ATAQS (Automated and Targeted Analysis with Quantitative SRM)

As a complement to the well-established discovery proteomic methods, targeted mass spectrometry based on SRM is becoming an important tool for the generation of reproducible, sensitive and quantitatively accurate data from biological samples. The method depends on the generation of target protein sets based on prior information and the one-time generation of verified mass spectrometric assays for each of the targeted proteins.  The development of these assays depends on the optimal selection of peptides that represent the proteins on the target list and the optimal set of transitions for their detection in biological samples. Once developed, these assays can be continually applied across a multitude of studies. 

The ATAQS pipeline (see figure below) and software provides a high throughput tool for organizing, generating and verifying transition lists and for the post acquisition analysis and dissemination of the data generated from applying the transition lists to studies of biological samples.  ATAQS uses information from publicly accessible databases for the optimization of the protein and peptide target lists and for the optimization of a transition set. ATAQS is an open source software that enables data-driven researchers to generate candidate protein lists and measure candidate proteins across a large number of biological samples, and allows algorithm-developing scientists to further develop the steps in the ATAQS pipeline. As needs arise, we plan to continuously expand on ATAQS functionalities (e.g., validation of quantification, support of SILAC type experiments, etc.)

The novel aspects of ATAQS are:

  1. Open source software for supporting large scale SRM verification workflow by multi users or research sites by managing projects and by running in a multi-threaded and distributed computing environment, to enable data processing on a compute cluster. This allows for timely processing of the typically large data sets generated in a high-throughput proteomics environment, and also ensures that the client computer’s resources are not drained.
  2. ATAQS provides a user friendly interface to access publically available transition resources to download and also contribute user optimized transitions to public database if researchers choose to do so.
  3. ATAQS produces an automated way of generating all of your verified transitions in Proteomics Standard Initiative format for SRM called TraML. Thus, it will be easier for exchanging data among proteomics community.
  4. A web-based GUI to provide the user with the ability to manage multiple projects and data analyses, as well as direct the data through the analytical and statistical modules, all via a web browser. The GUI also provides significant user control to customize the process for their needs and to output results in visual format as well as to generate TraML format of measured transitions.
  5. ATAQS includes extensive documentation to enable a bioinformatician to customize the ATAQS platform for their own and lab uses, by implementation of additional analytical tools, Bioconductor packages etc. as needed.
Additionally, our Institute has an open source policy, and we are committed to free access to ATAQS under an open source license (Apache 2.0). As needs arise, we plan to continuously expand on ATAQS functionalities.

We expect that ATAQS will find wide application as targeted proteomics increases in use to support hypothesis-driven research across all fields of life science.   


Figure. Summary of ATAQS workflow. ATAQS is composed of seven steps. The data flow is flexible in that the user can select which steps they want to use. For example, if user has already generated and optimized the list of transitions and decoy transitions, then the user can skip steps 4 and 5.

ATAQS article and contributing authors
ATAQS: A Computational Software Tool for High Throughput Transition Optimization and Validation for Selected Reaction Monitoring Mass Spectrometry, BMC Bioinformatics 2011, 12:78 (You can download the entire article by clicking this link).
Mi-Youn K. Brusniak, Sung-Tat Kwok, Mark Christiansen, David Campbell, Lukas Reiter, Paola Picotti, Ulrike Kusebauch, Hector Ramos, Eric W. Deutsch, Jingchun Chen, Robert L. Moritz, Ruedi Aebersold

ATAQS software installation instruction and source code
You can download software installation world document by the link ATAQS Installation Guide.doc. ATAQS_v1.0.tgz (downloadable from Corra-ATAQS project) contains complete source codes and libraries.

Corra-ATAQS developer code base and discussion group
Please join as project member for future development and biomedical research collaborators  and please join for  discussion.

ATAQS user guide and example data set
PDF format of ATAQS User guide using example yeast data set in the paper can be downloaded by the link ATAQS User Guide.pdf and (30 MB)

ATAQS demo site
If you would like to take a quick look without installation in your site, you can also use our demo website which is designed for “read only” pipeline. More specifically, it will not allow user to launch jobs to our server. However, this site can give you a pretty good idea on workflow and function so you can use ATAQS user guide mentioned in the previous section.

Discovery tool
While ATAQS is a computational tool for 
hypothesis-driven research across all fields of life science, Corra is a computational tool for discovery of candidate proteins of interest by utilizing label free quantification.

Thank you for interested in using ATAQS for your biological data application or enhancing current software or algorithm research.
We are looking forward to hearing from you and future collaboration as a community based code development.

Mi-Youn Brusniak, Ph.D.

 * Copyright (c) 2010 Institute for Systems Biology
 * Licensed under the Apache License, Version 2.0 (the "License");
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 * Contact info:
 * Mi-Youn K. Brusniak, Ph.D.
 * Insitute for Systems Biology
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