Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract Mascot is advanced software for protein identification using mass spectrometry (MS) data. Mascot takes the mass spectrometry data and searches it against molecular sequence databases to identify the constituent proteins and to characterize post-translational modifications (PTMs). The search procedure is computationally intensive, requiring complex statistical calculations to be performed rapidly while streaming through protein or nucleic acid sequence databases.

Products key features/capabilities include:

Supports all three (3) proven search strategies in a single, integrated package -- One of many approaches to proteome analysis is to use 2D gel electrophoresis to separate and visualize the proteins in a cell lysate. Individual spots, containing one or a few proteins, are then excised and digested with trypsin. Mass spectrometric analysis of the intact digest mixture from a spot provides a set of peptide molecular masses for a Peptide Mass Fingerprint search (first type of search). This is a rapid and sensitive technique, but may fail if the digest mixture represents a complex mixture of proteins.

For protein mixtures, or where greater specificity is required, a digest can be separated by High Performance Liquid Chromatography (HPLC), coupled directly to a tandem MS (MS/MS) instrument. Individual peptides are then selected and induced to fragment, yielding MS/MS spectra. A Mascot MS/MS Ions Search (second type of search) looks for the best peptide sequence match to each MS/MS spectrum, then groups these peptide matches into protein matches. This technique is applicable to even the most complex protein mixture, such as those generated by digesting a cell lysate without any gel separation step(s).

The third type of search supported by Mascot is a Sequence Query, an advanced and flexible tool that allows molecular and fragment ion mass values to be combined with amino acid sequence and composition data.

Unique, true probability based scoring allows standard statistical tests of significance to be applied -- Mascot computes the probability that the observed match between the experimental data and mass values calculated from a candidate peptide or protein sequence is a random event. The correct match, which is Not a random event, then has a very low probability. True probability based scoring is the key to recognizing and avoiding false positives. It is also an essential pre-requisite for automation. Only by establishing scores on a fixed, absolute scale, can the decision to accept or reject an identification be made by simple, rule-based software.

Search any FASTA database, whether protein, Expressed Sequence Tag (EST), or genomic DNA -- All calculations are performed on the fly, direct from the FASTA file, giving total flexibility. Search with or without enzyme specificity. ‘No-enzyme’ searches using MS/MS data are essential for finding non-specific cleavage products, and working with targets such as major histocompatibility complex (MHC) peptides. A wide range of chemical and post-translational modifications (PTMs) can be specified in a search. These modifications can be fixed (quantitative) or variable (non-quantitative). Arbitrary combinations of fixed modifications and up to nine (9) variable modifications can be included in a single search. If a peptide contains multiple potential modification sites, Mascot can identify precisely which residues have been modified.

Accepts mass spectrometry data from all the leading instrument manufacturers -- Mascot isn’t tuned for data from one (1) particular type of instrument. It is designed to extract all the statistically significant information and deliver optimum results, whatever the source of the data. Most instrument vendors now incorporate a Mascot interface into their data analysis packages. In addition, you can always use the Mascot Daemon to automate data processing and search submission. Mascot accepts MS data from the following leading instrument manufacturers: Agilent, Applied Biosystems, Bruker, MDS Sciex, Shimadzu, Thermo, and Waters.

Sophisticated client software to automate search submission without custom programming -- Data streams from multiple mass spectrometers can be routed to a Mascot Server for real-time searching by using Mascot Daemon, a Microsoft Windows application that is bundled with Mascot. Each Mascot Daemon task defines the data source (a list of data files or a file path), how the data are to be searched, when the searches are to take place, and any follow-up activities, such as conditional repeat searches. 1) Batch task: A batch of data files to be searched immediately or at a defined time; 2) Real- time monitor task: New files on a defined path are searched as they are created; 3) Score dependent follow-up task. For example, automatically repeating a search against a different sequence database.

Search parameters are defined in the Parameter Editor, which closely resembles the Hypertext Markup Language (HTML) form used for interactive Mascot searches. Tasks and their associated search results are displayed on the status tree. The full result report can be displayed in a web browser by clicking on a hyperlink. Mascot Daemon can take advantage of a variety of data import filters, including Mascot Distiller, to automate the processing of raw data files into peak lists.

Mascot Distiller -- offers a single, intuitive interface to mass spectrometry data files from Agilent, Applied Biosystems, Bruker, MDS Sciex, Shimadzu, Thermo, and Waters. A unique algorithm, which fits each peak to a calculated isotope distribution, processes the raw data into high quality, de-isotoped peak lists.

Mascot Wizard -- is a simple desktop tool that provides a drag and drop interface for submitting peptide mass fingerprint searches to a Mascot server. Internally, it uses the Mascot Distiller libraries to process raw data files into high quality peak lists.

Mascot Integra -- is a complete solution for managing and automating proteomics research. It will scale to the largest projects, yet has a very affordable entry level, making it a practical choice for laboratories of all sizes.

Mascot Cluster -- is a complete, turn-key solution for high throughput protein identification.

Note: Optional toolboxes support Mascot search results review, automatic and manual de novo sequencing, and batch processing. There is also a developer's package that provides access to the application programming interface (API) of the underlying Component Object Model (COM) library.

System Requirements

Mascot Server is available for all these popular computing platforms: Microsoft Windows NT / 2000 / XP / 2003; Linux; IBM AIX; Solaris; HP Tru64 Unix; and SGI IRIX.


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G6G Abstract Number 20087

G6G Manufacturer Number 101725