Mascot Server Download

[Myra Krallman]

MascotServer is a powerful search engine which uses mass spectrometrydata to identify proteins from DNA, RNA and protein sequence databasesas well as spectral libraries.While a number of similar programs are available, Mascot is uniquein that it integrates all of the proven methods ofdatabase searching: peptide mass fingerprinting, sequence query and MS/MS ions search.

Mascot has become firmly established as the standard for protein identification using mass spectrometry data. It will give excellent results with peak lists from instruments manufactured by: AB Sciex,Agilent,Bruker, Jeol,Shimadzu,Thermo Scientific,Waters.

You are welcome to use the free service running on this website. It is ideal for evaluation and searching smaller data sets. A selection of popular sequence databases are online, including SwissProt, Uniprot proteomes and the EST divisions of EMBL.

Mascot Server is available for Windows and Linux on Intel and AMD processors.The software is typically installed on a server grade computer at your own premises, but you can also run it on your workstation, virtualised infrastructure and in the cloud.All aspects of the hardware and software are fully under your control, and there are no restrictions on the number of users submitting searches to the Mascot server or the size of the searches.

The licence is perpetual, not an annual fee, and includes 1 year warranty covering technical support and all updates. After the first year, if you wish to continue receiving technical support and updates, you have the option of purchasing a support contract.

The Mascot search engine is very fast and the code is threaded for execution on multi-processor systems and clusters. Whatever throughput is required, it can be achieved by running Mascot on a sufficient number of processors.

Entry level is a single processor (1 CPU) licence. For licensing purposes, 1 CPU equals 4 cores. For example, a 1-CPU licence will use the first four cores in a system with 1 x 6-core processor or 2 x 4-core processors. If the system has more cores than are covered by the licence, the surplus cores are used for generating reports and web server/operating system overhead.

A licence can be upgraded to use additional processors at any time. Start with just the number of processors you need today and add additional processors to the licence as and when required. Note that there is no limit to the number of users that can submit searches to a Mascot server, even if it is just a single CPU licence.

You can continue receiving these benefits in subsequent years by purchasing an annual support contract.After the first year, if you wish to continue receiving technical support and updates, you have the option of purchasing a support contract for 20% of the licence fee per year. Alternatively, you can buy a version update, which includes one year of Premium Support.

Your Mascot Server licence entitles you to use the licensed version or any earlier version (at your option).We regularly release new versions with major new functionality.If have an active Premium Support contract when a new version is released, we will send it to you for free.

For example, if you have Mascot Server 2.5, and the latest version is 2.8, then the cost to update is 75% of the cost to buy a new licence with the same number of CPUs. When you update, you can optionally increase or decrease the number of licensed CPUs.

The standard Mascot Server has a 16kDa limit for precursor masses, making it unsuitable for most top-down experiments. An optional special version of Mascot, known as Mascot Top Down, is available which has a limit of 110kDa.

Mascot Parser provides an Application Programming Interface (API) to Mascot Server result files and Mascot Distiller project files, making it easy to access search results from programs written in C++, C#, Java, Python or Perl.

This is the home page for your in-house Mascot Server, apowerful search engine that uses mass spectrometry data to identify and characteriseproteins from sequence databases. To assist you, the help text for Mascot forms a substantialknowledge base concerning protein identification by MS.

Mascot incorporates a role based security model, which allows the system administrator tocontrol which functionality is available to individual users. If security has been enabled,you may be prompted to log in if you attempt to access a page or perform a taskthat requires authorisation. If security is not enabled, which is the default, the following links will simply confirm this.

Whether or not Mascot security is enabled, in order to comply with the licensing conditions,access to this Mascot server must be restricted to authorised users. We strongly recommend that your server is protectedby a secure firewall.

Help on using Mascot and understanding the results is contained in these HTML pages. Click on Help at the top of the page to browse the help topics or use the keyword search facility.The following documents are mainly of interest to system administrators.

For many users of Thermo instruments, Proteome Discoverer (PD) is their primary user interface for database searching, and Mascot is represented by a node in the workflow. This article collects together a few tips and observations concerning Proteome Discoverer 2.3 and Mascot Server 2.6.

Under Administration; Mascot Server, the setting Max. MGF File Size [MB] has a default value of 500. Some people increase this, thinking it is an upper limit on the size of the data set. In fact, PD splits larger peak lists into separate searches and transparently merges the results back into a single set of results. In most cases, this is a good approach, and avoids the possibility of running out of memory on systems with limited RAM. For typical Q-Exactive data, a 500 MB MGF corresponds to 150,000 spectra.

We sometimes get questions about the authentication settings. If you are not sure whether these are required, try opening a web browser on the PD PC, connect to your Mascot Server home page, then submit a small search. If you are immediately challenged for a user name and password by the web browser, in a pop-up dialog box, you need to enter the same credentials into the web server authentication fields in PD. If you can connect to the home page but are asked for a user name and password when you try to load the search form, as below, you need to enter the same credentials into the Mascot server authentication fields in PD. Otherwise, leave the authentication fields in PD blank; entering credentials when they are not required is likely to cause problems.

The Target Decoy PSM Validator node appears to report an FDR based on the excess of the Mascot score over the identity threshold. This is a calculated significance threshold, derived from the number of candidate peptides that were tested to find the best match. For large search spaces, such as no enzyme searches, searches with many variable modifications, or very large databases, this can be wildly over conservative. For all but the smallest data sets, Mascot reports use the homology threshold, which is an estimate of whether the score is an outlier from the distribution of scores for chance matches.

At an FDR of 1%, PD reported 36,036 target PSMs. The Mascot summary report, when using the identity threshold, gave essentially the same count of 35,978. Switching to the homology threshold, which is the default, the count was 42,043. Only a modest penalty for using the Target Decoy PSM Validator.

For an FDR of 1%, PD reported 2,762 target PSMs. The Mascot summary report, when using the identity threshold, gave essentially the same count of 2,682. Using the homology threshold, the count increased to 7,720, almost a factor of 3 greater, demonstrating the importance of using the homology threshold for such a data set.

Mascot software, by Matrix Science, is a widely used software for identification, characterization, and quantitation of proteins from peptide sequence databases. The software works well with peak lists generated by most mass specs. Although Mascot server is free, having a license is recommended as it can handle large files. Mascot software works well on Windows and Linux operating systems. Mascot Daemon is a Microsoft Windows client application that automates the submission of data files to Mascot Server in a batch mode.

Navigate to Administration->Configuration->Mascot and type in the name of the Mascot server in the Mascot Server URL field. It also recommended to run the Mascot Communication Tester from the Tools menu to confirm that the connection has been made.

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