Protein database search

Altschul S F, T L Madden, A A Schaffer, J Zhang, Z Zhang, W Miller and D J Lipman 1997. Gapped BLAST and PSI-BLAST A New Generation of Protein Database Search Programs. Nucleic Acids Research 25 3389-3402. 

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST a new generation of protein database search programs. Nucleic Acids Res 1997 25 3389-402. 

Mature PGE showed the highest homology - 79% (Fig. 2) - with PGC from A. niger based on a protein database search. 

Demirev, P. A. Ho, Y. P. Ryzhov, V. Fenselau, C. Microorganism identification by mass spectrometry and protein database searches. Anal. Chem. 1999, 71, 2732-2738. 

PSI-BLAST (Altschul et al., 1997) is rapidly becoming the tool of choice for protein database searching because of its speed, sensitivity and ease of use. It presents a very large improvement over the older versions of BLAST and new gapped-BLAST implementations (Altschul et al., 1997 Altschul et al., 1990). However, a naive user can easily be misled or not get the best possible results. PSI-BLAST is available as a stand-alone program from ftp //and as an interactive web tool at http //www.ncbi. nlm.nih.gov/cgibin/BLAST/nph-psi blast... 

Altschul, S., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST anmd PSI-BLAST a new generation of protein database search programs. Nucl. Adds Res. 25, 3389-3402. 

The development and use of various protein sequence databases for automated search routines (Eng et al., 1994 Clauser et al., 1999) are an essential component of protein analysis that uses mass spectrometry techniques. These programs (i.e., SEQUEST, MASCOT) require only a few peptides for matching therefore, the absence of a match for a particular peptide does not affect the search performance. Using protein database searches provides an efficient way of confirming a putative sequence from corresponding full-scan mass spectrometry and MS/MS data. 

S.F. Altschul, T.L. Madden., A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST A new generation of protein database search programs Nucleic Acids Res. 25 3389-3402. (PubMed) (Full Text in PMC)... 

An important development in high-throughput protein identifieation is the introduction of protein database searching [111]. After separation on ID- or 2D-GE, the proteins were blotted onto a membrane and enzymatically digested after reduction and alkylation. The tryptic peptide mixture is analysed by MALDl-MS to achieve a peptide map or peptide mass fingerprint (PMF). The m/z information of the peptides is used to search the protein database, e.g., the Protein Identification Resource (PIR) database [112-114]. If the mass of just 4-6 tryptic peptides is accurately measured (between 0.1 and 0.01%), a useful database search can be performed. 

S.F. Altschul, D.J. Lipman, Protein database searches for multiple alignments, PNAS, 87(1990)5509. 

Schaffer, A. A., Aravind, 1,., Madden, T. L., Shavirin, S., Spouge, J. L., Wolf, Y. I., Koonin, R, V., and Altschul, 8. F. 2001. Improving the ac-niracy of PSI-R1.A8T protein database searches with composition-based statistics and other refinements. Nucleic Acids Rfss. 29 2994-3005. 

Enter the accurate peptide monoisotopic mass assignments into a protein database search engine. 

V Output of protein database search lists the best protein match ... 

FIGURE 4.12 A flow chart showing the basic steps used to identify a protein. The protein is excised from a 2-D electrophoresis gel, the gel diced, and the stain is washed. The protein is reduced and digested in the gel. The newly formed peptides are extracted and analyzed using a MS and/or MS-MS scan mode. The resulting MS and MS-MS data are entered into a protein database search engine that performs the match. 

FIGURE 4.13 A MALDI-TOF mass spectrum acquired in reflectron mode showing the tryptic peptides from a digestion of bovine serum albumin. The m/z of the monoisotopic ions are assigned and can be entered into a protein database search engine to match to the theoretical trypsin digest of BSA. 

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