Peptide Search software

Besides sensitive methods for the analysis of proteins, bioinformatics is one of the key components of proteome research. This includes software to monitor and quantify the separation of complex samples, e.g., to analyze 2DE images. Web-based database search engines are available to compare experimentally measured peptide masses or sequence ions of protein digests with theoretical values of peptides derived from protein sequences. Websites for database searching with mass spectrometric data may be found at http //www.expasy.ch/tools, http //prospector.ucsf. edu/ and http //www.matrixscience.com. 

All four of the proteomic technologies mentioned above (2D-PAGE, HPLC, MS, and protein arrays) are dependent on the use of bioinformatics as a tool for data mining and elucidation. Often, MS runs generate lists of thousands of potential peptide biomarkers, and only with the help of dedicated software tools can the data be analyzed. Computer searches involving databanks of peptides and proteins are used to compare the lists of masses of the proteolytic peptides to theoretical proteolytic products. Matches between the observed mass and the calculated mass can serve as a way of identifying proteins of interest [28-32],... 

The mass spectra analysis of peptides was performed on an Ultraflex-TOF-TOF instrument (Bruker Daltonics, Germany) with a MALDI source equipped with UV laser (337 run) operated with positive ion detection m/z 700-2,000) and in reflection mode. The spectra were processed using Flex Analysis 2.4 software. A SwisProt database search was performed using the MASCOT program package (Matrix Science, UK). The exact monoisotope masses and... 

A third approach, pioneered by the group of Liebler [19, 34], involves a pattern recognition software called scoring algorithm for spectral analysis (SALSA) to search specific sequence motifs in the MS-MS data. Potential applications envisaged for SALSA include identification of specific protein modifications, e.g., PTM, identifications of peptides with common sequences, e.g., wild-type and mutant forms, and targeted analysis of isoforms and conformers in complex samples. 

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... 

Figure 2.6 Automated analysis of BSA tryptic digest at 26 fmol pL 1 from position 3 on the device. MS-MS spectra were generated for the observed peaks. The MS-MS spectra for the labeled peaks were successfully matched to BSA by searching a protein sequence database using the Sequest software. The numbers indicate the measured m/z ratio and the charge state of the peptide ions.

Studies of PTM have been benefited from the recent advancements in mass spectrometry, the introduction of new software and Internet-based MS data search facilities, computer-assisted topology prediction for a variety of PTMs (visit http // ca.expasy.org/), chemical synthesis of modified peptides and proteins, development of modified peptide specific antibody, in vitro modification techniques, exploitation of other eukaryotic cells such as insect cells for protein expression [4, 5, 16, 32], and progress in affinity purification of modified proteins. 

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