MStoolbox

Before you start

In order to use MSblender, you will need to run multiple search engines. MSBlender will integrate the results of all of the search engines, controlling the false discovery rate accordingly.

Repository

• https://github.com/marcottelab/MS-toolbox

Crux

• http://noble.gs.washington.edu/proj/crux/

Tide

• http://noble.gs.washington.edu/proj/tide/

DB setup

$ /project/marcotte/ms/bin/tide-index --enzyme=trypsin --digestion=full-digest --mods_spec=C+57.02156 --fasta UPS_combined.fa

MS-GFDB

• http://proteomics.ucsd.edu/Software/MSGFDB.html

DB setup

Using target only database.

$ java -cp /project/marcotte/ms/bin/MSGFDB.jar msdbsearch.BuildSA -tda 2 -d UPS_target.fa

X!Tandem

DB setup

• Setup database with the following command. You need to make 'combined' database (FASTA file) before this.

$ /project/marcotte/ms/bin/fasta_pro.exe <your fasta file>

Here is an example.

$ /project/marcotte/ms/bin/fasta_pro.exe UPS_combined.fa 
fasta_pro file conversion utility, v. 2006.09.15
 input path = UPS_combined.fa
output path = UPS_combined.fa.pro
db type = plain
taejoon@ada:~/project/ups2/DB$

InsPecT

• http://proteomics.ucsd.edu/Software/Inspect.html

OMSSA

• http://pubchem.ncbi.nlm.nih.gov/omssa/

MaxQuant

• http://www.maxquant.org/