MSblender TACC

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Before you start

  • To use this setting, your TACC account needs to be allocated to our lab project('A-cm10'). If you don't have an account, create it at Then, ask Edward to assign your account as a member of lab project.
  • Generally, 'longhorn' has shorter queue than 'lonestar'. So if you don't need large memory(> 4GB), use 'longhorn'.
  • Always work at $SCRATCH directory, not at /corral or your $HOME.
  • All source codes are available at /corral/utexas/A-cm10/src.MS/. Personally I use symbolic link for this directory under $HOME so I can use '~' shortcut.
 $ ln -s /corral/utexas/A-cm10/src.MS/ ~/src.MS 
$ ls ~/src.MS 
  • All packages are installed at /corral/utexas/A-cm10/src.MS/local/.
  • To run InsPecT, you need to set LD_LIBRARY_PATH for expat library. Type below command before running InsPecT (or put it on '$HOME/.profile_user'
 $ export LD_LIBRARY_PATH="/corral/utexas/A-cm10/src.MS/local/lib/" 
  • Default python interpreter is 2.4 at TACC. You need to load 2.7.1 as below.
 $ module load python

Currently installed packages

These packages are installed at lonestar.

  • TPP-4.5.1 + X!Tandem (2010.10.01.1)
  • /corral/utexas/A-cm10/src.MS/local/tppbin/xinteract (integrated wrapper for *Prophet)
  • /corral/utexas/A-cm10/src.MS/local/tppbin/tandem (X!Tandem with k-score support)
  • Crux 1.37
    • /corral/utexas/A-cm10/src.MS/local/bin/crux
  • Tide 1.0
    • /corral/utexas/A-cm10/src.MS/local/bin/tide-index
    • /corral/utexas/A-cm10/src.MS/local/bin/tide-msconvert
    • /corral/utexas/A-cm10/src.MS/local/bin/tide-search
  • MSGFDB (20120106)
    • /corral/utexas/A-cm10/src.MS/MSGFDB/current/MSGFDB.jar
  • InsPecT (20120109)
    • /corral/utexas/A-cm10/src.MS/local/bin/inspect

Install MS-toolbox & MSblender

  • I recommend to install MS-toolbox at your home individually, because everyone may want to use different search parameters.
$ module load git
$ cd ~
$ mkdir git
$ cd git
$ git clone
$ git clone
  • You don't need to compile MSblender codes under 'src' directory. Executable file is already available at /corral/utexas/A-cm10/src.MS/local/bin/msblender.

Let's start

$ module load python
$ mkdir my-project
$ cd my-project
$ python ~/git/MS-toolbox/bin/

It will make five directories (DB, mzXML, RAW, scripts, tmp), and one text file called 'mstb.conf'. Transfer your mzXML files to 'mzXML' directory. I also keep RAW files on the same directory. But it would be good to transfer them to corral & ranch(tape storage) to archive.

Setup your database

Transfer your FASTA file to 'DB' directory. You need 'combined' database, with target and decoy. It is recommended to use 'reverse' decoy sequences. If you use '' script on MS-toolbox, it generates reverse sequence with 'rv_'prefix.

$ python ~/git/MS-toolbox/bin/ XENLA_prot_v4.fasta 
$ mv XENLA_prot_v4_combined.fasta
$ cat XENLA_prot_v4.fasta.reverse >> XENLA_prot_v4_combined.fasta
$ head -n 1 XENLA_prot_v4.fasta
$ head -n 1 XENLA_prot_v4.fasta.reverse 

= DB setup for X!tandem