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Created Share Title Organism Instrument Spike In Publication Runs Folder
2018-01-31  Monitoring molecular contaminants and interferences in proteomic data sets  No1Amgen - Molecular Contaminants
2018-01-23 Global, site-resolved, quantitative analysis of the yeast redoxomeSaccharomyces cerevisiaeOrbitrap EliteNoUlrike Topf, Ida Suppanz, Lukasz Samluk, Lidia ...5Warscheid Lab - yeast_oxICAT
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, ABI 4000 QTRAP, ABI QTRAP 5500, Waters Xevo TQ, Agilent 6410, Agilent 6460NoAbbatiello SE, Mani DR, Schilling B, Maclean B,...15Study_9S
2018-01-03 Targeted Proteomics of HDL in People With Type 2 DiabetesHumanTSQ VantageNo2Vaisar - HDL_T2D_PlosOne
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, ...1Vitek - Vitamin D
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...1Schilling - JoVEsuccBSA
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...1U. of Lleida - Yeast
2017-11-02 SpkG kinase phosphorylates the ferredoxin 5 protein in Synechocystis 6803Synechocystis 6803TSQ VantageNoFEBS Lett, in submission1U of Turku - SpkG-Fd5-SYN_GT
2017-10-25 Targeted proteomics in triple negative breast cancer on FFPE samplesHomo sapiensOrbitrap Fusion LumosYes1.Gámez-Pozo, A. et al. Prediction of adjuvant ...2Chiva - La Paz_TN_Breast_Cancer
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...5Cristea - CobB PRM
2017-09-21 Cellular signaling underlying GSIS in pancreatic β-cellsRatThermo QE-HFNoKang T, Jensen P, Huang H, Lund Christensen G, ...1U of So Denmark - MCP-PRM_Skyline
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...3MacCoss - Homer2 Interactome
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 ...8Schilling - Longitudinal SSS
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 ...2Wollscheid - Bartonella_Proteogenomics
2017-05-18 Quantification of Mutant SPOP Proteins in Prostate CancerHomo sapiensTSQ Vantage, Waters NanoACQUITY UPLCYes16PNNL - Mutant SPOP Proteins
2017-05-03 Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancerHomo sapiensTSQ Vantage, Waters NanoACQUITY UPLCNo70PNNL _ SRM Ovarian Biomarkers
2017-05-03 PSB33 sustains Photosystem II D1 protein under fluctuating light conditionsArabidopsis thaliana Col-0TSQ vantage Thermo ScientificNo1UTurkuPlantBio - PSB33
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...2Berg - Skyline_Analysis_Idgfs
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...2Nunn - Geoduck Reproduction
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...16Borchers Lab - Double SIS-JPR
2017-03-03 Spatially and temporally resolved protein interaction networks in living cells.HumanTSQ QuantivaNoB. T. Lobingier, R. Hüttenhain, K. Eichel, A. Y...2Krogan - GPCR-APEX
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...1UTurku - SufR-SRM
2017-02-13 Stoichiometric surface density modelStreptococcus pyogenesThermo TSQ QuantivaYesKristoffer Sjöholm, Ola Kilsgård, Johan Teleman...2Lund U. IMP - Stoichiometric Density Model
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...5Liebler - Melanoma Paper
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...2UCSF-MSF MIB-PRM paper
2016-12-01 Photosynthesis-related phosphopeptides in Synechocystis 6803Synechocystis sp. PCC 6803TSQ VantageYesMartina Angeleri, Dorota Muth-Pawlak, Eva-Mari ...3UTurku - Angeleri_JProtRes_2016
2016-11-16 Impact of cystinosin glycosylation on protein stability by differential dynamic SILACHumanQexactive plusNoNathalie Nevo, Lucie Thomas, Cerina Chhuon, Zuz...6Guerrera - 3SDXiS
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, ...9Wiita - Protein Translation Model SRM data
2016-10-31 Plastin 1 widens stereocilia by transforming actin filament packing from hexagonal to liquidMouseOrbitrap FusionYesKrey JF, Krystofiak ES, Dumont RA, Vijayakumar ...3Barr-Gillespie - Stereocilia Crosslinker Targeted Data
2016-10-26 Osmolality/ salinity responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fishOreochromis mossambicusImpactHD UHR-QTOFNoWang X. and Kültz D2Kueltz - Wang and Kultz - 2016_1
2016-10-20 PECAN - A Library Free Peptide Detection Tool for DIA DataHuman, YeastQ-Exactive, Q-Exactive HF, TSQ-Vantage, TSQ-QuantivaNo5PECAN - A Library Free Peptide Detection Tool for DIA Data
2016-10-18 Robust Label-Free, Quantitative Profiling of Circulating Plasma Microparticle Associated ProteinsHumanQExactiveNoBraga-Lagache S, Buchs N, Iacovache MI, Zuber B...2Lagache - N1OHMk
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...2UTurku - IsaR1
2016-10-07 FLNc Calpain GluC SRM AnalysisHumanQExactive PlusNoLena Reimann, Heike Wiese, Yvonne Leber, Anja N...1Warscheid Lab - FLNc Calpain GluC SRM
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...9iPRG 2015
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...2Liebler - ASK PTM
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...2Bruce - PRM_XL_manuscript
2016-08-08 Detection of Low Abundance Ocean Bacteria PeptidesRuegeria pomeroyiThermo VantageNo2Nunn - Detection of Low Abundance Ocean Bacteria Peptides
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....1Schilling - Chris Adams_Gadd45a
2016-06-14 Identification and characterization of protein acetylation in Neisseria gonorrhoeaeNeisseria gonorrhoeaeTriple TOF 5600NoPost DMB, Schilling B, Reinders LM, D'Souza AK,...1Schilling - NGackA
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,...4Aebersold - GRB2 interactome by AP-SWATH
2016-06-02 PRM analysis of EC uterine aspirateHomo sapiensQExactive PlusYesMartinez-Garcia E, Lesur A, Devis L, Campos AR,...1Domon - EC
2016-05-25 Quantifiable peptide tags for targeted proteomics.Homo sapiensTSQ VantageYesGiel Vandemoortele, An Staes, Giulia Gonnelli, ...9Staes - PQS_peptides
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 QuadrupoleYes2Genome BC Proteomics Centre - PC Mouse uEiHq2
2016-05-12 In vivo kinase assay of mouse FLNcC2C12 mouse myotubesThermo Scientific Orbitrap Velos EliteNoLena Reimann, Heike Wiese, Yvonne Leber, Anja N...1Warscheid Lab - C-terminal FLNc in vivo kinase assays
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...1Warscheid Lab - FLNc d23-24 in vitro kinase assay
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...20PNNL_EGFR_pathway
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...2Barr-Gillespie - Annexin A5
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,...7Paulovich - FFPE_MRM_optimization
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 ...12Kockmann - MSQC1
2016-02-18 Differential light-dependent phosphorylation of Ser and Thr residues regulates plant STN7 kinaseArabidopsis thalianaTSQ vantage Thermo ScientificNo14UTurku-STN7
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....1Witkowska_DVH_TAP
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...1Greco - DBC1 SRM
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...1Biggin - Tagless_analysis_of_protein-protein_interactions_in_Desulfovibrio_vulgaris
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. ...4Liebler - ASK manuscript
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...1Parker - CiRT_Peptides
2015-10-15 Renal proteomes of marine and FW sticklebacksGasterosteus aculeatusImpactHD UHR-QTOFNoJournal of Proteomics. 2015 Sep;14(9):2331-40. ...1Kultz et al. (2015) Renal proteomes of marine and FW sticklebacks. J Proteomics
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...3Muth-Pawlak - SRM_irondepr_2015
2015-08-07 Population-specific plasma proteomes of marine and freshwater three-spined sticklebacksGasterosteus aculeatusImpactHD (Bruker)NoProteomics Volume 15, Issue 23-24, December 201...1Kultz et al. (2015) Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks. Proteomics
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 ...4Schilling - MRM_HR_TripleTOF_MS2_FullScanFiltering
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...8Schilling - MS1_MS2_SWATH
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...13Steiner - HER2 quantification in FFPE breast cancer tissues
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...3Goetze - Ariadne
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...1Dunkley - Neuronal Development SRM
2015-04-30 Analytical protein standardsHumanTSQ VantageNoSearle et. al.; Using Data Independent Acquisit...14Searle_PREGO_manuscript
2015-04-28 Mtb ALF-SWATH: Manual data analysis of the Top21 proteins (most intense) using SkylineMycobacterium TuberculosisTripleTOF 5600NoSchubert et. al; Absolute Proteome Composition ...1Ludwig_Mtb_requant
2015-04-28 Mtb ALF-SWATH: Dilution series of AQUA peptides used for anchor protein quantificationMycobacterium TuberculosisTripleTOF 5600YesSchubert et. al; Absolute Proteome Composition ...1Ludwig_Mtb_dilutions
2015-04-28 Mtb ALF-SWATH: Absolute quantification of Anchor proteins using AQUA peptidesMycobacterium TuberculosisTripleTOF 5600YesSchubert et. al; Absolute Proteome Composition ...1Ludwig_Mtb_anchors
2015-03-09 Protein acetylation in response to carbon overflow: detecting dynamic acetylation changes by mass spectrometryE. coliTripleTOF 6600 and TripleTOF 5600NoBirgit Schilling, David Christensen, Robert Dav...4Schilling - Ecoli_Glucose_Acetylome
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. ...54Schilling - main_Study_9