Mass Spectrometry Search Software

Three different mass spectrometry search algorithms dominate the database searching systems commercially available today. The Cornell University Probability Based Matching (PBM) software, The Integrated Control System (INCOS) and the MassLib system (see below) with the SISCOM search software. 

MS instruments measure the mass-to-charge ratio (m/z) values of the smallest of molecules very accurately. In addition, the development of translated genomic databases and specialized software algorithms that rapidly search MS data against theoretical spectra of known or predicted proteins within databases is an important component that greatly facilitated the emergence of mass spectrometry-based proteomics as a key approach for large-scale proteomic analysis.15... 

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. 

With the advent of accurate mass instruments, access to a reference database or library of compounds with the exact masses of precursor and product ions is becoming increasingly important. Many instrument manufacturers, as well as independent companies or institutions, are developing software that allows chemists to manage this type of information for specific applications such as proteomics or chemical contaminants. Examples of online resources that may be useful for searching for unknown residues based on molecular formulas obtained from accurate mass data inciude Metlin from the Scripps Center for Mass Spectrometry and ChemSpider from the Royal Society of Chemistry. " ... 

Part Mass Spectrometry by A. N. Davies gives an overwiew from a user s point of view. Commercially available mass spectral databases and software products for library searches are characterized. A statement from section 24.1 is repeated here because it seems to be essential not only for mass spectral database systems "... let the people who will be working with the systems have a major say in the testing and selection of the product to be purchased. .. . 

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