Search algorithm, MASCOT

The MS instrument returns LTQ or LTQ-FT raw data files that contain the mass spectral data. These may be analyzed by Bioworks, that features the SEQUEST [20] protein search algorithm for protein/peptide identification. The predicted peptides in the search analysis are verified for the fragmentation pattern in the MS/MS spectra. Alternatively, the data can also be uploaded to the Mascot server [21], and analyzed for peptides and corresponding protein identification. 

International Protein Index database for the species studied (available online at http //www.ebi.ac. uk/IPI) and its sequence-reversed version with the Mascot (Matrix Science, Boston, MA) search algorithm. Equivalent search software (Proteome Discoverer [Thermo Fisher Scientific], Protein Prospector [http //prospector.ucsf.edu/prospector/ mshome.htm], Phenyx [GeneBio, Geneva, Switzerland], XlTandem [http //www.thegpm.org/tandem/], etc.) may also be used. 

Mascot (Matrix Science) search algorithm and the International Protein Index (available online at http //www.ebi.ac.uk/IPI), or similar database. The search against the normal database combined with the corresponding reversed or randomized database is an excellent vahdation method for MS/MS searches of large data sets. 

Several software search engines, including MS-Fit, MOWSE, Prot-ID, Expasy tools, ProFound, Mascot, and PeptideSearch, are available for use with the peptide-mass fingerprinting data. During the search process, the algorithm matches the measured molecular masses of peptides in the query against the list of theoretical mass... 

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