A simple vendor-independent tool to optimize LC gradients in shotgun proteomics experiments.

D. C. Trudgian1, R. Fischer2, X. Guo1, B. M. Kessler2, H. Mirzaei1

1Dept. Biochemistry, UT Southwestern Medical Center, Dallas TX, USA

2Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, UK

Funding: Cancer Research and Prevention Institute of Texas (RP120613)

UPDATE - July 1st 2013: The GOAT download has been updated to 1.0.1. This version correctly supports folder-based vendor formats, and fixes a bug in gradient calculation that is likely to occur in 1.0.0. Apologies to those who tried the previous version after seeing the ASMS poster. Please use version 1.0.1. below.


About

GOAT optimizes LC gradients for shotgun proteomics experiments. Given a raw data file that was acquired with a standard gradient, it will produce an optimized gradient for increased sample coverage.

Results

An 8-way SAX separation of HeLa lysate was run on an Orbitrap Elite using 100 minute standard and GOAT gradients. Optimized GOAT gradients were generated individually for each fraction. A maximum 21% and average 10% increase in unique peptide sequences per fraction was achieved using the GOAT optimized gradients.

Poster

A poster describing GOAT was presented at ASMS 2013 in Minneapolis, MN:

Poster: MP18 - Informatics: General. Poster number: 357, Monday, Halls B&C.

Download

GOAT may be downloaded for non-profit academic use only, subject to the license terms below.

Goat 1.0.1 (including manual) - ZIP File

Potential non-academic users should contact the UTSW Office of Technology Development.

Contact

ProteomicsCore@UTSouthwestern.edu


License

a. Copyright ©2012, 2013 The University of Texas Southwestern Medical Center. All rights reserved;

b. This software and any related documentation constitutes published and/or unpublished works and may contain valuable trade secrets and proprietary information belonging to The University of Texas Southwestern Medical Center (UT SOUTHWESTERN). None of the foregoing material may be copied, duplicated or disclosed without the express written permission of UT SOUTHWESTERN. IN NO EVENT SHALL UT SOUTHWESTERN BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF UT SOUTHWESTERN HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. UT SOUTHWESTERN SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". UT SOUTHWESTERN HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

c. This software contains copyrighted materials from ProteoWizard. Corresponding terms and conditions apply.


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