TIQAM (Targeted Identification for Quantitative Analysis by MRM)

Introduction

TIQAM is developed as a suite of software tools to support targeted indentification and quantification using multiple reaction monitoring (MRM) mass spectum technology. More specifically, TIQAM software provided user friendly interfaces to assist process of peptide selection, transition generation and validation. The overview of the software supporting work flow is illustrated by the following figure.
TIQAM Work Flow
The detailed information on the work flow and the application using TIQAM software for targeted quantitative analysis of Streptococcus pyogenes virulenece factors has been written and submitted to a scientific journal for review. The article title and authors are "Targeted Quantitative Analaysis of Streptococcus Pyogenes Virulenece Factors by Multiple Reaction Monitoring" by

Vinzenz Lange, Johan A. Malmström, John Didion, Nichole L. King, Björn P. Johansson, Juliane Schäfer, Jonathan Rameseder, Chee-Hong Wong, Eric W. Deutsch, Mi-Youn Brusniak, Peter Bühlman, Lars Björck, Bruno Domon and Ruedi Aebersold.

Third party software requirement

Current TIQAM software supports Window, Mac and Linux OS and requires Java 1.6 java run time environment and MySQL community edition 5.0 database installed prior to running TIQAM software.

Installing MySQL

  1. download MySQL server, by unzipping mysql.zip and follow mysql instruction.
  2. installation instructions are available in mysql.com site. For example, the installation instructions for Windows are available at mysql document site.
  3. Start MySQL prior to running any of TIQAM software. The automatic start-up of your installed database server can be found at mysql document site.

Create Databases for TIQAM software

Please download sql scripts (createtrans.sql, createmrm.sql) carefully type the following statments exactly as written
>C:\where you installed mysql\bin\mysql -u root -p < createtrans.sql
>C:\where you installed mysql\bin\mysql -u root -p < createmrm.sql

Download and installing mzWiff for wiff file converter to mzXML

TIQAM software uses mzXML as an input standard. The mzWiff is a wiff file converter to mzXML.
mzWiff program can be downloaded from mzWiff beta version website.

Current release version of TIQAM software suite

TIQAM-Digestor 1.2.3
TIQAM-PeptideAtlas 1.0.3
TIQAM-Viewer 1.2.2

Download and installing TIQAM software suite

TIQAM for Win32_x86
TIQAM for  Linux_gtk_x86

Unzip the download folder and you can find TIQAM-digester, TIQAM-peptide-atlas and TIQAM-viewer with version number suffix folders. In each folder subdirectory, you will find .exe files to launch each TIQAM modules.

Download Tutorial Documentations and Demo Data Set

Tutorial documents for each module is in TIQAM-Tutorial.zip
The corresponding demo data set is in TIQAM-TutorialDemoData.zip

Download Data Set related to the above reference paper published in Molecular & Cellular Proteomics 2008

DataSet for TIQAM

Download TIQAM source code

TIQAM-src.tgz

More information is available in the following wiki site.

TIQAM Wiki at Seattle Proteomics Center

If you have any question on software installation, please contact using the following contact information.

Copyright (c) 2007 Mi-Youn Brusniak and Aebersold group
 Contact information:
Mi-Youn Brusniak, Ph.D.
1441 North 34th St.
Seattle, WA 98103 USA
mbrusniak@systemsbiology.org