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  • CPTAC Data Portal
    and proteoforms accurate relative quantitation of protein abundance in contrasting biospecimens and the localization of post translational protein modifications such as phosphorylation on a protein s sequence The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers PCCs for the CPTAC program The portal also hosts analyses of the mass spectrometry data mapping of spectra to peptide sequences and protein

    Original URL path: https://cptac-data-portal.georgetown.edu/cptacPublic/ (2015-06-01)
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  • DCC Contact Information
    Aspera and HTTP Data Download Help Frequently Asked Questions Aspera Installation Guides Aspera Installation Guide Windows Aspera Installation Guide Mac Checksums CPTAC DCC Software Contact Us Frequently Asked Questions Aspera Installation Guide Windows Aspera Installation Guide Mac Checksums CPTAC DCC Software Contact Us DCC Contact Information Print This Page If you are having problems with the CPTAC Public Data Portal please contact cptac dcc help esacinc com We welcome your

    Original URL path: https://cptac-data-portal.georgetown.edu/cptac/contact/showPublic (2015-06-01)
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  • DCC Contact Information
    Feedback Available Studies Query Data About the Data Responsible Use of CPTAC Data Overview Common Data Analysis Pipeline CDAP Aspera and HTTP Data Download Help Frequently Asked Questions Aspera Installation Guides Aspera Installation Guide Windows Aspera Installation Guide Mac Checksums CPTAC DCC Software Contact Us CPTAC 2006 2011 CPTAC 2011 present External Studies CPTAC Feedback Print This Page First Name Last Name Email Message Loading NCI Home Policies Accessibility FOIA

    Original URL path: https://cptac-data-portal.georgetown.edu/cptac/feedback/show (2015-06-01)
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  • CPTAC-DCC
    publish the initial global analyses of the data within a reasonable period of time In 2008 the National Cancer Institute organized a workshop to discuss how and when proteomics data should be released The result was the Amsterdam Principles that established guidelines for the timing of data release comprehensiveness of a dataset data format deposition to repositories quality metrics and responsibility for proteomic data release Participants agreed that mass spectrometry output data files should be available to support the claims of proteomics publications In 2010 the National Cancer Institute convened a follow on workshop to address quality metrics for proteomics with an emphasis on mass spectrometry As a sign of solidarity for these principles four peer reviewed journals simultaneously published the results Agreeing to abide by these principles and the CPTAC Publication Guidelines is required to gain access to CPTAC data Publication Guidelines CPTAC is a community resource project and data are made available rapidly after generation for community research use To act in accord with the Fort Lauderdale principles and support the continued prompt public release of large scale proteomic data prior to publication researchers who plan to prepare manuscripts or presentations involving CPTAC data and journal editors who receive such manuscripts are encouraged to coordinate their independent reports with CPTAC s publication schedule This may be done by contacting the CPTAC network at cancer proteomics mail nih gov CPTAC defines a global analysis publication as the first paper authored by one or more members of the Clinical Proteomic Tumor Analysis Consortium which includes analysis of much of the existing CPTAC data on the tumor type or sample set at the time of a data freeze Specifically these manuscripts report on the comprehensive integrated analysis of multiple CPTAC datasets available which may include global proteome profiling reverse phase protein

    Original URL path: https://cptac-data-portal.georgetown.edu/cptac/aboutData/disclaimer (2015-06-01)
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  • About the CPTAC Data
    by mass spectrometry characterizing and quantifying their constituent proteins or proteome Mass spectrometry enables highly specific identification of proteins and proteoforms accurate relative quantitation of protein abundance in contrasting biospecimens and the localization of post translational protein modifications such as phosphorylation on a protein s sequence Read more The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers PCCs for the CPTAC program The portal also hosts analyses of the mass spectrometry data mapping of spectra to peptide sequences and protein identification from the PCCs and from a CPTAC sponsored common data analysis pipeline CDAP All data is freely available to the public subject to the data use guidelines Data Analysis Proteomic analysis for each CPTAC study is carried out independently by the PCCs using a variety of protein fractionation techniques instrumentation and workflows The mass spectrometry and related data files are organized into datasets by study sub proteome and analysis site Currently available sub proteomes include global no protein fractionation phosphoproteome and glycoproteome PCCs may also provide higher level analyses of the mass spectrometry raw data computed with their custom bioinformatic pipelines for example matches of peptides to spectrum

    Original URL path: https://cptac-data-portal.georgetown.edu/cptac/aboutData/show?scope=about (2015-06-01)
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  • About the CPTAC Data
    using the ProteoWizard SeeMS tool and converted to other peak list formats suitable for analysis by tandem mass spectrometry search engines using the MSConvert tool A list of commercial and open source tools supporting the mzML format can be found at the PSI site Peptide Spectrum Match Data The primarily or first level analysis of the spectra uploaded by the Proteome Characterization Centers PCCs is the matching of tandem mass spectra to peptide sequences Tandem mass spectrometry search engines match the spectra to peptide sequences from protein sequence databases score the matches and output the best peptide spectrum matches PSMs for each spectrum PSMs are then filtered by score and statistical significance to ensure that only the most reliable PSMs are retained Typically in this process only the best PSM per spectrum is retained Each PSM links an identifier for the spectrum the peptide sequence any post translational modifications on the peptide and a list of identifiers for the protein sequences found to contain the peptide sequence In addition depending on the analysis pipeline PSMs may be annotated with additional information such as iTRAQ reporter ion intensities and post translational modification localization scores RAW PSM Format The Common Data Analysis Pipeline CDAP implemented for CPTAC by NIST produces tab separated value format files containing PSMs generated by MS GF for each CPTAC study The current reference protein database used for human in mouse xenograft tumor pooled samples is concatenated RefSeq H sapiens build 37 M musculus build 37 and the sequence for S scrofa porcine trypsinogen The FASTA file used for analysis of human TCGA samples and ovarian cancer tumors includes RefSeq H sapiens build 37 and the sequence for S scrofa porcine trypsinogen Download Common Data Analysis Pipeline Bioinformatic Methods PCCs may also analyze the spectral data and provide

    Original URL path: https://cptac-data-portal.georgetown.edu/cptac/aboutData/show?scope=dataLevels (2015-06-01)
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  • About the CPTAC Data
    Use of CPTAC Data Overview Common Data Analysis Pipeline CDAP Aspera and HTTP Data Download Aspera and HTTP Data Download Print This Page Data from the CPTAC Data Portal may be downloaded using either Aspera fasp technology or HTTP data transfer Aspera fasp Technology The CPTAC Data Portal has deployed an Aspera Connect Transfer Server to distribute data files Read more This server with fasp technology is ideal for the transport of large data files like those generated by mass spectrometry To use the Aspera service you must download the free client software to your computer download You can install this prior to selecting data to download or you can do this when prompted at the time of data download The Aspera Connect Server at CPTAC DCC uses nonstandard ports for security UDP 33001 for file transfer and TCP 33001 for User Authentication via SSH If you are working within a security firewall at a University or Research Institute these ports UDP 33001 and TCP 33001 may not be open To use the Aspera fasp technology you will need to contact you IT security staff to open these ports Alternatively you can download data using HTTP data transfer HTTP Data

    Original URL path: https://cptac-data-portal.georgetown.edu/cptac/aboutData/show?scope=dataDownload (2015-06-01)
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  • Frequently Asked Questions
    file transfer and TCP 33001 for User Authentication via SSH If a user is working at a University or Research Institute and within their own security firewall they need to contact their IT security staff to open these ports UDP 33001 and TCP 33001 My internet connection was interrupted is there a way I can set my transfers in the Aspera Connect Client to resume automatically Go to Aspera Connect Preferences on your machine and in the Transfers tab enable the auto retry function by checking the Automatically retry failed transfers box and entering a numerical value for the number of time to retry that suits your situation You can also manually click the retry icon to restart the download Can I use the Aspera command line to download data Yes there are two ways to use the Aspera Command Line 1 Direct Access from a Linux system Install the Aspera connect client on your linux system http asperasoft com software transfer clients connect web browser plug in The default install location will be the user home directory Modify the path in the below command line example if the Aspera connect client is installed in a different location Run the following command to test aspera connect bin ascp v i aspera connect etc asperaweb id dsa putty P 33001 O 33001 l 50M T Q user public host cptc xfer uis georgetown edu mode recv Phase II Data CompRef CompRef Proteome BI CompRef Proteome BI mzML cksum If c is successful simply replace the Phase II Data CompRef CompRef Proteome BI CompRef Proteome BI mzML cksum with the desired file or folder name Example folder names Phase II Data CompRef Phase II Data TCGA Colorectal Cancer Additional folder names and individual dataset names can be obtanied by browsing the web portal 2 A Python executable script allows direct file transfer from the CPTAC DCC public portal and is subjected to the CPTAC DCC public portal data use agreement The script can be run from the command prompt to perform whole directory or single file transfers The script can be obtained here Can I download the data without using Aspera The DCC offers access to the CPTAC data using the HTTP protocol Look for the Http Data Access link on each study page or access the URL https cptc xfer uis georgetown edu publicData directly How do I access the data in compressed files with a tar gz file extension On Linux and OSX systems the system tar and gzip command line tools should be used On Windows the 7z suite of file compression tools have been tested to successfully uncompress even the very large compressed files Data Integrity What are the cksum files for The checksum cksum files provide sha1 and md5 hashes and file size in bytes of each file to make it possible to verify that the contents of files after download from the CPTAC data portal match the content on the portal How can I verify the checksums On Linux and OSX systems the traditional ls md5sum and sha1sum programs compute the same file sizes and hashes and file sizes as those contained in the cksum files In addition the DCC offers a command line program cksum for generating and checking cksum files See Checksums under the Help tab How can the Aspera infrastructure help ensure file integrity The DCC has configured the Aspera Connect Server to use integrity verification for each transmitted data block Furthermore the Aspera client will only download files that are missing or different than the files on the server using file size and sparse checksums to determine if files on the local filesystem are different from those on the server The command line program cptacpublic see above for headless execution of Aspera downloads can also be configured to require the Aspera client compute full file checksums Finally checksum files see above can be used to provide an orthogonal check of downloaded file integrity Experimental Design and Data Formats Where can I find protocols for the preparation of tumor samples and methods for mass spectrometry Each laboratory reports details of their experimental protocol in their publications Links to the CPTAC publications can be found on the Available Studies tab in the third column Prior to publication metadata files are provided with details of sample file naming instruments and instrumental parameters These files are available for download from each study page under the data set column meta Where can I find the assignment of biospecimens to iTRAQ labels In studies using iTRAQ labels there is a file for iTRAQ Sample Mapping available for download from each study page under the data set column meta In the TCGA Ovarian and Breast Cancer Studies this file is also provided under the section Biospecimens and Metatdata Files What data formats are available Raw Vendor format RAW or vendor format files corresponding to the mass spectrometers used to acquire the spectra mzML The RAW format spectra are converted to HUPO Proteome Standards Initiative PSI compliant mzML format at the Data Coordinating Center DCC Raw PSM format The Common Data Analysis Pipeline CDAP implemented for CPTAC by NIST produces tab separated value format files containing peptide spectrium matches PSMs generated by MS GF for each CPTAC study mzIdentML PSM Format Raw PSMs from the CDAP or the PCCs are converted to HUPO Proteome Standards Initiative PSI compliant mzIdentML format at the Data Coordinating Center DCC Detailed descriptions are here Is original instrument data retrievable from the CPTAC Data Portal Yes on the data download pages specify raw as the data type desired Where can I find spectral data format information Spectral data is available in vendor RAW format and in HUPO PSI format mzML files from the study pages Select datatypes raw or mzML Where can I find details of the PSM data formats For example what do iTRAQ flags signify Data format details begin on Page 8 in Software Programs and Output Files of the Common Data Analysis

    Original URL path: https://cptac-data-portal.georgetown.edu/cptac/faq/showPublic (2015-06-01)
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