Database search algorithms

Demirev, P. A. Lin, J. S. Pineda, F. J. Fenselau, C. Bioinformatics and mass spectrometry for microorganism identification Proteome-wide post-translational modifications and database search algorithms for characterization of intact H. Pylori. Anal. Chem. 2001, 73, 4566 573. 

All of the three IC centers also provide facilities for sequence similarity search and alignment. The widely used database search algorithms are FASTA (Lipman and Pearson, 1985) at http //www.nbrf.georgetown.edu/pirwww/search/fasta.html and BLAST (Altschul et al., 1990) at http //www.ncbi.nlm.nih.gov/BLAST/. For BLAST... 

The SEQUEST database search algorithm (Ch. 17.6.2) is a powerful tool in protein identification, although like any statistical tool it relies on the jndgments of the user to critically evaluate its results. Problems may especially arise, when unanticipated modifications are present in the protein investigated. 

There are many other methods that can be used to separate proteins before characterization by mass spectrometry. Often in characterizing unknown proteins in a mixture, the constituent polypeptides are first enzymatically digested to yield a mixture of peptides. The peptides then are analyzed by MS either with or without some prior chromatographic or electrophoretic separation. With the aid of database search algorithms, the MS data are then evaluated to identify the proteins represented in the mixture (Abersold and Mann, 2003 Elia et ah, 2005). 

Three-dimensional database searching algorithms are available as add-on modules for some popular molecular modeling packages. An add-on module... 

Candidate peptide sequences from the mixture are later identified using a computerized database search algorithm (e.g., SEQUEST) [14] and validated using the STATQUEST probabilistic scoring program [15]. 

Institute for Molecular Bioscience (2006). University of Queensland (AU). Peptide mapping and database search algorithms, www.imb.uq.edu.au., last searched October 22, 2006. 

Kapp,E.,Schiltz,F. (2007) Overview of tandem mass spectrometry (MS/MS) database search algorithms. Current Protocols in Protein Science, 49,25.2.1—25.2.19. 

It should be noted that protein carbonylations occur via many different pathways. The hydrazide-coated glass beads are capable of enriching peptides harboring carbonyl modihcations other than those by HNE (e.g., 4-hydroxy-2-hexenal, 4-oxo-2-nonenal, metal-catalyzed oxidation, and others). These modifications can be included in the database search algorithms for in-depth mining of posttranslational protein carbonylations. 

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