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An intuitive software for visualizing & validating MS/MS protein identification data from any mass spectrometer.
Visualize
Scaffold displays a complete, experiment-wide view of the proteins identified in a tandem mass spectrometry
experiment. The side-by-side display of all the samples allows you to understand which proteins are differentially
expressed. Protein identification results are displayed as probability scores, allowing you to balance the number of
proteins and the confidence level of each identification. Automatic protein annotation aids in interpreting the biological relevance of data.
Validate
Identify proteins from MS/MS data by validating search engine results. Scaffold uses proven statistical algorithms of the Trans Proteomic pipeline (PeptideProphet and ProteinProphet) to calculate the probability that proteins are actually in your biological samples. Detailed results help detect false positives by focusing on a protein of interest, examining the peptide & spectra evidence supporting the identification.
Collaborate
With its free viewer, Scaffold makes it easy to share experimental results with colleagues. Scaffold also helps you prepare for publication, by capturing the information proteomics journals require in a paper’s methods section.
Additional features include:
- Tie protein identifications to key biological annotations
- Quantitative framework based on spectral counting
- Post-translational modification and mass tolerance filtering
- Advanced peptide assignment for protein grouping
- Improved false discovery rate estimation
- Export in ProtXML format
Data formats supported include :-
Data formats for SEQUEST® = *.dta and *.out, *.ms2 and *.sqt, and *.srf; Mascot® = *.dat; X! Tandem® = *.xml; Phenyx = *.scaffold-pidres.xml; OMSS = *.omx; Waters® IdentityE = *.xml (Note: These files must be created from our plugin in the new version of Waters PLGS); Proteome Discoverer = *.msf
Q+ is an additional module for Scaffold 3 enabling relative quantitation across multiple iTRAQ and TMT experiments.
This module enables Users to perform the following on their quantitation data:
- Viewing of experimental trends.
- Production of heat maps highlighting up & down regulated proteins.
- Filtering and sorting of differentially expressed proteins.
- Identification of proteins that deviate from the norm.
Scaffold PTM is a stand alone software for confident phosphorylation site assignment using Ascore by Beausoleil et al
(2006), as well as other PTM events such as oxidation, glycosylation etc..
It enables fast comparison of PTM rates across many samples with clear charts that make instant figures for powerpoint presentations & posters.
PTM embraces the HUPO open search engine standard mzIdentML, currently supported by Mascot & Scaffold, endorsed by every search engine vendor. SPTM files use an accesable open database format and the scaffold PTM console provides instant access to all underlying data.
MassQC is a software program that analyzes, displays, and compares standard LC-MS/MS runs to monitor and troubleshoot
the performance of your LC-MS instrumentation. MassQC enables Users to quickly answer the following questions:
- Is the LC-MS functioning well now?
- Is the LC-MS giving reproducible results?
- Is LC-MS performance degrading over time?
MassQC supports Thermo® Data Dependent Analysis (DDA) MS/MS *.RAW files from the following instruments:
- LTQ
- LTQ FT
- LTQ Orbitrap
- LTQ Velos
- LTQ Orbitrap Velos
Further Information
See Downloadable Resources for further technical information.
Newsletter
To access Proteome Software’s Newsletter please click on the following links.
Autumn 2009 - Newsletter No.1
January 2010 - Newsletter No.2
January 2011 - Newsletter No.3
August 2011 - Newsletter No.4
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