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  1. TPP:X!Tandem and the TPP (5454 bytes)
    1: ==What is X!Tandem?==
    2: X!Tandem is an open-source (and free) search engine, devel...
    5: ...xfordjournals.org/cgi/content/abstract/22/22/2830 Tandem score plug-in] implementing the COMET score funct...
    7: ...cs.fhcrc.org/CPAS/Project/Published%20Experiments/Tandem%20Pluggable%20Scoring/begin.view? here].
    9: To use the k-score plug-in, these three Tandem parameters should be set as follows:
  2. TPP Tandem search (19915 bytes)
    1: =Performing XTandem search using the Trans Proteomic Pipeline (TPP) T...
    6: It extends and uses some material from this earlier [[T...
    12: ...to perform a database search. The search engine X!Tandem will be used in this tutorial as it has two advan...
    16: ...e search engine [http://www.thegpm.org/TANDEM/ X!Tandem] is required, no separate installation is needed ...
    20: ... the installer: ''TPP_Setup_v4_0_JETSTREAM_rev_2.exe''. Run it and follow the installation instructio...

Page text matches

  1. Main Page (6445 bytes)
    12: *Active support: all users, both new and experienced, are encouraged to participate in our ve...
    14: ...pen proteomics data formats]]: mzXML, pepXML, protXML==
    15: ...ormats:pepXML|pepXML]], and [[Formats:protXML|protXML]] on the [[Formats:Overview|Formats]] page.
    21: ...on Linux and Windows systems and builds on Mac OS X as well. The TPP spans
    23: ...s popular search engines, including the bundled X!Tandem search software (from The GPM) and [http://comet-...
  2. TPP:Supported Search Engines (1578 bytes)
    2: In this context, a "search engine" is a tool that attempts to as...
    11: ===[[TPP:X!Tandem and the TPP|X!Tandem]]===
    12: ...!Tandem] is a open-source, free search engine. X!Tandem with the K-Score plugin is now distributed as par...
    24: ...http://www.ncbi.nlm.nih.gov/Web/Newsltr/V14N2/index.html OMSSA]
    27: .../index.html?root=myrimatch MyriMatch] open-source tandem mass spectral peptide identification by multivari...
  3. TPP:Windows Cygwin Installation (7499 bytes)
    9: ... on port 1441, so it should not conflict with an existing instance of IIS (the default Windows webser...
    11: === Downloading and Running the Setup.exe Installation Program ===
    14: ...g/software/TPP_Cygwin_Setup.exe TPP_Cygwin_Setup.exe installation program]. Note, you'll only need t...
    15: # Follow default installation by clicking "Next" at each installation step, until the installati...
    19: ==== Setup.exe Installation Walkthrough ====
  4. TPP:Installing on Mac OSX (12870 bytes)
    2: ...PP is not currently officially supported on Max OSX.''' This means that we cannot respond to install...
    8: ...idate) rev.0, Build 200805281113 (linux) on Mac OSX 10.5.2
    11: Latest Mac OSX version used for testing: '''Intel 10.5.2'''
    13: ...al is intended for someone comfortable running unix shell commands and installing and configuring sof...
    16: Intel-based Mac running OSX 10.5.2. At this time, certain parts of the code ...
  5. Software:PeptideProphet (1728 bytes)
    8: ...ommon standard by which the results of different experimental groups can be compared.
  6. Software:ProteinProphet (6941 bytes)
    14: NOOCCAM: non-conservative maximum protein list
    26: INSTANCES: Use Expected Number of Ion Instances to adjust the pepti...
    30: ...previously on all input interact datasets with mz/XML raw data format)
    32: EXCELPEPS: write output tab delim xls file including all peptides
    33: EXCELxx: write output tab delim xls file including all protein (group)s
  7. Software:ASAPRatio (1791 bytes)
    9: ... abundance, which is the goal of many proteomics experiments but was time- consuming and tedious befo...
    12: ...rom data generated by stable isotope dilution and tandem mass spectrometry." Anal Chem 75:6648-57.
  8. Software:TPP (8915 bytes)
    5: [[image:TPP.jpg|1200px]]
    8: ...760 88 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio]]
    9: ....proteomecenter.org/wiki/index.php?title=Software:XPRESS]]
    10: ...60 219 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:Libra]]
    11: ...250 88 [[http://tools.proteomecenter.org/wiki/index.php?title=Software:SBEAMS]]
  9. Formats:pepXML (2274 bytes)
    1: ...ers are available to transform output files to pepXML.
    3: ==PepXML Schema ==
    7: ...ision/pepXML/pepXML_v123.xsd pepXML 1.23 Schema] (xsd)
    14: **Expands list of possible aa- and term- modification ...
    26: ** Adds "X! Tandem (k-score)" search engine
  10. TPP:X!Tandem and the TPP (5454 bytes)
    1: ==What is X!Tandem?==
    2: X!Tandem is an open-source (and free) search engine, devel...
    5: ...xfordjournals.org/cgi/content/abstract/22/22/2830 Tandem score plug-in] implementing the COMET score funct...
    7: ...cs.fhcrc.org/CPAS/Project/Published%20Experiments/Tandem%20Pluggable%20Scoring/begin.view? here].
    9: To use the k-score plug-in, these three Tandem parameters should be set as follows:
  11. Software:Tandem2XML (1413 bytes)
    1: ...e TPP]] for important general information about X!Tandem support.'''
    7: ...ne. This tool converts Tandem result files to pepXML files suitable for use in the TPP.
    9: ==Running Tandem2XML==
    13: ===Converting X!Tandem results to TPP input files===
    15: ... on Cygwin but behaves exactly the same under linux.
  12. Software:SpectraST (70083 bytes)
    7: ...detected and reported by the mass spectrometer as tandem mass (MS/MS) spectra. Because peptide ions tend ...
    9: ...n remains the bottleneck of any given proteomics experiment. The requirement of computational resourc...
    11: ...ting and searching spectral libraries in the context of proteomics have been published within the pas...
    17: ...ons that are observed and identified in previous experiments will be included in spectral libraries a...
    21: ...n the other hand, armed with previously observed experimental spectra compiled into spectral librarie...
  13. TPP Tutorial v1 (43187 bytes)
    15: ...eir data a step further. This tutorial shows an example of how to run the TPP tools so that searched...
    18: ... results, and protein identification results. The XML backbone of this pipeline enables a uniform ana...
    22: ...MB of hard drive space. TPP itself requires approximately 190MB of disk space. The remaining space ...
    23: ...alysis software like TPP and data repositories. mzXML was developed by the Institute for Systems Biol...
    30: ...cs data analysis but do not have a great deal of experience with TPP.
  14. Software:ProbID (2453 bytes)
    2: ... the identifications and output the results in pepXML format, which subsequently can be analyzed by t...
    9: * example.dta This is the file format of MS/MS spectra...
    10: ...t takes a your_file.mzXML and returns a your_file.xml which can be analyzed by TPP (Trans-Proteomic P...
    19: tar -xzf ProbID.tgz
    33: perl runprobid.pl your_file.mzXML.
  15. Software:RAMP (2074 bytes)
    4: ...essly adapt to revisions to the [[Formats:mzXML|mzXML]] format, as well as handle other formats such ...
    8: *[[Software:MzXML2Search|MzXML2Search]] – RAMP
    10: *[[Software:XPRESS|Xpress]] – RAMP
    16: ==External Projects==
    17: *[http://dx.doi.org/10.1021/pr0705340 muxQuant] (M. Palmblad)
  16. TPP:Related Tools (6244 bytes)
    5: ===Thermo (Xcalibur) .RAW files===
    6: ===Waters (MassLynx) .RAW directories===
    7: ===MDS/Sciex (Analyst) .wiff files===
    10: ...to our open mzXML format. Please see [[Formats:mzXML]] for an overview of compatible formats and con...
    13: {| class="wikitable" style="text-align:center;" border="2" cellpadding="2"
  17. Expert search and TPP usage (12929 bytes)
    1: ...the TPP on MS/MS data from within ISB, using a Unix command line interface.
    12: /regis/sbeams/archive/<investigator>/<project>/<experiment_tag>/<search_descriptor>
    13: For example:
    14: ...beams/archive/youngah/HsUrine/HsNormFemUrine_163A/XTK_Hs3.38
    19: ...should be stored in the <experiment> directory. mzXML files should be symlinked (use ln -s) to each <...
  18. TPP:Installing on Ubuntu 8.10 (3812 bytes)
    1: ...rder-style: solid; border-color: #000; padding: 4px;"
    3: ... for instructions on how to build TPP for the Linux platform.
    13: ** libgd2-xpm(2.0.36~rc1~dfsg-3ubuntu1)
    14: ** libgd2-xpm-dev (2.0.36~rc1~dfsg-3ubuntu1)
    17: ** libexpat1-dev (2.0.1-4)
  19. Terry's compbio links (11123 bytes)
    15: ...servations] [http://www.paychexflex.com paychexflex] (terry.farrah 6char plus that year) [https://int...
    17: .../www.dropbox.com/home/price%20lab Price Lab dropbox]
    22: ...ogle.com/document/d/1qsYYMgGTYOWpgTAPMG72wh7aNiuU8xLI15M-i-A181k/edit Running ProbAnno standalone] at...
    41: ...le.com/document/d/1PCHWWVLl453x9ow76XgDrWVoFXKWJ1JXGhl6hf4d30k/edit How to build Kaviar]
    43: ...cument/d/1OLsShhl7TeMCBPk6Al6O9sH_n0sgL51OhExVtVwjXTQ/edit RCF specification]
  20. Terry's blog (18394 bytes)
    5: ... urine data with David's latest flags as in finishtandemsearch, plus PROTLEN,
    10: ...eral Swiss-Prot entries from different species in XML format; come up with list
    11: of XML fields we want & review with Eric. Load these f...
    19: X!Tandem semitryptic no refinement parametric model.
    20: finishtandemsearch with TESTDEVPATH.

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