X!!Tandem with PTMTreeSearch


PTMTreeSearch is a program developed for identification of Post-Translational Modification in MS/MS data and it is embedded to the X!Tandem project. This server is hosted by Protein Structure and Bioinformatics Group [link]
International Centre for Genetic Engineering and Biotechnology (ICGEB) [link],
Trieste,Italy.
Note that this server has been created for demonstration purposes and some parameters are fixed. For full control of PTMTreeSearch, please download it from here.

Reference

For citation please use:
PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra
Attila Kertesz-Farkas, Beata Reiz, Roberto Vera, Michael P Myers, Sandor Pongor
Bioinformatics 30 (2), 234-241, 2014
[Download article here from the publisher]<
contact: Prof. Sandor Pongor: pongor at icgeb /dot/ org.

Introduction

X!Tandem is a software application to identify proteins and peptides from tandem mass spectrometry (MS/MS) data. The X!tandem is an open source project conducted at Rockefeller University by P.I. Robert Craig. link

X!!Tandem is a parallel version of the X!Tandem that has been mad parallel with MPI technology. link

PTMTreeSearch is an exhaustive approach to identify Post Translational Modifications (PTMs) in MS/MS data.
The PTMTreeSearch is an untargeted method that means PTMTreeSearch uses a large database of known PTMS for modified peptide identification. No PTMs can be identified, that is not included to the PTM Database. Currently the PTM database contains 524 unique PTMs obtained from the OMMSA, RESID, UNIMOD and UNIPROT. PTMTreeSearch has been implemented as a pluggable scoring function into the open-source X!tandem project.

Current version and Download

  • PTMTreeSearch. The source code of the PTMTreeSearch is available here. See the readme.txt file how to include it to the source code of X!tandem. The complete source code of parallel X!!tandem with PTMTreeSearch is available here. This is exactly the same that runs here.
  • X!!Tandem v2010.12.01 was downloaded at 2011.07.25 from the ftp site of Yale University. The parallelization of the X!tandem is based on the MPI technology.
  • Protein sequence databases were downloaded at 2010.10.10. The human protein IPI database was downloaded at 2011.07.25. All protein sequence database were downloaded from theGPM's FTP site.
  • PTM databases were downloaded at 2011.10.10 from omssa from here, unimod from here, uniprot from here, and resid from here
  • This application runs on a Linux cluster server, called Beetle. Beetle has one frontend node and 10 backend nodes. Each node has two 2Ghz processors and 6Gb RAM. The server is located at ICGEB at Trieste, Italy.

    • Overview

    At the first stage X!Tandem identifies peptides and collect proteins. These proteins will be passed to the second stage for more exhaustive analysis.
    In the second stage (also called error-tolerant search) X!tandem uses the following refinements:
    1. comparison with multiple potential modification
    2. full [X]|[X] cleavage
    3. N-terminal modifications
    4. C-terminal modifications
    5. point mutations, and
    6. PTMTreeSearch for untargeted PTM identifications

    All of these refiniement steps can be turned on/off independently from each other.

    For further information about the X!Tandem go theGPM project page.

    PTMTreeSearch parameters:

    use PTMTreeSearch: turns on/off PTMTreeSearch method in the second refinement stage.
    Default is: On

    PTMBound: Sets the maximum number of PTMs to be identified per peptide, used in the exhaustive search.
    Minimum value: 1
    Maximum value: 3
    Default value: 2
    Note: The larger the PTMBound the exponentially longer the running time.

    mass lower bound (defines mass loss)
    Minimum value: 0
    Maximum value: 200
    Default value: 50

    mass upper bound:
    Minimum value: 0
    Maximum value: 400
    Default value: 200 Note: The wider the mass range the more the peptides to be compared and the longer the PTMTreeSearch running time.
    Please note that only few parameters can be controlled in this webserver. For full access to all the parameters of PTMTreeSearch please download and use it locally on your system.

    Privacy statement

    We do not use or store your private data or email address. After the processing of your data has finished your uploaded data is deleted. Only a weblink to the result file will be sent to the email address you provided once.
    The result file will be kept for a while (couple of weeks) for you, hence we recommend downloading it for your own record. Email addresses will not be stored.