ISSN 1524-0215
Vol. 31, Issue Suppl, 2020August 01, 2020 EDT
Multi-User, High-Throughput PEAKS Online Workflow, for large scale DIA and DDA Proteomic Analysis
Multi-User, High-Throughput PEAKS Online Workflow, for large scale DIA and DDA Proteomic Analysis
Krieger Jonathan, Xin Lei, Shan Baozhen (Paul),
Articles in Vol. 31, Issue Suppl, 2020
Vol. 31, Issue Suppl, 2020
- How to perform quantitative single cell proteomics with SCoPE2Emmott EdwardHuffman R. GrayKharchenko PeterKoller AntoniusPerlman David H.Petelski AleksandraSerra MarcoSlavov NikolaiSpecht Harrison
- Hands on Training Module in Rigor and Reproducibility: Promoting Credible ScienceMedina-Lopez AidynMyers MeganRoberts JacquelynMartinez-Rivera NoraidaRosa-Molinar EduardoDragavon JoeWhite Nicole
- A Practical Guide to Quantitative FLIM/FRETVogel Steven
- The Entrepreneurial Core DirectorHockberger PhilMundoma ClaudiusMyers Ben
- ABRF Light Microscopy Research Group Study 3: The Development and Implementation of New Tools for Microscope Quality Assurance TestingAbrams BenBrown ClaireCallahan LindaCole RichardPengo ThomasWee Tse-Luen
- Administrating core facilities supported under multiple funding sources, including center grantsKarungi JustineMeyn SusanRichards Heather
- High Throughput Targeted Metabolomics Panels to Support Large StudiesDhungana SurajMolloy BillyPlumb RobLi Jinxi
- Technologies for Reading, Writing & Editing OmesChurch George
- Collective Leadership in Core Facilities: What we can learn from Native Americans and Aboriginal CulturesWhite Nicole
- Mapping Regulatory Elements Using Single-cell ATAC-SeqSimon VernaRakhshan FariborzPotluri SandeepMazzone AmeliaLi YingEckloff BruceCunningham JulieMaia Alexandre Gaspar
- Next Generation Genotyping (NGG) Using Riptide™. Performance Specifications when Best Practices are AppliedBrown KeithSiddique AzeemSuckow GaiaHomer NilsCarey JayOrdoukhanian PhillipHead StevePickrell JosephKim RyanAshworth RoxannChittur SridarKermack Justin
- Using Cyclic Traveling Wave Ion Mobility Mass Spectrometry to Investigate native and Deuterated Proteins and peptides - new capabilities for core labsMartin RoyCooper-Shepherd Dale
- Utilizing peptide centric DIA on an Orbitrap Lumos and diaPASEF on a Bruker timsTOF Pro for Complex Proteomics QuantitationPhinney BrettHocke JustinGrigorean GabrielaSalemi MichelleChien AllisMartin RoyWeis-Garcia Frances
- Using Cyclic Traveling Wave Ion Mobility Mass Spectrometry to Investigate native and Deuterated Proteins and peptides - new capabilities for core labsMartin RoyCooper-Shepherd Dale
- Utilizing peptide centric DIA on an Orbitrap Lumos and diaPASEF on a Bruker timsTOF Pro for Complex Proteomics QuantitationPhinney BrettHocke JustinGrigorean GabrielaSalemi MichelleChien AllisMartin RoyWeis-Garcia Frances
- Label Free Quantitative Proteomic using Progenesis QI proteomics Reveals Novel Mechanism of Redox Regulation in Skeletal MusclesKumar VikasGao LieRudebush Tara L.Yu LiSchultz Harold D.Zucker Irving
- RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library methodFei SuzanneHarrington ChrisMinnier JessicaCarbone LuciaSearles RobertDavis BrettOgle KimberlyPlanck StephenRosenbaum James TChoi Dongseok
- FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parametersSasada RyanWeinstein MichaelPrem AishaniJin MingdaBhasin Jeff
- Multi-User, High-Throughput PEAKS Online Workflow, for large scale DIA and DDA Proteomic AnalysisKrieger JonathanXin LeiShan Baozhen (Paul)
- Tips and Tricks for PTM AnalysisLee KimberlySheeley Douglas
- Significant reduction in mitochondrial DNA contamination improves sequencing power for ATAC-seq librariesAntunes JoanaJin MingdaLiu ZhenfengBhasin JeffYang Xiaojing
- Case study: Centralized management of shared research equipment through the BioCore at the University of Colorado BoulderQuandt DustinRamirez-Aguilar KathrynWhite NicoleGirard Isabelle
- Pushing the limits of single-cell RNA-seq with SMART-Seq single cell technologyBansal NidhanjaliDuong TommyBostick MagnoliaFarmer Andrew
- Standardizing Gut Microbiome Studies: Applying the use of a mock gut microbial community for DNA extraction optimizationSasada RyanWolfe ElaineTang Shuiquan
- Small Core Facility Management - Lessons LearnedSmith DianeOxford Julia
- Muropeptide LC-MS Analysis and Data Processing Protocols for Core FacilitiesHelm RichardJutras BrandonDeHart TannerHildreth SherryRay W. Keith
- ThruPLEX HV: a simplified system for preparation of molecular-tagged NGS librariesSherlin LukeFarmer AndrewMartin PatrickRotsinger JosephLaliberte JulieChakrabarty SudakshinaAbe Kensuke
- DSRG Research Study: Hybrid Capture Methods for Targeted RNA sequencingAdams Marie
- Subclonal identification of driver mutations and copy number variations from single-cell DNA sequencing of tumorsAinali ChrysanthiManivannan ManimozhiSahu SombeetSciambi AdamParikh Anup
- Tips and Tricks for PTM AnalysisLee KimberlySheeley Douglas
- High throughput proteome and phosphorpoteome sample processing coupled to fast gradient DIAStoychev StoyanBekker-Jensen DorteMartinez del Val AnaSteigerwald SophiaBatth TanveerGerber IsakJordaan JustinOlsen JesperChien AllisKnudtson KevinMartin Roy
- Purification of FFPE Samples Using Isotachophoresis to Improve the Yield and Quality of Amplifiable DNAMarshall LewisDyer Randy
- Single cell sorting - a survey of practicesBrundage KathleenAbshari MehrnooshAdams DaveBispo ClaudiaBowen SaraCochran MatthewHarley ReginaHassel ChristianeHeyward FeliciaKollipara AvinashLoof NicolasNiziolek ZacharyThornton Sherry
- The Panorama Data Repository for Skyline UsersSharma Vagisha
- A Rapid and Comprehensive Targeted Approach for Investigating the Lipidome of Bladder Cancer SubjectsDhungana SurajMunjoma NyashaIsaac GiorgisGethings LeePlumb Rob
- Development of automated mass spectrometry data evaluation workflows for analysis of therapeutic proteinsBitsch FrancisYang YangHug ChristianHensinger Heloise
- Nanoscale Automation of a Full-Length RNA Sequencing Library Preparation Method on a Microfluidic CircuitGoralski ThomasAlipaz JulieBrockman JoelChamnongpol SangpenFowler BrianGeis JenniferKubu ChristopherKung RaphaelLacar BenjaminPark CharlesPhelan MichaelSun Gang GangKing David
- Characterization of Protein Biotinylation Sites by Peptide-Based Immunoaffinity EnrichmentLee KimberlyZhu YiyingNelson AlissaRen Jian MinYang VickyFarnsworth CharlesStokes MatthewChien AllisKnudtson Kevin
- Use Of FlashGel™ DNA Cassettes For Separations In Gene Editing WorkflowsWhite Hugh
- Fluorescent Imaging: Ensuring Reproducibility and Finding the Best DyeMatiukas Arvydas
- Reducing compression effects and expanding the multiplex capabilities on a trapped ion mobility Q-TOFAdams ChristopherWilletts MattSrikumar TharanKrawitzky Michael
- Miniaturization of Ribosomal RNA Depletion and Total RNA Library Preparation in Single CellsWegener MarcRhodes MaryJohnson BenjaminSheridan RachaelHimadewi PamelaFoy KellyShen HuiTriche TimothyAdams Marie
- A cytometry-based assay to determine optimal Janelia Fluor dye labelling of Halo and SNAP tagsSchaefer KathyXie Frank (Liangqi)Weis-Garcia FrancesWhite Nicole
- Molecularly guided digital spatial profiling for multiplexed analysis of gene expression with spatial and single cell resolutionFuhrman KitKuhar Jamie RoseMerritt Chrisnyugen karenSorg KristinaZhang BingqingMa Xiao-junDikshit AnushkaDikshit Anushka
- The Usual Suspects? An Assessment of Biospecimen Collection DeviationsO'Neal JamyeBarnes HeatherDahlman KimberlyStein Jonathan
- Comparing Reagents Used on Applied Biosystem's 3730xlPetros ChristinaMunger HeidiWei Chia-Lin
- New approaches to phosphoproteomics: Clinical scale characterization of the AKT/mTOR pathway targetsSinghal KratikaLeib RyanMatney RowanChen EmilyWagh DhananjayColler JohnLiu FangChien AllisKnudtson KevinMartin RoyWeis-Garcia Frances
- Whole transcriptome profiling of germinal center B-lymphocytes using a universal, integrated workflow of FACS cell sorting and TempO-Seq® assaySeligmann BrucePechhold KlausSchrader CarolRaghunathan MeghaBabic MilosWilliams Travis
- Proteomics Data Science: Online Data ResourcesSearle BrianWeintraub Sue
- GERG Study 2019: Reproducibility of indel formation rates by comparing guideRNA format and delivery methodSergison ElizabethDelventhal KymPruett-Miller ShondraModarai ShirinKmiec EricRegan MaureenMiller Brandon
- SimpliFi: a data-to-meaning analytics engine to bring omics understanding to allWilson JohnPalmeri JimPappin Darryl
- RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library methodFei SuzanneHarrington ChrisMinnier JessicaCarbone LuciaSearles RobertDavis BrettOgle KimberlyPlanck StephenRosenbaum James TChoi Dongseok
- FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parametersSasada RyanWeinstein MichaelPrem AishaniJin MingdaBhasin Jeff
- Multi-User, High-Throughput PEAKS Online Workflow, for large scale DIA and DDA Proteomic AnalysisKrieger JonathanXin LeiShan Baozhen (Paul)
- Tips and Tricks for PTM AnalysisLee KimberlySheeley Douglas
- Significant reduction in mitochondrial DNA contamination improves sequencing power for ATAC-seq librariesAntunes JoanaJin MingdaLiu ZhenfengBhasin JeffYang Xiaojing
- Case study: Centralized management of shared research equipment through the BioCore at the University of Colorado BoulderQuandt DustinRamirez-Aguilar KathrynWhite NicoleGirard Isabelle
- Pushing the limits of single-cell RNA-seq with SMART-Seq single cell technologyBansal NidhanjaliDuong TommyBostick MagnoliaFarmer Andrew
- Standardizing Gut Microbiome Studies: Applying the use of a mock gut microbial community for DNA extraction optimizationSasada RyanWolfe ElaineTang Shuiquan
- Small Core Facility Management - Lessons LearnedSmith DianeOxford Julia
- Muropeptide LC-MS Analysis and Data Processing Protocols for Core FacilitiesHelm RichardJutras BrandonDeHart TannerHildreth SherryRay W. Keith
- Development of a simple and versatile enzymatic DNA synthesis system that enables accurate, fast, and long oligos on demandEimerman PatrickJeddeloh JeffreyChampion ElisePeponnet ChristineGariel SylvainGodron XavierYbert Thomas
- Puerto Rico-INBRE Metabolomics Research CoreChorna NataliyaCadilla CarmenMedina Jose Rodriguez
- An efficient, tunable solution for pre-capture multiplexing in targeted sequencing via novel chemistry and semiconductor DNA synthesis technologySong IreneMiller RaymondWang JiashiWang JianpengFan LongYe LumengLi HongHuang Heidi
- Next Generation Genotyping (NGG) for Population Scale Genomic Studies Using Riptide™ DNA Library PreparationSiddique AzeemBrown KeithSuckow GaiaHomer NilsOrdoukhanian PhillipHead StevePickrell JosephKim RyanAshworth RoxannChittur SridarKermack Justin
- Scalable and Highly Sensitive Single Cell RNA-seq through Combinatorial BarcodingRoco CharlesO'Connor EmilyHills EthanTran VuongRosenberg Alexander
- Everything you wanted to know about ABRF Research Groups (but didn't know who to ask)Mason Chris
- Building Robust Quality Management Systems in Core Labs (GLP, GMP and QA Best Practices)Blum DavidDavies RebeccaGregory Christopher
- FASEB & ABRF: Partners in Science Policy and AdvocacySeger Yvette
- Gene Activity Quantification in Real Time RT-PCRChornyy AnatoliyChorna NataliyaZuazaga Humberto Ortiz
- 4D Cell Biology: Adaptive optics lattice light-sheet imaging and AI powered big data processing of live stem cell-derived organoidsSchoeneberg Johannes
- Disaster preparedness to maintain sample and reagent integrityBonk Aaron
- Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing StudyMason Chris
- iPRGPalmblad Magnus
- Customizable Management Database for Day-to-Day Corea Facility OperationsHsia Ru-ching
- Using organoids to understand mechanisms and consequences of aging in breastLaBarge MarkMiyano MasaruSayaman RosalynTodhunter Michael
- Advanced Imaging Approaches in Drug Discovery: Exploring Macromolecular Biodistribution to Brain TargetsCalvert MeredithSanchez PascalZuchero JoyThorne RobertDe Vos SarahPizzo MichelleInnocent CvicWeis-Garcia Frances
- Empowering Team Science 101: Collaborating for Reproducible Outcomes Across Diverse TechnologiesLopez PeterSchock-Kuster Elke
- Progress Towards Standardizing Metagenomics: Applying Metagenomic Reference Material to Develop Reproducible Microbial Lysis Methods with Minimum BiasSasada RyanWeinstein MichaelDanko DavidWolfe ElaineTang ShuiquanJarvis KarenGrim ChristopherLagishetty VenuJacobs JonathanArnold JasonKemp RyanMason Christopher
- Location, Location, Location! An Evaluation of Spatial Transcriptomics Methods Using Embryonic Chick TissueHall KateGogol MadelaineHassan HuzaifaKasemeier JenniferLi HuaMalloy SethMcKinney SeanMcLennan RebeccaMorrison JasonWang YongfuKulesa PaulPerera Anoja
- Evaluation and Optimization of Sample Processing and Bioinformatics Analysis for Long-Read Metagenomic SequencingSasada RyanGonzalez AngelWeinstein MichaelTang Shuiquan
- Methods to preserve individual bacteria and microbiome samples for nucleic acid analyses without altering cellular structure or integrityRanjan RaviGreen Stefan J.Mason ChristopherButler DanVinas Natalia ReyeroHsu Chuan-YuWagner NicoleThomas W. KelleySimpson SteveBivens NathanKehoe PhoebeTighe Scott
- Using organoids to understand mechanisms and consequences of aging in breastLaBarge MarkMiyano MasaruSayaman RosalynTodhunter Michael
- Novel Strong Cation Exchange Ultra-Performance Liquid Chromatography Coupled to UV and MS Detectors for Robust Characterization of ADC Charge VariantsKliman MichalAistars ArnieMatsuda YutakaMendelsohn Brian A.
- Journals, ABRF and You: Partners Addressing Rigor and ReproducibilityWeis-Garcia Frances
- Utilizing the Rheonix NGS OnePrep™ Solution to automate the Takara Bio ThruPLEX® Tag-Seq HV library preparation kitHiggins HazelZhu HuiKim Beum JunYasmin RubinaSherlin LukeLaliberte JulieMartin PatrickFarmer AndrewMontagna Richard
- Close Encounters of the Third Kind; Circumventing the Effects of Extraterrestrial DNATighe Scott
- Submitting Successful Cancer Center Support Grants (P30) from the Core PerspectiveFox JayHe MinLoughran ThomasSynold TimothyUthamanthil Rajesh
- Multi-omics: Traversing the Central Dogma of Molecular BiologyHettich RobertJagtap PratikMathe EwyMishra TejaswiniRuggles Kelly
- A high throughput single cell workflow for paired genomic and phenotypic analysisFlynn JamesDhingra DaliaMendez PedroOoi AikWang ShuGulati SaurabhRuff Dave
- High Spatial Resolution Molecular Tissue Imaging by Desorption Electrospray Ionization using Novel Sprayer AssemblyShrestha BindeshRoman GregoryHattan StephenLeveille WadeMurphy JimMichienzi JosephMusacchio JeffreyJones EmrysPringle StevenInnocent CvicKnudtson KevinWeis-Garcia Frances
- Evaluation and Optimization of Sample Processing and Bioinformatics Analysis for Long-Read Metagenomic SequencingSasada RyanGonzalez AngelWeinstein MichaelTang Shuiquan
- Methods to preserve individual bacteria and microbiome samples for nucleic acid analyses without altering cellular structure or integrityRanjan RaviGreen Stefan J.Mason ChristopherButler DanVinas Natalia ReyeroHsu Chuan-YuWagner NicoleThomas W. KelleySimpson SteveBivens NathanKehoe PhoebeTighe Scott
- Using organoids to understand mechanisms and consequences of aging in breastLaBarge MarkMiyano MasaruSayaman RosalynTodhunter Michael
- Novel Strong Cation Exchange Ultra-Performance Liquid Chromatography Coupled to UV and MS Detectors for Robust Characterization of ADC Charge VariantsKliman MichalAistars ArnieMatsuda YutakaMendelsohn Brian A.
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- Utilizing the Rheonix NGS OnePrep™ Solution to automate the Takara Bio ThruPLEX® Tag-Seq HV library preparation kitHiggins HazelZhu HuiKim Beum JunYasmin RubinaSherlin LukeLaliberte JulieMartin PatrickFarmer AndrewMontagna Richard
- Close Encounters of the Third Kind; Circumventing the Effects of Extraterrestrial DNATighe Scott
- Submitting Successful Cancer Center Support Grants (P30) from the Core PerspectiveFox JayHe MinLoughran ThomasSynold TimothyUthamanthil Rajesh
- Multi-omics: Traversing the Central Dogma of Molecular BiologyHettich RobertJagtap PratikMathe EwyMishra TejaswiniRuggles Kelly
- A high throughput single cell workflow for paired genomic and phenotypic analysisFlynn JamesDhingra DaliaMendez PedroOoi AikWang ShuGulati SaurabhRuff Dave
- High Spatial Resolution Molecular Tissue Imaging by Desorption Electrospray Ionization using Novel Sprayer AssemblyShrestha BindeshRoman GregoryHattan StephenLeveille WadeMurphy JimMichienzi JosephMusacchio JeffreyJones EmrysPringle StevenInnocent CvicKnudtson KevinWeis-Garcia Frances
- Adapting a high-throughput clinical sample pipeline for proteomic characterization of adipose tissueHutchinson ChelseaPiehowski PaulSanford JamesGritsenko MarinaHansen JoshuaMoore RonaldQian Wei-JunAdkins Joshua
- CRISPR-Mediated Depletion of Ribosomal RNA-Derived DNA from RNA-Seq NGS LibrariesSiddique AzeemSuckow GaiaHead SteveOrdoukhanian PhillipSussman HallieRamachandran DhanyaHomer NilsBajena JorgeBrown KeithChittur SridarKnudtson KevinKermack Justin
- Enzymatic Methyl-seq: Next Generation MethylomesHoppers AmandaWilliams LouisePonnaluri V K ChaithanyaSexton BrittanySaleh LanaCampbell MatthewMarks KatherineSamaranayake MalaEttwiller LaurenceGuan ShengxiChurch HeidiLanghorst BradleySun ZhiyiEvans Thomas C.Vaisvila RomualdasDimalanta EileenStewart Fiona
- Collective Leadership in Core Facilities: What we can learn from Native Americans and Aboriginal CulturesWhite Nicole
- Cathepsin B/ SAPC inhibition deregulates apoptosis-related proteins in neuronal cells exposed to supernatants from HIV-infected macrophagesMelendez LoydaPhDZenon-Melendez CamilleMSLima Abiel RocheCarrasquillo-Carrión KelvinMSCantres-Rosario YadiraBS
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- Ultra-low input single tube linked read library method enables NGS systems generate accurate & economical long read information for broad applicationsWang Yong
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- Mapping whole brain structure and activity at cellular resolution: iDISCO+ and ClearMapKirst Christoph
- Efficient high-throughput sequencing for quantitative immune profiling using unique molecular identifiersBostick MagnoliaLi QiangTazawa RyujiXiang WenwenSwaminathan KarthikeyanFarmer Andrew
- Planning for Core Sustainability and Addressing Usage Challenges: Lessons from Core Research Facilities Seeded by NIH IDeA FundingBaker JonathanEdmondson RickyHaley RandMackintosh SamOxford Julia
- Molecular Characterization and Cytotoxic Activity of McTI, a Novel Cystine-Knot Inhibitor from Momordica charantiaKhurshid YamnaSaeed MariaLam JerikaSimjee Shabana UHaq Zaheer-Ul-Ahmed AftabChien AllisMartin Roy
- Viral vector manufacturing: quality attributes of rAAV used in clinical developmentAlcudia JavierWright John Fraser
- RNAscope® and BaseScope™: In-situ RNA analysis for formalin-fixed paraffin-embedded tissues and beyondSelvaraj ShanmugapriyaMezzano ValeriaLoomis CynthiaHanniford Douglass
- Suitability of RNA for NGS analysis after co-extraction with metabolites from limiting biological samplesSiwicki RebeccaMadaj ZacharyPettinga DeanWegener MarcEllis AbigailIsaguirre ChristineDeCamp LisaRohrer DanKirchoff MeganJones RussellGivan ScottJewell ScottSheldon RyanAdams MarieAshworth RoxannKnudtson Kevin
- MethylSeq Direct workflow: a fast method for DNA methylation analysisSchreiber Edgar
- Multi-well, In-Incubator Imaging Platform for Biological ImagingLy Victoria
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- HONEY I SHRUNK THE KITS: Practical Adventures in Reducing Assay VolumesLevine Stuart
- ISOLATION, CHARACTERIZATION AND CYTOTOXIC ACTIVITY OF NON- SPECIFIC LIPID TRANSFER PROTEIN (nsLTP) FROM FENNEL (FOENICULUM VULGARE Mill.) SEEDSMegeressa MekdesKhurshid YamnaAhmed Aftab
- Electron Microscopy: adding cryoEMBelnap DavidChambers MelissaDryden KellyEgelman Ed
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- Real-time, high-resolution microscopy of invasive cancer cells in the tumor microenvironment contextGligorijevic Bojana
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1.
Jonathan K, Lei X, Baozhen (Paul) S. Multi-User, High-Throughput PEAKS Online Workflow, for large scale DIA and DDA Proteomic Analysis. JBT. 2020;31(Suppl):S22-S23.