About the software:
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.
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.
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.
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's primary report enumerates the proteins found in a
sample along with the peptides in evidence for each (also generated in
- 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.
- The alignment report aligns all the peptides found for each
protein against each other to produce sequence contigs.
- 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
- 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 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.
- 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
- Calculation of the isoelectric point for a protein is described in
this brief paper.
- 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
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
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"
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.
DTASelect and Contrast are copyright 2001 by David L. Tabb, The Scripps Research