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.
  • This document is for 'stampede'.
  • Currently in most cases I use three search engines: comet, X!Tandem, and MS-GF+.
  • You don't need to run 'MSblender' modeling on TACC, because it does not take that long. I normally run all searches at TACC, then transfer the output to my local machine to run MSblender. So it only covers 'search' part. For running MSblender, please see MSblender page.

Install MSblender (and comet, MSGF+, X!Tandem)

$ cd ~
$ mkdir git
$ cd git
$ git clone

Prepare a working space

$ module load python
$ mkdir myProject
$ cd myProject
$ mkdir mzXML
$ mkdir DB
$ mkdir comet
$ mkdir MSGF+
$ mkdir tandemK

Prepare database

  • You can run this process on any computer. If it takes longer than a minute, it would be better to process it on other than TACC login node (your account may be locked).
$ python $HOME/git/MSblender/pre/ my_seq.fa
$ cat my_seq.fa.* > my_seq.combined.fa

DB setup for X!tandem

 $ $HOME/git/MSblender/extern/fasta_pro.exe my_seq.combined.fa

You may see the message like below:

$ ~/git/MSblender/extern/fasta_pro.exe my_seq.combined.fa 
fasta_pro file conversion utility, v. 2006.09.15
 input path = my_seq.combined.fa
output path =
db type = plain

DB setup for comet

You don't need to do anything for this.

DB setup for MSGF+

It uses significant amount of computing resources (i.e. memory), so it may not be suitable to run on login node.

$ module load jdk64
$ java -Xmx4000M -cp /home1/00992/linusben/git/MSblender/extern/MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA -d XenopusHybrid_xlJGIv16_xtJGIv83.combined.fa -tda 0

Prepare mzXML files

Copy your mzXML files on this diretory ($SCRATCH/myProject/mzXML).

Run comet

$ cd $SCRATCH/myProject/comet
$ ~/git/MSblender/extern/comet.linux.exe -p

Edit '' file. Typically, you need to change the following lines.

num_threads = 16

peptide_mass_tolerance = 20.0
peptide_mass_units = 2

search_enzyme_number = 2   ## See the end of param file for the type of enzymes

output_txtfile = 1
output_pepxmlfile = 0

Then, create the launcher script (called '') as below.

#SBATCH -n 16
#SBATCH -p normal
#SBATCH -t 24:00:00

#SBATCH -o cmt.o%j

DBNAME=$(basename $DB)


#SBATCH -J "cmt"
for MZXML in $(ls ../mzXML/*mzXML)
  OUT=$(basename $MZXML)

Then, submit the job by typing 'sbatch'


Create '' file as below.

#SBATCH -n 16
#SBATCH -p normal
#SBATCH -t 24:00:00

#SBATCH -o mg+.o%j
set -x

module load jdk64



DBNAME=$(basename $DB)

#SBATCH -J "mg+"
for MZXML in $(ls ../mzXML/*mzXML)
  OUT=$(basename $MZXML)
  time java -Xmx20000M -jar $MSGFplus_JAR -d $DB -s $MZXML -o $OUT -t 20ppm -tda 0 -ntt 2 -e 1 -inst 3
  time java -Xmx20000M -cp $MSGFplus_JAR edu.ucsd.msjava.ui.MzIDToTsv -i $OUT -o $TBL -showQValue 1 -showDecoy 1 -unroll 0

Then, submit the job by typing 'sbatch'

Run X!Tandem

$ cd $SCRATCH/myProject/tandemK
$ ~/git/MSblender/search/ ../mzXML/ ../DB/

First argument of is a directory for mzXML, and second one is for .pro database generated by fasta_pro.exe as above.

You will see *.xml files matched to your mzXML files (X!Tandem input), 'tandem-taxonomy.xml' file (another X!Tandem input), and (a script to run X!tandem).

Make the following launcher (''), and submit it as 'sbatch'.

#SBATCH -n 16
#SBATCH -p normal
#SBATCH -t 24:00:00

#SBATCH -o tK.o%j
set -x

bash ./

If you have many mzXML files, you can run it parallel by splitting with 'split -l' command, and run individual splitted script at ''.