Can I have a copy of XXXXX software?

The answer is, in most, instances, no. The proprietary software that is provided with instruments often includes a free results viewer, but will lack most analytical capabilities. Further, the raw data that derive from the instrument are usually subject to high level processing for discovery or comparative analyses. We have paid a great deal of money for these packages, and they are usually copy-protected and restricted to single computers. These computers are usually very highly specified, running 64-bit OS, with every enhancement for handling large data files, and also for speed.

In general, external users will expect us to perform most of the analyses as well, and thus, we will access these packages on your behalf. If you wish to become adept at running the software yourself, that is no problem, but access to the computers is chargeable as well, and we will also have to make a charge for training. This is the only way we can operate without PFG subsidising other groups research
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Accessing the MASCOT server at Liverpool

We no longer operate a MASCOT server for University of Liverpool users. Access is now limited to PFG and affiliates. This is regrettable, but there are no external input streams to support this package.

From the manufacturers's web site:

Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases. While a number of similar programs available, Mascot is unique in that it integrates all of the proven methods of searching. These different search methods can be categorised as follows:

Peptide Mass Fingerprint in which the only experimental data are peptide mass values, Sequence Query in which peptide mass data are combined with amino acid sequence and composition information. A super-set of a sequence tag query,

MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides,

The general approach for all types of search is to take a small sample of the protein of interest and digest it with a proteolytic enzyme, such as trypsin. The resulting digest mixture is analysed by mass spectrometry

Different types of mass spectrometer have different capabilities. A simple instrument will measure a set of molecular weights for the intact mixture of peptides. An instrument with MS/MS capability can additionally provide structural information by recording the fragment ion spectrum of a peptide. Usually, the digest mixture will be separated by chromatography prior to MS/MS analysis, so that MS/MS spectra from individual peptides can be measured.

The experimental mass values are then compared with calculated peptide mass or fragment ion mass values, obtained by applying cleavage rules to the entries in a comprehensive primary sequence database. By using an appropriate scoring algorithm, the closest match or matches can be identified. If the "unknown" protein is present in the sequence database, then the aim is to pull out that precise entry. If the sequence database does not contain the unknown protein, then the aim is to pull out those entries which exhibit the closest homology, often equivalent proteins from related species
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