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X! Tandem open source is software that can match tandem mass spectra with
peptide sequences, in a process that has come to be known as protein
identification.
This software has a very simple, sophisticated application programming
interface (API): it simply takes an XML file of instructions on
its command line, and outputs the results into an XML file, which
has been specified in the input XML file.
This version of X! Tandem is a full release and it includes extensive source level
documentation.
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Please read the artistic license
under which this software is distributed.
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Introduction
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The X! Tandem MS Protein Sequence Modeler is a software package that includes a number of c++ and xml files:
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all c++ source code required to build new versions of the executable
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a c++ executable (tandem.exe)
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an xml "template" (default_input.xml)
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an xml taxonomy input file (taxonomy.xml)
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an xml test input file (input.xml)
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a spectrum input test file (spectrum_1.pkl)
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Download
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1.
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Download and extract compressed file
- tandem-win32-{release-date}.zip,
- tandem-linux-{release-date}.tar.z
or
- tandem-osx-{release-date}.tar.z
from here into a temporary folder. If you are using Linux or OS X use the
following command to extract the files:
tar -xzf tandem-[linux|osx]-tar.z. This will create a folder named
tandem which contains 3 sub folders:
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src - contains the source files for tandem
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bin - contains the binary for tandem, as well as example files and mass spectra.
You can run tandem from the command line in this directory, by typing:
tandem input.xml or
./tandem.exe input.xml (Linux or OS X)
The output from the program will appear in the output file
specified in the input.xml file with a date stamp appended
to the filename. Check the path names in taxonomy.xml and input.xml
if there is trouble doing this check. Read the default_input.xml
file for more information on how the input parameter file format
works. For more information on these xml files please read the FAQ.
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fasta - contains an example FASTA protein sequence list file. This
type of file is often referred to as a "database" file or
simply a "database". However, it is not a database of any
type: it is simply a file with a simple (but poorly specified)
format. X! Tandem does not search databases of protein sequences.
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Altering the Program
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The "bin" folder contains the tandem.exe program which runs the search algorithm.
If you are using Windows to create a new version of tandem, either double click
on the file called x-bang-msms.sln or create a new project in Visual Studio.
Add all the .cpp and .h files from the "src" folder to the newly created project.
The Windows version of tandem.exe program was originally compiled using Microsoft Visual Studio 7.0 on Windows XP.
If you are using Linux or OS X, from the command prompt, navigate to the src folder.
Type the command "make" (without the quotes). This will create a new tandem.exe
in the bin folder. The Linux version of tandem.exe was originally compiled on RedHat Linux 9.0 with the g++ compiler version 3.2.2.
The OS X version of tandem.exe was originally compiled using an Apple Computer, GCC version 1175, based on gcc 3.1 20020420.
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If you have any troubles installing or running X! Tandem, please consult the
Tandem FAQ. If you are using a
version of Linux other than Red Hat, please consult the
Linux FAQ.
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Here are some journal articles that describe ideas associated with Tandem:
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The Biopolymer Markup Language; David Fenyö
Bioinformatics.. 1999; 15:339-40.
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Informatics and data management in proteomics; David Fenyö and Ronald C. Beavis
Trends Biotechnol. 2002; 20:S35-8.
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A Method for Assessing the Statistical Significance of Mass Spectrometry-Based
Protein Identifications Using General Scoring Schemes; David Fenyö and Ronald
C. Beavis
Anal. Chem.; 2003; 75:768-774.
- Further references ...
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Copyright © 2004-2011, The Global Proteome Machine Organization
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