MStoolbox

From Marcotte Lab
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Contents

Before you start

For using MSblender, you need to run multiple search engines.

Repository

Crux

Tide

MS-GFDB

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

OMSSA

MaxQuant