Welcome: Take the Tour

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Welcome Take the Tour
Scaffold is a software tool for extracting more
detailed and accurate information from your
SEQUEST or Mascot results.
Please take a few minutes and see how can
Scaffold can benefit your lab. You can navigate
through the slides by either using the links menu
to the right, or using the navigation buttons.
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What is Scaffold?

• As a proteomics scientist, you may have spent
  days even weeks running SEQUEST or Mascot on
  your MS/MS data, only to be left with such
  questions as
• Were any of the protein identifications false
  positives?
• Were any critical identifications missed?
• What supporting data can I use to verify my
  results?
• How do I compare identified proteins between my
  treated sample and control?
• Can I speed up the search for post-translational
  modifications?

To help solve such problems, Proteome Software
developed Scaffold, a software tool for
extracting more detailed and accurate information
from your SEQUEST or Mascot results.
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Scaffold Increases Sensitivity
Scaffold fits separate probability curves to
correctly and incorrectly identified proteins in
your samples. Given a discriminant score D,
Bayesian statistics then compute the probability
p(D) that a match is correct.
Threshold optimization
Arbitrary Thresholds Miss Identifications
incorrect
Number of spectra in each bin
correct
Scaffold statistically analyzes your sample set,
rendering obsolete the need to set an arbitrary
acceptance threshold. Probability scores strike a
balance between more protein identifications and
increased confidence. Your results can also be
automatically cross-validated with X! Tandem,
further increasing confidence. Clear tabular
overviews make it easy to confirm consistent
results in replicate samples. Plus, you can drill
down through underlying data to see the spectra
supporting the identification of a peptide.
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Scaffold Finds More Valid Identifications
Scaffold readily combines results from multiple
search engines, as well as automatically running
X! Tandem on your data. Identifications may
overlap, but, as the diagram below shows, less
than you might think. By combining results from
several applications, you get more good,
cross-validated protein identifications.
Scaffold also lets you export unmatched spectra
to search against other databases. Importing the
new results back into Scaffold results in a more
complete list of valid protein identifications.
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Scaffold Enhances the Search for PTMs
Identifying post-translational modifications can
add valuable information to the results of your
proteomics experiment, but searching for them
often requires excessive computer time. To speed
the process, Scaffold can export a subset FASTA
database containing only your initially
identified proteins. Using this subset database,
you can quickly rerun the original search engine
with fixed or variable modifications, to find
protein modifications. Scaffold also enables you
to exploit X! Tandems rapid search for
modifications.
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Scaffolds Visualization Tools Enable Comparisons
Scaffold summary view
Scaffold makes it easy to compare and contrast
protein expression between samples. A click of
the mouse switches between an overview of
proteins by biosample categories (for example,
control vs. diseased samples) to an overview of
proteins at each gel spot, or in each mass
spectrometry sample. Summaries display
identification probabilities, numbers of
identified peptides, and also the number of
spectra matched for each protein, giving you a
rough estimate of differential expression.
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Scaffolds Lets You View the Supporting Spectra
Viewing a spectrum
For more detail, Scaffold displays the supporting
MS samples and underlying MS/MS spectra for any
identified protein.
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Scaffold Uses Proven Algorithms
Scaffold uses proven algorithms 1 2 3 that have
been documented and verified by the proteomics
community. We have independently implemented
these algorithms in a system thats easy to
install, easy to learn, and easy to use and one
that facilitates the management of large
quantities of data. Additionally, you can manage
the peak lists and search results from your MS/MS
runs, and use the database-like functionality
easily sorting, filtering, and linking - without
the headache of maintaining a database.
Can your software keep up with your
hardware? Upgrade to Scaffold today!

• References and Trademarks
• Craig, R., and Beavis, R. C., "TANDEM matching
  proteins with tandem mass spectra."
  Bioinformatics.
• 2004 Jun 1220(9)1466-7. Epub 2004 Feb 19.
  PubMed
• 2. Keller, A., Nesvizhskii, A. I., Kolker, E.,
  and Aebersold R., "Empirical statistical model to
  estimate the accuracy of peptide identifications
  made by MS/MS and database search." Anal. Chem.
  2002 Oct 1574(20)5383-92. PubMed
• Nesvizhskii AI, Keller A, Kolker E, Aebersold R.
  , A statistical model for identifying proteins
  by tandem mass spectrometry. Anal Chem. 2003 Sep
  175(17)4646-58. PubMed
• SEQUEST is a registered trademark of the
  University of Washington
• Mascot is a registered trademark of Matrix
  Science Ltd.

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How Scaffold Benefits You

• Maximize your SEQUEST or Mascot results
• Increase sensitivity
• Increase confident protein identifications
• Visually compare and contrast samples
• Manage up to 300,000 MS/MS spectra in a single
  file
• Analyze either 2-D gel or MuDPIT MS/MS results
• Integrated X! Tandem searching

Easy to install, easy to learn, easy to use, easy
to maintain
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Want More Information?
As youve seen in this overview, Scaffold can
offer great benefits to any lab currently using
SEQUEST or Mascot to analyze their MS/MS data.
To get your free 14 day trial of the Scaffold
software all you need to do is call or
e-mail. Proteome Software 800-944-6027 info_at_prote
omesoftware.com