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.
Known bug - spaces and special characters in filenames not supported - GOAT does not pass filenames and paths that contain spaces or other special characters to ProteoWizard msaccess correctly. If you try to run GOAT on a file that has a name including spaces, or which is inside a directory with a name including spaces, you are likely to receive an error message. Please rename your input files and directories so that they do not included spaces in their names, to work around this problem. We apologize that this bug will not be fixed, as the developer has left the laboratory.
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.
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.
A poster describing GOAT was presented at ASMS 2013 in Minneapolis, MN:
Poster: MP18 - Informatics: General. Poster number: 357, Monday, Halls B&C.
GOAT may be downloaded for non-profit academic use only, subject to the license terms below.
Potential non-academic users should contact the UTSW Office of Technology Development.
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