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    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

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    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

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    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

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    Any thoughts on getting around this will be highly appreciated Thanks Saul more less Skyline File Error png view request Error building spectral library 2 responses tanya0290 2015 05 11 09 22 Hello I have generated raw files using a waters G2 Si instrument in a DDA experiment I then ran a database search using the trans proteomic pipeline from which I produced the pepXML files I tried to add these when building a spectral library under peptide settings However it gives an error that there were no spectra found for the new library I do not know how to correct this issue and have tried generating different file types that are compatible but have so far been unsuccessful Is there any advice that you could give me I followed the videos on line to get to this point more less view request Failed to build a cache 2 responses SF 2015 05 07 12 09 Hi I am continually getting an error message that says Failed to build a cache for File name ThermoRawFile ScanInfo Impl initizalie GetFilterforScanNum Failed call to XRawfile The handle is invalid I ve tried importing individually or in batches in case it was a single corrupt file but it appears everytime Thanks Sarah more less view request Lock both peak boundaries for multiple samples MRM 4 responses cmk35 2015 05 07 08 55 Dear Brendan and the Skyline team I am new to MRM data analysis and really appreciate how easy it is to use Skyline We are doing experiments to calculate heavy light ratios across multiple samples where the same peptides have been targeted I was wondering if the following feature already exists in Skyline or you might be able to add it I am currently using Skyline daily For each biological sample targeting a peptide I have a series of spectra and retention times the RTs can change slightly over the course of the experiment Is it possible to set lock a left and right peak boundary width and then apply this window of integration across multiple samples It would be great if the peak width could be locked and then I could drag that integration area for other samples to center on specific RT peaks Currently I am manually dragging peak boundaries for each sample and trying to match the peak integration widths by eye to keep things consistent across samples Please let me know if you need any more details on my question Thanks again for all your hard work in improving Skyline Best Tina more less view request the fragment ion not detected yueg 2015 05 05 14 18 Hi Brendan I just noticed some problem when I used Skyline to look for my data One problem is about looking the precursor isotope pattern You will see in the first slide when my mouse pointed the peak 44 3min the isotope pattern showed is in 42 42mins I noticed there is one red circle in 42 42min but my mouse pointed in 44 3mins no matter I clicked once or double clicked Did I have some setting wrong Or I just do not do the right way the another question is about fragment issue You will see in my second slide there is no any fragment ions which was picked with Skyline I could not figure out what is wrong some others are just fine in the slide 3 with same setting in the same file could you help me what I did wrong Thank you Eileen more less Presentation3 pptx view request Spectral Library Creation 2 responses j philip 2015 05 05 12 00 Hi I did a Mascot search for some standards we use in the lab I created a spectral library with some of the better standards by importing the Mascot DAT files during the build library function Is there any way of getting Skyline to select a particular MS2 spectrum for a particular peptide instead of automatically picking the spectrum thanks john more less view request Area calculation in Report 4 responses j philip 2015 05 05 11 43 Hi When creating a custom report I went to Proteins Peptides Precursors Precursor Results In that section there are three calculations that I am interested in Total Area Total Area MS1 and Total Area Fragment CustomReports 2 5 pdf defines Total Area as The summed Area values of all individual transitions for the particular precursor So what is Total Area MS1 and Total Area Fragment These definitions are not in the CustomReports 2 5 pdf Is there a more recent version of that file If not can someone fill in the missing definitions thanks john more less view request Method export failure 2 responses bret cooper 2015 05 04 05 19 Dear Brendan I m running Skyline 2 6 unplugged on Win XP with Xcalibur 2 0 7 on the computer that runs our Orbi XL When following the Targeted MSMS low res tutorial for method export pg 11 I get an error attempting to export ERROR failure opening template method C Skyline TargetedMSMS template meth I get similar errors using other meth files in Xcalibur Is this a backwards compatibility issue If so can you suggest a solution and or send a generic methods file or manual settings description for PRM that will help me get started in my system Thanks and sincerely Bret Cooper more less view request Waters Synapt DDA peptide search from Mascot DAT file 10 responses Abraham Escobedo 2015 04 30 08 42 Dear Skyline developers I am having troubles when I want to import a DAT file for MS1 Full Scan Filtering purpouses When I select the file an error appears Data truncation in library header File may be corrupted Other exported files like XML pepXML MZTAB or MZID are not recognized When I continue with the peptide search process with the previous imported DAT file and I submit the FASTA database NCBI or Swissprot it indicates that there were no matching spectra But the same data produces several matches when runs with MASCOT previously My RAW files come from a Synapt HDMI Waters which are processed with ProteinLynx 4 1 to generate the PKL files and then are submitted to a MASCOT search producing the DAT exported file My operating system is Windows 8 64 bit and the Skyline version is 3 1 0 7382 64 bit I am attaching the DAT file and the NCBI database is for Mus musculus Could you indicate me if I am doing something wrong or if I need to do something not specified in the tutorial MS1 filtering Thank you Abraham E more less Prueba Plasma8 dat view request results import from chorus fails 2 responses tobias kockmann 2015 04 30 07 25 Dear skyline support I am trying to import results from chorus into a skyline 3 1 doc but I am not getting any chromatograms The raw file stored on chorus is fully translated and contains data from a DIA type experiment Importing from a local copy works without any problem Any clue what might go wrong here Best Tobi more less view request myrimatch IDPicker data importing 1 response mvillal1 2015 04 28 21 54 Hello Skyline developers and community I have been trying to create a spectral library from some Myrimatch IDPicker output files but I am not able or don t know how to export them to the idpXML mzXML formats that Skyline requires My files are either in pepXML or mzIdentML formats but I don t know how to convert either of these outputs to idpXML or mzXML Can anyone point me out a way to do this The raw data comes from a Thermo LTQ XL which is then processed through the Bumberdash IdPicker pipeline Many thanks P S I am new to targeted proteomics but Skyline is proven to be a great tool Keep up the good work and thanks again Ivan more less view request Waters Synapt DDA peptide search from Mascot DAT file Abraham Escobedo 2015 04 28 19 09 I am having troubles when I want to import a DAT file for MS1 Full Scan Filtering purpouses When I select the file an error appears Data truncation in library header File may be corrupted Other exported files like XML pepXML MZTAB or MZID are not recognized When I continue with the peptide search process with the previous imported DAT file and I submit the FASTA database NCBI or Swissprot it indicates that there were no matching spectra But the same data produces several matches when runs with MASCOT previously My RAW files come from a Synapt HDMI Waters which are processed with ProteinLynx 4 1 to generate the PKL files and then are submitted to a MASCOT search producing the DAT exported file My operating system is Windows 8 64 bit and the Skyline version is 3 1 0 7382 64 bit more less Prueba Plasma8 dat view request Global normalization standard for small molecules 1 response r bagshaw 2015 04 28 13 18 Hello Thank you again for this wonderful tool you provide So for the small molecule stuff it is possible to set a compound as a normalization standard and have peak areas of the other compounds normalized to it ie a global standard I can do this easily for peptides when looking at real peptides that is but it doesn t seem to work for me for small molecules Thanks Rick more less view request XIC in the absence of MS2 data 1 response CtrlAltDel 2015 04 27 13 17 Hello I am working with data from purified proteins I am interested in finding a tool to perform XICs using a list of masses of my choosing in the absence of MS2 data preferably from the command line Is this something that skyline can perform Basically 1 Input m z and RT 2 extract all matches withing tolerance more less view request Export of replicate data in Skyline 1 response rle041 2015 04 27 01 43 Hi Skyline team First of all thank you for a great software I am currently using skyline to investigate DIA data I am wondering if it is possible to export data from skyline with replicate information in columns So that there is only one row pr transition and precursor and that replicate values for area dotproduct and idotp are in columns This would make things much easier in the post analysis I do not know if this is already possible but I have only been able to export this information in rows In advance Thank you for your help Ragnhild more less view request Comparing isotope abundancies measured by SRM 2 responses sarahabollinger 2015 04 26 11 03 1 I would like to know is it possible to determine the isotopic distribution of a peptide from monitoring its transitions If so please direct me to a tutorial or other useful information as to how the data can be analyzed using Skyline 2 I have also tried to setup a parent scan to try and find the isotopes that way but it was unsuccessful and I cannot find any useful information on how to setup a scan in this way on your website more less view request Failure to install Skyline 1 response psemchuk 2015 04 24 11 45 I have been trying to update Skyline on my computer and after many failures with downloading files which I think has been sorted out by the Skyline team I am still unable to install skyline on the computer I have followed the support guide for How to recover from broken installation and I have restarted my system but it still fails to install Skyline Here is the error message I got PLATFORM VERSION INFO Windows 6 1 7601 65536 Win32NT Common Language Runtime 4 0 30319 18444 System Deployment dll 4 0 30319 34244 built by FX452RTMGDR clr dll 4 0 30319 18444 built by FX451RTMGDR dfdll dll 4 0 30319 34244 built by FX452RTMGDR dfshim dll 4 0 41209 0 Main 041209 0000 SOURCES Deployment url https skyline gs washington edu software Skyline release 64 3 1 Skyline application Server Apache Coyote 1 1 Deployment Provider url https skyline gs washington edu software Skyline release 64 3 1 Skyline application Application url https skyline gs washington edu software Skyline release 64 3 1 Application 20Files Skyline 3 1 0 7382 Skyline exe manifest Server Apache Coyote 1 1 IDENTITIES Deployment Identity Skyline application Version 3 1 0 7382 Culture neutral PublicKeyToken e4141a2a22107248 processorArchitecture msil Application Identity Skyline exe Version 3 1 0 7382 Culture neutral PublicKeyToken e4141a2a22107248 processorArchitecture msil type win32 APPLICATION SUMMARY Installable application ERROR SUMMARY Below is a summary of the errors details of these errors are listed later in the log Activation of https skyline gs washington edu software Skyline release 64 3 1 Skyline application resulted in exception Following failure messages were detected Value does not fall within the expected range COMPONENT STORE TRANSACTION FAILURE SUMMARY No transaction error was detected WARNINGS There were no warnings during this operation OPERATION PROGRESS STATUS 24 04 2015 12 44 14 PM Activation of https skyline gs washington edu software Skyline release 64 3 1 Skyline application has started 24 04 2015 12 44 14 PM Processing of deployment manifest has successfully completed 24 04 2015 12 44 14 PM Installation of the application has started 24 04 2015 12 44 15 PM Processing of application manifest has successfully completed 24 04 2015 12 44 15 PM Found compatible runtime version 4 0 30319 24 04 2015 12 44 15 PM Request of trust and detection of platform is complete ERROR DETAILS Following errors were detected during this operation 24 04 2015 12 44 15 PM System ArgumentException Value does not fall within the expected range Source System Deployment Stack trace at System Deployment Internal Isolation IStore LockApplicationPath UInt32 Flags IDefinitionAppId ApId IntPtr Cookie at System Deployment Application ComponentStore LockApplicationPath DefinitionAppId definitionAppId at System Deployment Application SubscriptionStore LockApplicationPath DefinitionAppId definitionAppId at System Deployment Application FileDownloader PatchFiles SubscriptionState subState at System Deployment Application FileDownloader Download SubscriptionState subState at System Deployment Application DownloadManager DownloadDependencies SubscriptionState subState AssemblyManifest deployManifest AssemblyManifest appManifest Uri sourceUriBase String targetDirectory String group IDownloadNotification notification DownloadOptions options at System Deployment Application ApplicationActivator DownloadApplication SubscriptionState subState ActivationDescription actDesc Int64 transactionId TempDirectory downloadTemp at System Deployment Application ApplicationActivator InstallApplication SubscriptionState subState ActivationDescription actDesc at System Deployment Application ApplicationActivator PerformDeploymentActivation Uri activationUri Boolean isShortcut String textualSubId String deploymentProviderUrlFromExtension BrowserSettings browserSettings String errorPageUrl at System Deployment Application ApplicationActivator ActivateDeploymentWorker Object state COMPONENT STORE TRANSACTION DETAILS No transaction information is available more less view request retention time predictor and retention time filtering still problems 1 response guadalupe espadas 2015 04 24 08 51 We have installed the version 3 1 and we have the same problem We have been seend you a dropbox with the info skyline and 1 raw in order you could reproduce the error If you have any problema to download the files please let us konw Thanks a lot Guadalupe more less view request I am not possible to download Skyline upgrade 2 responses hubalek 2015 04 23 03 27 Since the beggining of this week I am trying to download Skyline upgrade and it always failed giving me the following message see attached file thanks for help Martin more less RZRDMW65 log txt view request chromatogram doesn t match with spectra data 5 responses pengchao0160 2015 04 22 11 41 Dear skyline support I tried to do quantification with PRM using MS2 data I noticed that the chromatogram generated by skyline didn t match with the identified spectra For example in the attached screen shot there are only two identified spectra but skyline generated a really complicate curve which has many peaks without supporting spectra data I am wondering how skyline generate the chromatogram Thank you very much more less screen shot jpg view request building spectral library from waters MSe data 4 responses chiara nitride 2015 04 22 08 38 Hi Brendan I am working with MSe data from a Waters Synapt G2 in Skyline 3 1 0 7382 I am creating the spectral library using the final fragment csv generated by PLGS In the Import Peptide Search DIA with DDA spectral library Configure Transition Setting Default Configure Full Scan Setting Default except for the isolation scheme All Ions I associated the FASTA sequence of the protein I can see the spectral library but I can only see one precursor chromatogram see the attached screen shot I think there can be something wrong in the setting Can you be so kind to help me understanding where the problem is Thank you more less 20150422CN docx view request peptides with identified spectrum but no green dots for precursor and product ions 9 responses yuancx 2015 04 21 13 29 Hi Most of peptides have green dots for their precursor ions and fragment ions as expected A few peptides have good identified spectra from search engines Skyline matched the correct spectrum with its corresponding peptide but no green dots for their precursor ions and fragment ions For those peptides without green dots I decreased the cutoff score when I made the library so that Skyline can find the correct spectrum from database search results How can I get Skyline to give green dots to those peptides so that Skyline can produce chromatogram information of quantitation Thanks Chao Xing more less view request error during results import from chorus 2 responses tobias kockmann 2015 04 20 07 58 Dear skyline support I am getting the following error message during a results import from chorus Failed to build cache for path to file There is an error in XML document 2 2 Any idea what this is about Best wishes Tobi more less Screen Shot 2015 04 20 at 16 51 17 png view request Strage MS2 results from PRM runs 1 response marten sundberg 2015 04 20 07 14 Hi I have been running some PRM runs and have experience really strange result when I imported the last runs to Skyline In the first runs I had peaks for the peptide in both the native sample and the AQUA peptide But when I am now rerunning the samples with a new but similar dilution of the samples the results looks really strange It looks that the peaks have no starting point but an endpoint It is not the same for all the peptides but as you can see the behavior is the same in both the native and AQUA peptides in this example This is run on a Q Exactive plus instrument Is there anyone that have seen this and have any suggestion what to do Best regards Marten more less PRM problems pptx view request Peptide Quantitation with and without IS 1 response snigdha 2015 04 19 21 17 1 Is it possible to do relative quantitation without using any internal standard We are currently running 5 replicates for each sample control and performing relative quantitation of our interested proteins MRM transitions are generated using in silico on SKYLINE software and selection was based on cross reference from SRM Atlas MRM Based public libraries and literature Acquisition has performed using AB Sciex 4000 Q TRAP LC MS MS So far the results obtained are at par with our discovery data of 2 D DIGE iTRAQ and validation data of Western Blot Can we proceed in this way Looking forward for your suggestion 2 Is it possible to use 2 or 3 heavy isotopically labelled peptides as internal standard and normalise a set of more than 50 proteins 3 Is it possible to use a standard peptide like angiotensin or renin as internal standard and normalise a set of proteins If so is their any option in SKYLINE software to use this peptide for normalization 4 How much retention time variation is acceptable for a peptide Cheers Snigdha more less view request Transition list export wrong polarity 1 response r bagshaw 2015 04 17 09 12 Hi I noticed a potential bug When exporting a transition method for TSQ containing negative ion transitions the polarity is exported as a 1 meaning positive mode rather than a 0 meaning negative mode this is for small molecule work Additionally when I am fine tuning a list of targets using the Modify and a change is made the tree collapses the branch at that point and the highlighted target moves to the target entry above the modified entry I would expect that the tree should not collapse after modification and the selected target should stay selected Cheers Rick more less view request Can not download TargetedMSMS 2 zip 3 responses ebbingdejong 2015 04 17 08 07 I ve been trying to download the example files from the Targeted MS MS PRM tutorial at https skyline gs washington edu tutorials TargetedMSMS 2 zip Long before the download finishes I get an error saying failed network error Google Chrome provides further explanation here https support google com chrome answer 2898334 p ui download errors rd 1 In Firefox the download also fails but no explanation is given I ve also checked with our IT department and they do not think that anything on our end should be preventing this download from succeeding Are there any browser or network settings that I should correct Is there another way to get the files Cheers Ebbing more less view request Skyline for glycosylated peptides 2 responses hui chung liang 2015 04 17 01 56 I am currently developing the SRM method for glycopeptides from a specific plasma protein using Thermo TSQ Vantage I have made my own list csv of precursors and transition ions with optimised CE and RT and I would like to know how to convert the raw data to Skyline file in order to investigate my glyco SRM assay for the quantification of glycoforms Since they are glycosylated peptides instead of deglycosylated peptides which are mostly used using glycan oxonium ions as fragmentation ions the FASTA files or other libraries do not work for me I have tried Pinpoint and it seemed not well suited for the analysis of glycopeptides Please can you let me know first how to convert the raw file to skyline file and what would you recommend me to do when manually importing the file and method for tailored quantitative analysis Many thanks more less view request change email 1 response hgiebler 2015 04 16 16 03 I would like to change my account s email address Do you still need to ask an administrator more less view request Error downloading updating Skyline 5 responses psemchuk 2015 04 16 10 23 Hello Skyline Team I have been getting errors whenever I try to update the new version of Skyline I also uninstalled Skyline but I could t re install it back because there is an error that shows up during the download process Here I have attached the error report that I received Please look into this matter Thanks more less 3EMZHM4V log view request Error when downloading new Skyline daily 2 responses Will Thompson 2015 04 16 08 55 Hi Brendan and team When i have tried to download the update this week i have gotten a failed to download skyline and the attached error Cannot update Do I just need to update directly Thanks for your input Cheers Will more less Applicationdownload error txt view request Can skyline choose unique peptide without matching spectral library 1 response chenb37 2015 04 15 21 39 Hi I want to look at all the unique tryptic peptides against certain background proteome regardless whether their spectrum will have a match from the library or not Is there a way to do that in skyline more less view request Small molecule feature precursor mass vs m z vs neutral mass 3 responses r bagshaw 2015 04 15 17 20 Hi I want to establish use of Skyline for small molecules a bit better but I find an issue with the way the molecular formulas and precursor masses are handled When entering molecules in the transition list page I expect that when I enter the chemical formula it will calculate the neutral monoisotopic mass of the parent compound which it does The mass that is calculated however is also used as the precursor m z which is wrong as it should be of course either 1 or 1 or however it becomes charged maybe that could be specified too This is indicated by the pop ups when hovering the cursor over the compound name and the parent mass in the targets window Neutral mass and Precursor m z report the same value The workaround I have been using is to just enter the correct singly charged m z that I expect which leaves the chemical formula and precursor charge columns without meaning I would rather use chemical formulas though Cheers Rick more less view request Collision Energy Optimization Question how sensitive is the Optimization algorithm 1 response kvancott2 2015 04 15 15 39 I have a set of transitions for a trace protein and want to do CE Optimization to get as much sensitivity as I can out of the LC MRM I went through the tutorial and followed the process and got some really good results I tested 2 steps at 5V intervals so the steps are 2 1 0 1 and 2 I want to optimize for each transition so I set the optimize by to transition and then exported my transition list I then looked at the csv file and compared with the peak areas for several of the transitions I found that many of the transitions were not using the optimized CE level Some were some weren t There were some cases where the difference between the steps is not very much so that doesn t matter too much But there were a lot of cases where Skyline clearly did not choose the optimal CE for the transition I m looking at one case in particular where the optimized CE Skyline chose the Step0 CE resulted in 2x lower area than what the data state Step 2 CE It s a big file 500 transitions so inspecting each transition will be laborious Is there some sort of threshold the CE Optimizer algorithm uses or some sort of CE limit it imposes more less view request Is using Skyline to QA QC DDA standards possible 2 responses j philip 2015 04 15 14 22 Hi We are using PTRC peptides spiked in a solution with some bovine proteins as our lab standard The PRTC peptides are heavy SILAC peptides with retention times that are distributed evenly Before and after each LC MS experiment in the lab we run this standard with a quick DDA top 10 method I created a spectral library by searching a good performing standard with Mascot and importing the results into Skyline From the standard for each of the peptides we want to get ppm area retention symmetric peak shape yes no tailing yes no MS MS quality I know Skyline can get us ppm area and retention time I am not sure about the remaining parameters I can try to create proxies for them For example to look at peak shape I can see where Retention time is between Start Time and End time If it s not near the middle then I can assume peak shape is not symmetric or is tailing But I don t know how to get skyline to get the MS MS quality Can I get a list of all the product ions matched to the spectral library containing the good MS MS with dalton difference from calculated m z If I can get this for each PRTC peptide that could work as a proxy for MS2 quality Or is there another way that I am missing Any suggestions would be helpful and appreciated thanks john more less view request Tutorials cannot be downloaded 1 response Darwin 2015 04 15 12 27 Hi I tried to download the Targeted PRM tutorials and I received a network error and could not download the tutorial files and the pdf I have tried on different browsers Chrome and IE Would someone help me with the downloads Thanks more less view request retention time predictor and retention time filtering 4 responses guadalupe espadas 2015 04 14 09 53 After doing the retention time prediction I re import the data to have only 5 minutes of scan from the retention time predicted The retention time filtering is not working fine see document attached Version 2 6 0 6851 Thanks for your answer Guadalupe more less retention time predicor and filtering CRG docx view request error during results import and proteome digestion 5 responses tobias kockmann 2015 04 14 03 41 Dear skyline support I am getting the following error message when trying to import results into a skyline document failed to build cache for path to file Array dimensions exceeded supported range see screenshot In the background skyline daily is digesting a reference proteome This task also fails with an I O exception see screenshot I am working on a RDS system Windows server I suspect that this is the problem because certain task do not get sufficient privileges But the document folder is clearly writeable but stored on a NAS mounted on the server Any idea what needs to be done more less Screen Shot 2015 04 14 at 12 27 34 png Screen Shot 2015 04 14 at 12 29 42 png view request Importing spectral library from peptideatlas 3 responses chenb37 2015 04 13 23 26 Hi I m trying to import some liver peptide spectral information from peptide atlas this is the link I went to http www peptideatlas org builds when I chose a link under the column spectral library I download a file that ends with tgz I don t think that is a supported format but I don t know where should I get the correct form either Could you help me with this Thank you so much more less view request Failed install of new Skyline update 24 responses Tomas Vaisar 2015 04 13 12 52 Not sure if this is common but when I tried to update Skyline today after the new patch the download started fine but then I got error Below Any suggestions Tomas Server Apache Coyote 1 1 IDENTITIES Application Identity Skyline exe Version 3 1 0 7382 Culture neutral PublicKeyToken e4141a2a22107248 processorArchitecture msil type win32 ERROR SUMMARY Below is a summary of the errors details of these errors are listed later in the log Activation of C Users Tomas AppData Roaming Microsoft Internet Explorer Quick Launch User Pinned StartMenu Skyline appref ms resulted in exception Following failure messages were detected Downloading https skyline gs washington edu software Skyline release 64 3 1 Application Files Skyline 3 1 0 7382 Skyline pdb did not succeed Unable to read data from the transport connection An existing connection was forcibly closed by the remote host An existing connection was forcibly closed by the remote host COMPONENT STORE TRANSACTION FAILURE SUMMARY No transaction error was detected WARNINGS There were no warnings during this operation OPERATION PROGRESS STATUS 4 13 2015 12 49 06 PM Activation of C Users Tomas AppData Roaming Microsoft Internet Explorer Quick Launch User Pinned StartMenu Skyline appref ms has started 4 13 2015 12 49 07 PM Performing necessary update check as specified by the deployment 4 13 2015 12 49 07 PM Consuming new update 4 13 2015 12 49 09 PM Installation of the application has started 4 13 2015 12 49 09 PM Processing of application manifest has successfully completed 4 13 2015 12 49 09 PM Found compatible runtime version 4 0 30319 4 13 2015 12 49 09 PM Request of trust and detection of platform is complete ERROR DETAILS Following errors were detected during this operation 4 13 2015 12 49 22 PM System Deployment Application DeploymentDownloadException Unknown subtype Downloading https skyline gs washington edu software Skyline release 64 3 1 Application Files Skyline 3 1 0 7382 Skyline pdb did not succeed Source System Deployment Stack trace at System Deployment Application SystemNetDownloader DownloadSingleFile DownloadQueueItem next at System Deployment Application SystemNetDownloader DownloadAllFiles at System Deployment Application FileDownloader Download SubscriptionState subState at System Deployment Application DownloadManager DownloadDependencies SubscriptionState subState AssemblyManifest deployManifest AssemblyManifest appManifest Uri sourceUriBase String targetDirectory String group IDownloadNotification notification DownloadOptions options at System Deployment Application ApplicationActivator DownloadApplication SubscriptionState subState ActivationDescription actDesc Int64 transactionId TempDirectory downloadTemp at System Deployment Application ApplicationActivator InstallApplication SubscriptionState subState ActivationDescription actDesc at System Deployment Application ApplicationActivator ConsumeUpdatedDeployment SubscriptionState subState ActivationDescription actDesc at System Deployment Application ApplicationActivator PerformDeploymentUpdate SubscriptionState subState String errorPageUrl at System Deployment Application ApplicationActivator ProcessOrFollowShortcut String shortcutFile String errorPageUrl TempFile deployFile at System Deployment Application ApplicationActivator PerformDeploymentActivation Uri activationUri Boolean isShortcut String textualSubId String deploymentProviderUrlFromExtension BrowserSettings browserSettings String errorPageUrl at System Deployment Application ApplicationActivator ActivateDeploymentWorker Object state Inner Exception System IO IOException Unable to read data from the transport connection An existing connection was forcibly closed by the remote host Source System Stack trace at System Net ConnectStream Read Byte buffer Int32 offset Int32 size at System Deployment Application SystemNetDownloader DownloadSingleFile DownloadQueueItem next Inner Exception System Net Sockets SocketException An existing connection was forcibly closed by the remote host Source System Stack trace at System Net Sockets NetworkStream Read Byte buffer Int32 offset Int32 size COMPONENT STORE TRANSACTION DETAILS No transaction information is available more less view request No spectra were found for the new library 2 responses stephan michalik 2015 04 13 03 44 I try to import searches from TripleTOF data mzML files and I get the error No spectra were found for the new library The searches and results are OK I tried the same pipeline convert to mzML Comet TPP for QExactive data and it worked out fine Do you have a guess cheers thanks for your help more less view request Blib file generated by BiblioSpec Spectral Library Tools is different to skyline blib 2 responses stephan michalik 2015 04 12 10 44 Dear Skyline Team I downloaded and installed the latest BiblioSpec Spectral Library Tools to generate the blib files in a batch It worked out fine but the blib and blib redundant files were different size from those skyline generated with the same input files I used Skyline 2 6 and imported TPP iProphet files with a cut off score from 0 9 in skyline For Blib files generation with BiblioSpec Spectral Library Tools I used BlibBuild exe input file pep xml output redun blib BlibFilter exe s0 9 output redun blib output blib Did I do something wrong Does Skyline use the old Blib file format and not the sqlite3 Thanks for the help cheers STEPHAN more less view request 3 1 back compatibility issues 1 response j sikora 2015 04 10 14 08 Recently I upgraded to Skyline 3 1 on my office machine but have some back compatibility issues with 3 1 release My TSQ is running on win XP and planning to upgrade to win7 but it will take some time I would like to interchange files between computers Is there any way to temporarily downgrade to XP compatible Skyline release 2 6 more less view request problem to install BiblioSpec Spectral Library Tools 2 responses stephan michalik 2015 04 10 04 39 Hi Skyline team I need to install the BiblioSpec Spectral Library Tools to convert my files in order to read them in the SpecL package in R I downloaded the build as suggest svn checkout svn svn code sf net p proteowizard code trunk proteowizard code I tried compilation under MacOS Yosemite and Windows macOS error sudo quickbuild sh j4 hash optimization space address model 64 pwiz tools BiblioSpec build

    Original URL path: https://brendanx-uw1.gs.washington.edu/labkey/project/home/support/begin.view (2015-06-01)
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