DTASelect and Contrast: Informatics for Shotgun Proteomics

About the software:

DTASelect

SEQUEST is very powerful for matching uninterpreted tandem mass spectra to database peptide sequences. DTASelect is designed to reassemble this peptide information into usable protein information. The program can do more than simply report the protein content of a sample; it features many customizable filters to specify which identifications should be kept and which discarded. It also features reports to investigate post-translational modifications, align sequences of peptides to identify poorly sequenced regions, and analyze chromatography efficiency. The software makes the process of analyzing SEQUEST results far faster, more powerful, and more consistent than possible before, even for data sets containing a million spectra or more. By automating SEQUEST analysis, DTASelect enables experiments of far greater scope.

Contrast

Differentiating biological samples by protein content is an important application of proteomics. The Contrast program uses the filters present in DTASelect to highlight the most important identifications of samples and then compares them. Unlike most relatively simple comparison algorithms, Contrast can differentiate up to 63 different samples at once. Contrast handles differential analysis between experimental and control samples simply and flexibly.

Availability

Both programs can now be licensed for use at your university, institute, or company. Academic and nonprofit use is free of charge. Commercial use is available for a license fee.

Publication

Tabb DL, McDonald, WH, Yates JR 3rd, DTASelect and Contrast: Tools for Assembling and Comparing Protein Identifications from Shotgun Proteomics. J. Proteome Res. 2002 1:21-26.

Reports and Screenshots

DTASelect.html: DTASelect's primary report enumerates the proteins found in a sample along with the peptides in evidence for each (also generated in text form).
DTASelect-mods.html: This report focuses on the post-translational modifications found in the peptides remaining after filtering. The peptides showing the presence of each modification are aligned against each other.
DTASelect-align.html: The alignment report aligns all the peptides found for each protein against each other to produce sequence contigs.
DTASelect-chroma: The chromatography report shows how many +1, +2, and +3 precursor ions remained from each round of chromatography after filtering, aiding the improvement of chromatography for proteomic experiments.
Spectrum Viewer: DTASelect features a graphical user interface (GUI) which can display spectra more effectively than the standard tool shipped with SEQUEST.
Sequence Coverage Viewer: The GUI can also be used to show sequence coverage for proteins where multiple peptides are observed.
Bird's Eye: DTASelect can represent all proteins found in a sample in a single graphic, suitable for presentations.
Contrast.html: Contrast produces its own report in combination with DTASelect reports. Its main output shows the pattern of presence and absence for each protein across a set of samples. Each protein is shown with its sequence coverage, which is a link to corresponding DTASelect files like DTASelect.html above.

Downloads

DTASelect and Contrast Manual for version 1.9 (last updated 9/27/04): For a complete description of the features and use of the programs, the manual is the best bet. Instructions for installing the software are included.
DTASelect and Contrast User Manual for version 1.8 (last updated 12/16/02): The manual for the previous edition of the program.
DTASelect and Contrast FAQ (last updated 3/18/02): The FAQ attempts to address commonly asked questions. New questions are welcome!
Isoelectric Point Calculation Algorithm.: Calculation of the isoelectric point for a protein is described in this brief paper.
TupleTable.java: DTASelect's GUI uses a java library called "TupleTable" to create a clickable table of text elements onscreen. This library's source code is licensed under the GNU Lesser General Public License

Acquiring DTASelect and Contrast

A Materials Transfer Agreement Request Form is necessary to acquire a license for DTASelect / Contrast. Fill in the blanks on this form, and fax it to the number at the bottom of the form. Scripps will then send you the full MTA for signatures.

About the Logo

"The statue is already in the stone, has been in the stone since the begining of time, and the sculptor's job is to see it and release it by carefully scraping away the excess material"
-Michelangelo

DTASelect is designed to highlight the most important identifications from a sample. Like the sculptor, the program must trim away all the bits that get in the way of seeing these identifications.