Mascot Server - Mass spectrometry data analysis software

Mascot has become established as the cross platform standard for protein identification using mass spectrometry data. Cross platform in the sense that it runs on all these mainstream computing platforms:

Linux
Microsoft Windows 2000 / XP / 2003 / Vista / 2008
Solaris (Sun)

... and cross platform in the sense that it accepts peak list data from all these manufacturer's instruments:

Agilent
Bruker
ThermoFisher Scientific (Finnigan)
Shimadzu (Kratos)
Waters (Micromass)
AB SCIEX (Applied Biosystems)

Although Mascot can be accessed for free on our web site, here are some of the many reasons why people choose to license Mascot for in-house use:

Confidentiality issues prohibit transmission of sensitive data to a third party across the internet.
To search custom or proprietary sequence databases.
For high throughput work and closed loop automation.
Search results can be imported into a database for data mining.
The HTML forms and Perl scripts can be customised.

The Mascot search engine is very fast, and the code is threaded for execution on multi-processor systems or PC clusters. Whatever throughput is required, it can be achieved by running Mascot on a sufficient number of processors.
This doesn't have to mean a heavy investment up-front. Start with just the number of processors you need today, and add additional processor licences as and when required. Note that there is no limit to the number of users who can submit searches to a Mascot server, even if it is just a single processor licence. The licence cost is based purely on the number of processors actually used by Mascot, which can be less than the total number of processors in the system.
A Mascot licence includes a one year warranty, providing:

Access to expert technical support
Free updates to all new releases of Mascot
No charge to swap to another supported platform

You can continue receiving these benefits in subsequent years by purchasing an annual support contract.

Software Link: Mascot Server - Mass spectrometry data analysis software