Author: Title: Organism: Instrument:
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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 sapiens4000 QTRAP,QTRAP 5500,TSQ Vantage,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ MS,Xevo TQ-SAbbatiello SE, Schilling B, Mani DR, Zimmerman ...Yes54 
2015-03-09 Protein acetylation in response to carbon overflow: detecting dynamic acetylation changes by mass spectrometryEscherichia coliTripleTOF 6600,TripleTOF 5600Schilling B, Christensen D, Davis R, Sahu AK, H...No4 
2015-04-28 Mtb ALF-SWATH: Absolute quantification of Anchor proteins using AQUA peptidesMycobacterium tuberculosisTripleTOF 5600Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ...Yes1 
2015-04-28 Mtb ALF-SWATH: Dilution series of AQUA peptides used for anchor protein quantificationMycobacterium tuberculosisTripleTOF 5600Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ...Yes1 
2015-04-28 Mtb ALF-SWATH: Manual data analysis of the Top21 proteins (most intense) using SkylineMycobacterium tuberculosisTripleTOF 5600Schubert OT, Ludwig C, Kogadeeva M, Zimmermann ...No1 
2015-04-30 Analytical protein standardsHomo sapiensTSQ VantageSearle BC, Egertson JD, Bollinger JG, Stergachi...No14 
2015-06-09 Characterization of a human pluripotent stem cell-derived model of neuronal development using multiplexed targeted proteomicsHomo sapiensTSQ VantageDunkley T, Costa V, Friedlein A, Lugert S, Aign...Yes3 
2015-06-14 Ariadne’s thread: a robust software solution leading to automated absolute and relative quantification of SRM datasynthetic peptides, Drosophila melanogasterTSQ Quantum EMRNasso et. al.; Ariadne's Thread: A Robust Softw...Yes3 
2015-06-16 Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded Breast Cancer TissuesHomo sapiensTSQ VantageSteiner C, Tille JC, Lamerz J, Kux van Geijtenb...Yes13 
2015-06-18 MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic ExperimentsMus musculusTripleTOF 5600Rardin MJ, Schilling B, Cheng L, MacLean BX, So...No8 
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.Bos taurus, Saccharomyces cerevisiae, Escherichia coliTripleTOF 5600Schilling B, MacLean B, Held JM, Sahu AK, Rardi...No4 
2015-08-06 Evaluation of multi-tRNA synthetase complex by multiple reaction monitoring mass spectrometry coupled with size exclusion chromatographyHomo sapiensQTRAP 5500Park SJ, Ahn HS, Kim JS, Lee C. Evaluation of M...Yes4 
2015-08-07 Population-specific plasma proteomes of marine and freshwater three-spined sticklebacksGasterosteus aculeatusimpact HDProteomics Volume 15, Issue 23-24, December 201...No1 
2015-08-10 Development of a quantitative SRM-based proteomics method to study iron metabolism of Synechocystis sp. PCC 6803Synechocystis sp. PCC 6803TSQ VantageDevelopment of a quantitative SRM-based proteom...No3 
2015-10-15 Renal proteomes of marine and FW sticklebacksGasterosteus aculeatusImpactHD UHR-QTOFJournal of Proteomics. 2015 Sep;14(9):2331-40. ...No1 
2015-10-27 Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry.Homo sapiens, Mus musculus, Saccharomyces cerevisiaeOrbitrap/HCD,TripleTOF 5600Parker SJ, Rost H, Rosenberger G, Collins BC, M...No1 
2015-12-07 Assembly dynamics and stoichiometry of the apoptosis signal-regulating kinase (ASK) signalosome in response to electrophile stressHomo sapiensQ Exactive PlusJoel D. Federspiel, Simona G. Codreanu, Amy M. ...No4 
2015-12-18 A quantitative tagless co-purification method to validate and identify protein-protein interactionsDesulfovibrio vulgaris str. Hildenborough4800 Plus MALDI TOF/TOF,5800 TOF/TOFMaxim Shatsky, Ming Dong, Haichuan Liu, Lee Lis...No1 
2015-12-21 Proteomic profile of deleted in breast cancer 1 (DBC1) protein-protein interactionsHomo sapiensLTQ Orbitrap VelosGiguère SS, Guise AJ, Jean Beltran PM, Joshi PM...No1 
2016-02-08 Bacterial interactomes: interacting protein partners share similar function and are validated in independent assays more frequently than previously reportedDesulfovibrio vulgaris str. HildenboroughLTQ Orbitrap Velos,LTQ XL,QSTAR XLM. Shatsky, S. Allen, B.L. Gold, N.L. Liu, T.R....No1 
2016-02-18 Differential light-dependent phosphorylation of Ser and Thr residues regulates plant STN7 kinaseArabidopsis thalianaTSQ VantageTrotta A, Suorsa M, Rantala M, Lundin B, Aro EM...No14 
2016-03-07 Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspectiveHomo sapiensTSQ Vantage,QTRAP 5500,Q Exactive,Q Exactive HF,TripleTOF 5600Tobias Kockmann, Christian Trachsel, Christian ...Yes12 
2016-03-18 Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissuesHomo sapiensQTRAP 5500Kennedy JJ, Whiteaker JR, Schoenherr RM, Yan P,...Yes7 
2016-03-23 Annexin A5 is the Most-Abundant Membrane-Associated Protein in Stereocilia but is DispensableMus musculusOrbitrap FusionKrey JF, Drummond M, Foster S, Porsov E, Vijaya...No2 
2016-05-06 Conserved protein abundance pattern of the EGFR-MAPK pathway reveals its regulatory architectureHomo sapiensTSQ VantageTujin Shi, Mario Niepel, Jason E. McDermott, Yu...Yes20 
2016-05-12 In vitro kinase assay of human and mouse FLNc domain 23-24Homo sapiens, Mus musculusObritrap Velos Elite,Q Exactive PlusLena Reimann, Heike Wiese, Yvonne Leber, Anja N...No1 
2016-05-12 In vivo kinase assay of mouse FLNcC2C12 mouse myotubesThermo Scientific Orbitrap Velos EliteLena Reimann, Heike Wiese, Yvonne Leber, Anja N...No1 
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 musculus6490 Triple Quadrupole LC/MSYes2 
2016-05-25 Quantifiable peptide tags for targeted proteomics.Homo sapiensTSQ VantageGiel Vandemoortele, An Staes, Giulia Gonnelli, ...Yes9 
2016-06-02 PRM analysis of EC uterine aspirateHomo sapiensQ Exactive PlusMartinez-Garcia E, Lesur A, Devis L, Campos AR,...Yes1 
2016-06-08 Robust temporal profiling of GRB2 protein complexes in primary T cells using SWATH mass spectrometryMus musculusTripleTOF 5600Etienne Caron, Romain Roncagalli, Takeshi Hase,...No4 
2016-06-14 Identification and characterization of protein acetylation in Neisseria gonorrhoeaeNeisseria gonorrhoeaeTripleTOF 5600Post DMB, Schilling B, Reinders LM, D'Souza AK,...No1 
2016-07-13 Gadd45a Promotes Skeletal Muscle Atrophy by Forming a Complex with the Protein Kinase MEKK4Mus musculusTripleTOF 5600Bullard, S.A., Seo, S., Schilling, B., Dyle, M....No1 
2016-08-08 Detection of Low Abundance Ocean Bacteria PeptidesRuegeria pomeroyiTSQ VantageNo2 
2016-09-21 A general method for targeted quantitative cross-linking mass spectrometryHomo sapiens, Bos taurusQ-Exactive Plus HF,Q Exactive PlusJuan D. Chavez, Jimmy K. Eng, Devin K. Schweppe...No2 
2016-09-22 Dynamic phosphorylation of apoptosis signal regulating kinase 1 (ASK1) in response to oxidative and electrophilic stress Q Exactive PlusCarlos Morales Betanzos, Joel D. Federspiel, Am...No2 
2016-10-03 ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experimentsSaccharomyces cerevisiaeQ ExactiveChoi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS...Yes9 
2016-10-07 FLNc Calpain GluC SRM AnalysisHomo sapiensQ Exactive PlusLena Reimann, Heike Wiese, Yvonne Leber, Anja N...No1 
2016-10-17 Acclimation of oxygenic photosynthesis to iron starvation is controlled by the sRNA IsaR1 in cyanobacteriaSynechocystis sp. PCC 6803TSQ VantageGeorg J, Kostova G, Vuorijoki L, Schön V, Kadow...No2 
2016-10-18 Robust Label-Free, Quantitative Profiling of Circulating Plasma Microparticle Associated ProteinsHomo sapiensQ ExactiveBraga-Lagache S, Buchs N, Iacovache MI, Zuber B...No2 
2016-10-20 PECAN - A Library Free Peptide Detection Tool for DIA DataHomo sapiens, Saccharomyces cerevisiaeQ 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-QTOFWang X. and Kültz DNo2 
2016-10-31 Plastin 1 widens stereocilia by transforming actin filament packing from hexagonal to liquidMus musculusOrbitrap FusionKrey JF, Krystofiak ES, Dumont RA, Vijayakumar ...Yes3 
2016-11-15 Time-resolved proteomics vs. ribosome profiling reveals translation dynamics under stressHomo sapiensQTRAP 5500Tzu-Yu Liu, Hector H. Huang, Diamond Wheeler, ...No9 
2016-11-16 Impact of cystinosin glycosylation on protein stability by differential dynamic SILACHomo sapiensQ Exactive PlusNathalie Nevo, Lucie Thomas, Cerina Chhuon, Zuz...No6 
2016-12-01 Photosynthesis-related phosphopeptides in Synechocystis 6803Synechocystis sp. PCC 6803TSQ VantageMartina Angeleri, Dorota Muth-Pawlak, Eva-Mari ...Yes3 
2017-01-10 An optimized chromatographic strategy for multiplexing in parallel reaction monitoring mass spectrometry: Insights from quantitation of activated kinasesHomo sapiensQ Exactive PlusUrisman A, Levin RS, Gordan JD, Webber JT, Hern...No2 
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 PlusMorales-Betanzos CA, Lee H, Gonzalez-Ericsson P...Yes5 
2017-02-13 Stoichiometric surface density modelStreptococcus pyogenesTSQ QuantivaKristoffer Sjöholm, Ola Kilsgård, Johan Teleman...Yes2 
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 VantageLinda Vuorijoki, Arjun Tiwari, Pauli Kallio, Ev...No1 
2017-03-03 Spatially and temporally resolved protein interaction networks in living cells.Homo sapiensTSQ QuantivaLobingier BT, Hüttenhain R, Eichel K, Miller KB...No2 
2017-03-21 Role of type 2 NAD(P)H dehydrogenase NdbC in redox regulation of carbon allocation in Synechocystis sp. PCC 68031Synechocystis sp. PCC 6803TSQ VantageHuokko T, Muth-Pawlak D, Battchikova N, Allahve...No1 
2017-03-29 Quantitative Proteomics Method ComparisonHomo sapiensTSQ Quantiva,Q Exactive PlusHoffman MA, Fang B, Haura EB, Rix U, Koomen JM....No2 
2017-04-13 Multiplexed MRM-based Protein Quantitation Using Two Different Stable Isotope Labeled Peptides for Calibration  André LeBlanc, Sarah A. Michaud, Andrew J. Perc...No16 
2017-04-17 Proteomic assay development for reproductive maturation state determination in Geoduck: towards a non-invasive proteomic assay for improving aquaculturePanopea generosaTSQ VantageEmma B. Timmins-Schiffman, Grace A Crandall, Br...No2 
2017-04-20 Proteomics analysis identifies orthologs of human chitinase-like proteins as inducers of tube-morphogenesis defects in DrosophilaDrosophila melanogasterTSQ VantageSandra G. Zimmerman, Gennifer E. Merrihew, Mich...No2 
2017-05-03 PSB33 sustains Photosystem II D1 protein under fluctuating light conditionsArabidopsis thalianaTSQ VantageNo1 
2017-05-03 Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancerHomo sapiensTSQ Vantage,nanoACQUITY UPLCNo70 
2017-05-03 Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and TissuesHomo sapiensTSQ Vantage,nanoACQUITY UPLCNie S, Shi T, Fillmore TL, Schepmoes AA, Brewer...No8 
2017-05-18 Quantification of Mutant SPOP Proteins in Prostate CancerHomo sapiensTSQ Vantage,nanoACQUITY UPLCYes16 
2017-06-14 An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomicsBartonella henselae str. Houston-1Orbitrap FusionUlrich Omasits, Adithi R. Varadarajan, Michael ...No2 
2017-06-21 MSstatsQC: Longitudinal system suitability monitoring and quality control for targeted proteomic experimentsHomo sapiens, Bos taurus4000 QTRAP,QTRAP 5500,TSQ Vantage,6410 Triple Quadrupole LC/MS,6460 Triple Quadrupole LC/MS,Xevo TQ MSDogu, E, Mohammad-Taheri, S, Abbatiello, SE et ...No8 
2017-07-05 A mass spectrometry-based proteomic analysis of Homer2-interacting proteins in the mouse brainMus musculusLTQ Orbitrap Elite,TSQ QuantivaScott P. Goulding, Karen K. Szumlinski, Candice...No3 
2017-08-03 Proteomic comparison of three clinical diarrhoeagenic drug-resistant Escherichia coli isolates grown on CHROMagarTMSTEC media.Escherichia coliQ ExactiveKalule JB, Fortuin S, Calder B, Robberts L, Ked...No2 
2017-08-29 A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen PeroxideSalmonella typhimuriumBruker Amazon SL ion trap and Shimadzu 8050 QQQ,LCMS-8050Karash S, Liyanage R, Qassab A, Lay JO Jr, Kwon...No3 
2017-09-15 Quantification of Plasma proteins using PlasmaDive kit on nanoflow LC-MS system and standard flow LC-MS systemHomo sapiensTSQ Vantage,6495A Triple Quadrupole LC/MSYin X, Baig F, Haudebourg E, Blankley RT, Gandh...Yes2 
2017-09-21 Cellular signaling underlying GSIS in pancreatic β-cellsRattus norvegicusQ Exactive HFKang T, Jensen P, Huang H, Lund Christensen G, ...No1 
2017-09-21 Streptococcus pyogenes infection and the human proteome with a special focus on the IgG-cleaving enzyme IdeSHomo sapiens, Streptococcus pyogenesTSQ Vantage,TSQ QuantivaChristofer A. Q. Karlsson, Sofia Järnum, Lena W...No2 
2017-09-27 The conservation of sirtuin lipoamidase activity in bacteria as a regulator of metabolic enzyme complexesEscherichia coliQ Exactive,LTQ Orbitrap VelosRowland EA, Greco TM, Snowden CK, McCabe AL, Si...No5 
2017-10-17 DDR panel radiation responseHomo sapiensQTRAP 6500Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, S...No3 
2017-10-25 Targeted proteomics in triple negative breast cancer on FFPE samplesHomo sapiensOrbitrap Fusion LumosGámez-Pozo, A. et al. Prediction of adjuvant ch...Yes2 
2017-11-02 SpkG kinase phosphorylates the ferredoxin 5 protein in Synechocystis 6803Synechocystis sp. PCC 6803TSQ VantageAngeleri M, Zorina A, Aro EM, Battchikova N. In...No1 
2017-11-02 Nitric oxide prevents Aft1 activation and metabolic remodeling in Frataxin-deficient yeastSaccharomyces cerevisiae6420 Triple Quadrupole LC/MSAlsina D, Ros J, Tamarit J. Redox Biology. Vo...Yes1 
2017-11-20 Quantification of Site-Specific Protein Lysine Acetylation and Succinylation Stoichiometry using Data-Independent Acquisitions (DIA) Mass Spectrometry --Protocol ExampleBos taurusTripleTOF 5600Wei L, Meyer JG, Schilling B. Quantification of...No1 
2017-11-29 Measurement by a Novel LC-MS/MS Methodology of Vitamin D–Binding ProteinHomo sapiensQ Exactive PlusHenderson CM, Lutsey PL, Misialek JR, Laha TJ, ...Yes1 
2017-12-18 Curated DIA assay for consistent ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus)Gasterosteus aculeatusImpactHD UHR-QTOFJ. Li, B.B. Levitan, S. Gomez-Jimenez and D. Kü...No4 
2018-01-03 Targeted Proteomics of HDL in People With Type 2 DiabetesHomo sapiensTSQ VantageVaisar T, Couzens E, Hwang A, Russell M, Barlow...No2 
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
2018-01-23 Global, site-resolved, quantitative analysis of the yeast redoxomeSaccharomyces cerevisiaeLTQ Orbitrap EliteUlrike Topf, Ida Suppanz, Lukasz Samluk, Lidia ...No5 
2018-01-26 Mass spectrometry identification and quantitation of proteins from small pools of developing auditory and vestibular cellsMus musculusQ Exactive HFNo3 
2018-01-31 Monitoring molecular contaminants and interferences in proteomic data sets  Rardin MJ. Rapid assessment of contaminants and...No1 
2018-02-02 Targeted mass spectrometry enables robust quantification of FANCD2 mono-ubiquitination in response to DNA damageHomo sapiensQTRAP 6500Whiteaker JR, Zhao L, Ivey RG, Sanchez-Bonilla ...No5 
2018-03-05 Discovery of a testis-specific complex TEX101-DPEP3 and selection of its disrupting antibodiesHomo sapiensTSQ QuantivaSchiza, C., Korbakis, D., Panteleli, E., Jarvi,...Yes4 
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
2018-03-15 PknG physiological substratesMycobacterium bovis BCGQ ExactiveKehilwe C Nakedi, Bridget Calder, Mousumi Barne...No1 
2018-03-16 Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK PathwayHomo sapiensTSQ Vantage,nanoACQUITY UPLCYi L, Shi T, Gritsenko MA, X'avia Chan CY, Fill...Yes4 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - Ochsner cohort datasetHomo sapiens6490 Triple Quadrupole LC/MSShah AK, Hartel G, Brown I, Winterford C, Na R,...Yes4 
2018-03-21 Serum glycoprotein biomarker validation for esophageal adenocarcinoma - PROBE-NET cohort datasetHomo sapiens6490 Triple Quadrupole LC/MSShah AK, Hartel G, Brown I, Winterford C, Na R,...Yes4 
2018-03-22 Identification of functional TEX101 interactome through proteomic profiling of human spermatozoa homozygous for a missense variant rs35033974Homo sapiensTSQ Quantiva,Q Exactive PlusSchiza C, Korbakis D, Jarvi K, Diamandis EP, Dr...Yes5 
2018-03-22 Targeted Quantification of the Peroxisome Proteome during Human Cytomegalovirus InfectionHuman Cytomegalovirus, Homo sapiensQ Exactive HFInfection-Induced Peroxisome Biogenesis Is a Me...No1 
2018-03-26 Global Characterization of Human IgG1 under Oxidative Stresses—Combining dual independent protease digestions and LC-HRMS Data Independent Acquisition (DIA)Homo sapiensQ Exactive PlusChen Y, Doud E, Stone T, Xin L, Hong W, Li Y. R...No8 
2018-03-27 Combining discovery and targeted proteomics reveals a prognostic signature in oral cancerHomo sapiensXevo 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 MeasurementsEscherichia coliQ Exactive HFTaumer C, Griesbaum L, Kovacevic A, Soufi B, Na...No5 
2018-05-22 HR-SRM-baseds analysis of mouse/human SGLT2 in kidney and heart tissue.Mus musculus, Homo sapiensTripleTOF 5600+Mustroph et al., ESC Heart Failure, in revision...No1 
2018-05-25 Quality Assessment and Interference Detection in Targeted Mass Spectrometry Data using Machine LearningHomo sapiensQTRAP 5500Toghi Eshghi S, Auger P, Mathews WR. Quality as...Yes3 
2018-06-11 Modular Engineering of L-Tyrosine Production in Escherichia coliEscherichia coli4000 QTRAPJuminaga, Darmawi, et al. "Modular engineering ...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