaga, Darmawi, et al. "Modular engineering ...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 Metabolic engineering of Escherichia coli for limonene and perillyl alcohol productionEscherichia coliAB Sciex 5500NoAlonso-Gutierrez, Jorge, et al. "Metabolic engi...1 
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 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 
2018-07-05 Streptococcus pyogenes evades adaptive immunity through specific modification of host IgG glycosylationhuman and mouseTSQ VantageNoNaegeli, A., Bratanis, E., Karlsson, C., Shanno...8 
2018-07-05 Identification of novel protein lysine acetyltransferases in Escherichia coliEscherichia coliTripleTOF 6600NoD.G. Christensen, J.G. Meyer, J.T. Baumgartner,...2 
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 
2018-08-01 Regulation of UCP1 and Mitochondrial Metabolism in Brown Adipose Tissue by Reversible SuccinylationMus musculusTripleTOF 5600Nosubmission to cell1PXD010205
2018-08-06 Mechanical force induces rapid phosphorylation dependent signaling in Xenopus embryosXenopus laevisQ Exactive HFNo6 
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 
2018-08-22 Enhanced validation of antibodies for research applicationsHomo sapiensQ Exactive HFYesEdfors F, Hober A, Linderbäck K, Maddalo G, Azi...2