Welcome: Take the Tour

1
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.
2
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.
3
Scaffold Increases Sensitivity
Threshold optimization
Arbitrary Thresholds Miss Identifications
Scaffold applies curves to the peptide IDs to
gauge the probability of being a correct ID.
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.
4
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.
5
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.
6
Scaffold Enables Comparative Proteomics
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. Easily switch between
views of probability, numbers of identified
peptides, and also the number of spectra matched
for each protein.
7
Scaffolds Lets You View the Supporting Spectra
Viewing a spectrum
For additional confidence, Scaffold displays the
supporting MS samples and underlying MS/MS
spectra for any identified protein.
8
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 yet
also facilitates the management of large
quantities of data.

• 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.

9
Share Data Easily with the Free Scaffold Viewer

• Scaffold Viewer reads all Scaffold files. With it
  you can
• View protein identifications compiled with
  Scaffold by your mass spec core
  laboratory.
• Share the proteins identified by your mass
  spectrometer with your colleagues.
• Scaffold Viewer, like other browsers and readers,
  is free. Just download and install Scaffold, then
  click "Free Scaffold Viewer" the first time you
  run Scaffold.
• No software "key" is needed to use Scaffold in
  viewer mode.

10
How Scaffold Benefits You

• Maximize your SEQUEST or Mascot results
• Increase sensitivity
• Increase confident protein identifications
• Visually compare and contrast samples
• Manage large datasets
• Share data with the free viewer
• Integrated X! Tandem searching

Easy to install, easy to learn, easy to use, easy
to maintain
11
Would You Like 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 please download the latest version from
our website, and then submit a request via the
website for an evaluation key. Proteome Software
800-944-6027 info_at_proteomesoftware.com
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.