Proteome Software Scaffold

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract Scaffold is a software tool for extracting more detailed and accurate information from your SEQUEST (see Note 1) or Mascot (see Note 2) results. Scaffold identifies proteins from tandem mass spectrometry (MS/MS) data by validating the results from SEQUEST or Mascot (see G6G Abstract Number 20087) searches. It uses proven statistical algorithms to calculate the probability that proteins are accurately identified. Detailed results help you catch false positives or missed proteins, and you can drill down to examine the evidence supporting each identification. Product features/capabilities include:

Validate Protein Identifications -- Clear, visual representations of spectra, peptide coverage and supporting data are conveniently linked to your protein IDs. Scaffold allows you to drill down and examine the various peptides and spectra supporting the identification.

Compare Results Across Samples -- Because MS/MS results can be difficult to interpret, Scaffold graphically compares protein expression between samples. The 'Scaffold Viewer' presents results as probability scores, allowing you to balance the number of proteins and the confidence level of each identification. Scaffold displays a complete experiment-wide view and automatically annotates your protein IDs with relevant biological documentation. With Scaffold, you can sort and visualize your experiments according to location and function, while automatically annotating your protein IDs.

Scaffold Finds More Valid Identifications -- Scaffold readily combines results from multiple search engines, as well as automatically running ‘X! Tandem’ (see Note 3) on your data. By combining results from several applications, you get better, 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. Scaffold uses an independently written subroutine that implements the same algorithm as PeptideProphet (see Note 4).

Scaffold Analyzes MuDPIT and 2D Gel MS/MS -- Scaffold is flexible, enabling direct comparisons among proteins that were identified using 2D gels, 1D gels, or liquid chromatography (LC). It can just as easily analyze Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC/MS/MS) experiments (also known as MuDPIT or shotgun proteomics) -- Scaffold combines the digested peptides in each LC/LC fraction for complete protein identification.

Scaffold Enhances the Search for PTMs -- Identifying post-translational modifications (PTMs) 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! Tandem’s rapid search for modifications.

Scaffold Enables Visual Comparison -- 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.

Note 1: SEQUEST is the original, and still one of the leading, programs that correlate un-interpreted tandem mass spectrometry (MS/MS) spectra of peptides with the amino acid sequences from protein databases. SEQUEST is the search engine sold by Thermo Finnigan with its mass spectrometers.

Note 2: Mascot is a widely used program that also uses mass spectrometry data to identify proteins from protein databases. Mascot has a extensive set of web help pages that includes a lot of information on protein identification by MS. You can use Mascot, in a limited way, on the web for free.

Note 3: ‘X! Tandem’ is a very fast search engine which searches for matches of MS/MS spectra to a protein database. X! Tandem is free to use on the web or to download. X! Tandem works in conjunction with (The Global Proteome Machine Organization) and can take advantage of the information gleaned from previous searches. It has an option, PPP, which searches first only the peptides that have been found most frequently for each protein. This can speed searches up by a factor of 20. X! Tandem was created by Craig and Beavis of the Manitoba Proteomics Center as an open-source alternative to SEQUEST, Mascot and similar search engines.

Note 4: PeptideProphet was developed by Keller, Nesvizhskii, et al. at The Institute for Systems Biology as a Bayesian statistical algorithm to convert SEQUEST scores into probabilities.

System Requirements


• Windows XP or 2000 or Apple Mac or Linux

• 512 MB RAM minimum, 1GB RAM recommended

Scaffold Capabilities

• Data formats for SEQUEST® = *.dta and *.out; Mascot® = *.dat; X! Tandem® = *.xml

• Maximum dataset size in one Scaffold file = 500,000 spectra.


Manufacturer Web Site Proteome Software Scaffold

Price $5995 ($4995 for academic or non-profit labs).

G6G Abstract Number 20081

G6G Manufacturer Number 102231