If software developers are going to join what Oracle's ads call "the new gold rush," the hardware suppliers have to develop machines that make customers feel like prospectors, not tools.
To obtain theoretical masses, the Protein Prospector MS-Product tool was used (v.5.10.4. UCSF).
Spectra were analyzed with the MSFit tool of the Protein Prospector program [ 47] at http://www.prospector.ucsf.edu/prospector, using taxonomy filters for microorganisms or Haemophilus.
The system also includes a number of data visualization and query tools, such as Geothermal Prospector (Getman et al. 2015).
All searches were done using MS-fit peptide mass fingerprint tool from the UCSF Mass Spectroscopy facility (Protein Prospector, UCSF) on SwissProt database (2005.01.06) with mass tolerance of 50 ppm, maximum number of missed cleavage of 1, and protein/peptide modifications (peptide N-terminal Gln to pyroGlu, oxidation of M, and protein N-terminus acetylation).
The sum of all these changes led to significant improvements in the number of peptides identified in all datasets tested, and by comparing the results to those reported by other search engines it indicated that the older version of Protein Prospector (version 5.3) appeared to already outperform alternative tools, and the new version further increased this edge (Baker et al. 2010).
Threading tools like 3D-PSSM [25] (now Phyre [26]), TASSER [27], which uses PROSPECTOR [28], [29] derivatives as the threading engine, or MUSTER [30] all take into account sequence-, as well as structural (secondary and/or tertiary) features when scoring hits and therefore outperform purely structure-based techniques.
"It can claim that it is supplying superior picks and shovels to the entire industry, the best mining tools for gold prospectors in the Internet economy".
"Not bad," the prospector allowed.
"I'd be a prospector of the prospectors.
