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  • Video 1: Method Editing: /home/software/Skyline
    version of the free Flash Player by downloading here Download the full video for faster access to repeat viewing recorded using Skyline v0 2 discussion Discussion Search Search Pages Skyline Targeted Proteomics Environment Install 64 bit Skyline v3 1 Install 64 bit Skyline v3 1 Unplugged Install 32 bit Skyline v3 1 Install 32 bit Skyline v3 1 Unplugged Release Notes Videos Video 1 Method Editing Video 2 Results Analysis Video 3 Existing Quantitative Experiments Video Trailer Tutorials 教程 中国语文 靶向 方法编辑 靶向方法优化 处理已有定量实验数据 MS1 全扫描筛选 靶向 MS MS PRM iRT 保留时间预测 チュトリアル 日本語版 ターゲットメソッドの編集 ターゲットメソッドの最適化 既存データ処理および定量実験 MS1フルスキャンフィルタ ターゲットMS MS PRM iRT保持時間予測 Targeted Method Editing Targeted Method Refinement Processing Grouped Study Data Existing and Quantitative Experiments Small Molecule Targets MS1 Full Scan Filtering Targeted MS MS PRM Data Independent Acquisition Absolute Quantification Custom and Live Reports Advanced Peak Picking Models iRT Retention Time Prediction Collision Energy Optimization Spectral Library Explorer QuaSAR Quantitative Statistics SRM Course Tutorials Tips Chorus Cloud Chromatogram Extraction Working with Other Quantitative Tools How to Display Multiple Peptides Terminology Cheat Sheet How Skyline Builds Spectral Libraries ID Annotations Missing with Mascot Search Results Slides Explaining Data Independent Acquisition DIA Methods for Thermo Q Exactive How Skyline Calculates

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=video_0-2 (2015-06-02)
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  • Video 3: Existing & Quantitative Experiments: /home/software/Skyline
    your version of the free Flash Player by downloading here Download the full video for faster access to repeat viewing recorded using Skyline v0 5 Preview discussion Discussion Search Search Pages Skyline Targeted Proteomics Environment Install 64 bit Skyline v3 1 Install 64 bit Skyline v3 1 Unplugged Install 32 bit Skyline v3 1 Install 32 bit Skyline v3 1 Unplugged Release Notes Videos Video 1 Method Editing Video 2 Results Analysis Video 3 Existing Quantitative Experiments Video Trailer Tutorials 教程 中国语文 靶向 方法编辑 靶向方法优化 处理已有定量实验数据 MS1 全扫描筛选 靶向 MS MS PRM iRT 保留时间预测 チュトリアル 日本語版 ターゲットメソッドの編集 ターゲットメソッドの最適化 既存データ処理および定量実験 MS1フルスキャンフィルタ ターゲットMS MS PRM iRT保持時間予測 Targeted Method Editing Targeted Method Refinement Processing Grouped Study Data Existing and Quantitative Experiments Small Molecule Targets MS1 Full Scan Filtering Targeted MS MS PRM Data Independent Acquisition Absolute Quantification Custom and Live Reports Advanced Peak Picking Models iRT Retention Time Prediction Collision Energy Optimization Spectral Library Explorer QuaSAR Quantitative Statistics SRM Course Tutorials Tips Chorus Cloud Chromatogram Extraction Working with Other Quantitative Tools How to Display Multiple Peptides Terminology Cheat Sheet How Skyline Builds Spectral Libraries ID Annotations Missing with Mascot Search Results Slides Explaining Data Independent Acquisition DIA Methods for Thermo Q Exactive How

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=video_0-5b (2015-06-02)
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  • Start Page: /home/software/Skyline
    MO May 31 2015 Spring Computation and Statistics for Discovery and Targeted Proteomics at Northeastern Boston May 18 22 2015 Spring Targeted Quantitative Proteomics Course at UW Seattle March 23 27 2015 Spring Short Course at US HUPO Tempe March 15 2015 review the slides Winter Targeted Proteomics Workshop at IIT Bombay Dec 10 11 2014 Winter Targeted Proteomics Workshop at Kyoto University Nov 26 2014 Fall Proteomics Informatics Short Course in Seoul October 13 14 2014 Fall Targeted Proteomics Course at PRBB Barcelona Sep 28 Oct 3 2014 watch presentations Summer Panorama Webinar III August 19 2014 watch the recording Summer EU Proteomics Summer School Workshops in Brixen Bressanone August 3 9 2014 Summer Skyline User Group Meeting at ASMS 2014 review the presentations Summer ASMS 2 Day Courses in Baltimore MD June 14 15 2014 More Events Recently Published Egertson Nature Protocols Multiplexed peptide analysis using data independent acquisition and Skyline abstract Abbatiello Mollecular Cellular Proteomics Large scale inter laboratory study to develop analytically validate and apply highly multiplexed quantitative peptide assays to measure cancer relevant proteins in plasma abstract Sharma Journal of Proteome Research Panorama A Targeted Proteomics Knowledge Base abstract Broudy Killeen Bioinformatics A framework for installable external tools in Skyline abstract More Publications Pages Skyline Targeted Proteomics Environment Install 64 bit Skyline v3 1 Install 64 bit Skyline v3 1 Unplugged Install 32 bit Skyline v3 1 Install 32 bit Skyline v3 1 Unplugged Release Notes Videos Video 1 Method Editing Video 2 Results Analysis Video 3 Existing Quantitative Experiments Video Trailer Tutorials 教程 中国语文 靶向 方法编辑 靶向方法优化 处理已有定量实验数据 MS1 全扫描筛选 靶向 MS MS PRM iRT 保留时间预测 チュトリアル 日本語版 ターゲットメソッドの編集 ターゲットメソッドの最適化 既存データ処理および定量実験 MS1フルスキャンフィルタ ターゲットMS MS PRM iRT保持時間予測 Targeted Method Editing Targeted Method Refinement Processing Grouped Study Data Existing and Quantitative Experiments Small Molecule Targets MS1

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/begin.view? (2015-06-02)
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  • Start Page: /home/software/Topograph
    because Topograph does report chromatographic areas Topograph also performs retention time alignment based on the location of MS2 peptide identifications to enable finding peptides in samples which do not have an MS2 ID for that particular peptide Installing Topograph version 2 Topograph install page Topograph Daily Build Future version of Topograph The Topograph Daily build is released more frequently than the official Topograph V2 release As bugs are fixed in

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Topograph/begin.view (2015-06-02)
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  • Start Page: /home/software/BiblioSpec
    not compatible There is however a conversion tool for turning a version 1 0 library into a sqlite3 library BiblioSpec components The BiblioSpec package contains the following programs BlibBuild creates a library of peptide MS MS spectra from a variety of different database search results BlibFilter removes redundant spectra from a library BlibSearch searches a spectrum library for matches to query spectra printing the results to a report file BlibToMS2

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/BiblioSpec/begin.view (2015-06-02)
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  • Start Page: /home/software/Topograph/support
    are certain you are encountering a defect in the software you may also choose to post to the Issues List Messages Showing all messages MSe Data from Waters PLGS software wkray 2015 04 30 12 07 We are trying to determine incorporation of 15N from MS E data that has been processed using PLGS 3 0 2 Topograph recognizes the search results final fragment csv but it is having a problem using the mzML files exported from the PLGS software I was wondering if anyone else has reported a problem like this What version of mzML and mzXML does Topograph recognize Do you have any suggestions to remedy this problem The error message is below 4 30 2015 2 33 25 PM Exception trying to open E 2015 Cyano peptide DB Ion Accounting 150423 Cyano Pep UHM100 15N C IA final fragment mzML System Exception ChromatogramList mzML chromatogram Index out of bounds at pwiz CLI msdata ChromatogramList chromatogram Int32 index Boolean getBinaryData at pwiz ProteowizardWrapper MsDataFileImpl GetScanTimes at pwiz Topograph Model MsDataFileData Init MsDataFileImpl msDataFileImpl in C Users nicksh svn topograph 1 1 pwiz pwiz tools Topograph TopographLib Model MsDataFileData cs line 51 at pwiz Topograph MsData MsDataFileUtil TryInitMsDataFile Workspace workspace MsDataFile msDataFile String message in C Users nicksh svn topograph 1 1 pwiz pwiz tools Topograph TopographLib MsData MsDataFiles cs line 101 Exception caught at at pwiz Topograph MsData MsDataFileUtil TryInitMsDataFile Workspace workspace MsDataFile msDataFile String message at pwiz Topograph ui Forms TurnoverForm EnsureMsDataFile MsDataFile msDataFile Boolean alwaysPrompt at pwiz Topograph ui Forms TurnoverForm EnsureMsDataFile MsDataFile msDataFile at System RuntimeMethodHandle InvokeMethod Object target Object arguments Signature sig Boolean constructor at System Reflection RuntimeMethodInfo UnsafeInvokeInternal Object obj Object parameters Object arguments at System Delegate DynamicInvokeImpl Object args at System Windows Forms Control InvokeMarshaledCallbackDo ThreadMethodEntry tme at System Windows Forms Control

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Topograph/support/begin.view (2015-06-02)
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  • Sign Up for Support and Notification Email: /home/support
    to the Skyline web site please do not submit this form again The information you provide will not be shared with any outside organizations A confirmation email has been sent to you Please check your email to confirm your address and complete the sign up process Fill out the form below to register and sign up for free support and to receive notification email of new releases and events You

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/support/page.view?name=signup-form (2015-06-02)
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  • MacCoss Lab Software: /home
    to employ cutting edge technologies for creating and iteratively refining targeted methods for large scale proteomics studies Build Targeted Methods Use prior knowledge of your proteins and peptides of interest to improve your measurement selectivity and precision See Quantitative Results Learn more about your quantitative measurements through the rich and interactive Skyline graphical data displays Store and Share Experiments Panorama stores the entire Skyline data model where you and your collaborators can explore it with a web browser Build Chromatogram Libraries Use Panorama to build fully validated chromatogram assay libraries you can use in Skyline for new experiments Project Page Support Panorama is a freely available open source targeted proteomics website knowledgebase for sharing experiments and validated assays that integrates into a Skyline proteomics workflow It can be installed on a local server or you can request a project on the PanoramaWeb org server hosted by the MacCoss Lab at the University of Washington Access privileges within a project may be customized allowing you to control fully who has access to data you publish to Panorama Project Page Support Topograph is a freely available open source Windows client application designed to analyze data in protein turnover experiments using chromatographic peak

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/project/__r2/begin.view? (2015-06-02)
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