Mascot

Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases.

While a number of similar programs available, Mascot is unique in that it integrates all of the proven methods of searching.

These different search methods can be categorised as follows:

• Peptide Mass Fingerprint in which the only experimental data are peptide mass values



• Sequence Query in which peptide mass data are combined with amino acid sequence and composition information. A super-set of a sequence tag query



• MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides

Project which uses mascot - HUPO Brain Proteome Project Pilot Studies

Purpose of this project:
Proteomics studies driven by large consortia often led to heterogeneous data due to different strategies, techniques and equipment. Nevertheless, results have to be implemented into one database to assure a common, standardized interpretation. This is why this pilot study is initiated as high degree of standardization are extremely important in order to obtain reliable results.

Objective of this project:
To come out a solution to data standardization by analyzing data by four different search engine (Mascot,Sequest,PFF-Solver and Phenyx).

For more information, visit
http://www.medizinisches-proteom-center.de/lehre/poster/HUPO/Christian_Stephan_HUPO_2005.pdf

For information on mass spectrometry, visit
http://bioisit.blogspot.com/2007/11/mass-spectrometry.html

References:
http://www.matrixscience.com/
http://www.hbpp.org/