Mascot Cluster - Spectroscopy Software

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

Mascot has been designed to be embarrassingly parallel, which means that each search can be divided to run in parallel on multiple processors. Support for parallel execution is built-in to Mascot, and does not require any special operating system or grid engine. If you wish, you can license the software and set up a cluster using your own hardware. On this page, we describe the other option: a turn-key system with Mascot pre-installed on reliable, high performance IBM hardware.

Hardware

Any current IBM server that uses Intel or AMD processors can be used as the hardware platform. For a small cluster, up to around 6 processors, the most cost-effective solution is to use a number of dual processor servers, either tower or rack mount. For larger systems, we recommend the IBM BladeCenterTM, which is more compact and easier to manage than a large number of standard servers.

Mascot licensing is socket based. That is, if a processor has multiple cores, Mascot will use all of them for searching. For a given architecture, search speed (or throughput) goes as the processor clock speed multipled by the total number of cores.

Only the processors used for searching require a Mascot licence. It is often a good idea not to run searches on the master (head) node of the cluster, but leave it free to run the web server, handle database updates, and generate reports. This makes the server very responsive even when there are several searches running, using all the processor time on the search nodes. Having a non-searching master node also gives you a spare node, in case one of the search nodes has a hardware failure.

Result files are stored on the master node, so this needs access to plenty of disk storage. Search nodes only need local storage for program files and the compressed sequence database files; a single hard drive of modest size is usually sufficient. All nodes should have at least 2 GB RAM.

Software Link: Mascot Cluster - Spectroscopy Software

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Mascot Daemon - Spectroscopy Software

Mascot Daemon is a client application which automates the submission of data files to Mascot server. It runs under Microsoft Windows 2000, XP, Server 2003, Vista, Server 2008, and 7. Daemon functionality includes:

Batch mode, in which an arbitrary group of files can be defined for searching, either immediately or at some pre-set time.
Real-time monitor mode, in which new files on a pre-defined path are searched as they are created.
Score dependent follow-up tasks. For example, automatically repeating a search at a later date or against a different sequence database.

Multiple Daemon clients can submit searches to a single Mascot server. If you have several mass spectrometers, you can install separate copies of Daemon on each instrument data system or just have a single copy of Daemon somewhere on the LAN marshalling searches for all instruments.

The functional unit of Mascot Daemon is a task, which is defined by 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.

Search parameters are defined in the Parameter Editor, which closely resembles the HTML form used for interactive Mascot searches. Fields can also contain HTML-like tags which are automatically substituted at run time with information such as a file name or a sample description.

Every time a new task is run, it creates a task node on the status tree. The results from each task are attached to the task node, just like directories and sub-directories in Windows Explorer. Key information for each result can be displayed by clicking on the result node. The full result report can be displayed in a web browser by clicking on the blue hyperlink.

Daemon's follow-up function is extremely powerful and can be used in many different ways. A couple of simple examples would be:

A batch of data files can be searched at specified intervals against database updates. Each data file will stay in the loop until it's score exceeds a pre-set level.
Sequence databases of increasing size or decreasing quality can be searched serially. For example, a small database of common contaminants such as keratins might be searched first. Spectra which are unmatched can then be searched against a comprehensive non-redundant protein database, such as NCBI nr. Data which still fail to find a match can then proceed to a search of dbEST.

Arbitrary numbers of follow-up tasks can be chained together to implement complex decision trees. This is only possible because Mascot scores reflect true probabilities, permitting rule based software to determine whether a match is significant according to user specified criteria.

The default database engine used by Mascot Daemon is Microsoft Jet 4.0, the engine used by Access 2000. Alternatively, Daemon can be configured to use any database engine which supports either OLE DB or ODBC, such as Microsoft SQL-Server or Oracle, enabling multiple Daemon clients to share a common task database.

 Software Link: Mascot Daemon - Spectroscopy Software

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AnalyzerPro - Spectroscopy Softwares

AnalyzerPro is a data deconvolution software application for LC-MS and GC-MS data. It utilizes proprietary algorithms to detect obscured components that existing software is unable to find without additional information.

Some of the key features of AnalyzerPro are shown below:

Deconvolution of GC-MS & LC-MS data
Supports for all major manufacturer's instruments and legacy instruments
Targeted and non-Targeted Analysis
Correction for baseline drift
Extraction of closely co-eluting peaks
Automatic spectral enhancement
Qualitative Analysis
Quantitative Processing using external or internal standards
Combined Quan and Qual reports
Batch processing
Component purity calculation
Command line interface
Mass defect processing
DFTPP processing
Multiple sample comparison
Overlay multiple component chromatograms
Overlay component ions
M/Z searching
Seamless Integration with NIST libraries
Elemental composition
Results searching
Tabular display of results
Processing Trail
Audit Trail
Integration with RemoteAnalyzer®
Background file subtraction
Accurate mass compatible
Print chromatograms / spectra
Copy chromatograms / spectra as metafiles
Charge State Deconvolution
Multiple screen layout
Custom Reports
Online, telephone and email support

Many other features and benefits come as standard. Some are more specialised than others and by downloading a trial coy or requesting a demonstration we can show you how AnalyzerPro can assist with your particular application.

Software Link: AnalyzerPro - Spectroscopy Softwares

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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

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Mnova MS - Spectroscopy Software

Processing & analyzing LC GC MS data that emphasizes minimalism, simplicity, and agility.

By providing a common interface for different vendor data and automating all functionality (data read in and display, integration, background subtraction and complicated computational analysis), Mnova MS opens the power of the technique to all non expert users.

This allows you to remove bottlenecks in your organization by taking routine work off the hands of your experts and by maximizing the time they can spend on higher value work.

Multivendor LC GC MS data visualization, processing and analysis:
Open automatically, by simply dragging and dropping, LC, GC and/or MS data coming from Agilent, Bruker, JEOL, Thermo, Waters equipment, as well as data in mzData or mzXML formats. (Find the complete list of supported formats here)
Automatically or manually integrate peaks in the TIC, MS, and UV traces. Automatic peak picking and integration are carried out upon importing the spectrum, automatic results can be edited by manually interacting with the data.
Select spectra based on TIC peaks, with / without background subtraction
Co-add spectra manually
Display different TICs and MS Spectra from different functions, as well as DAD and PDA traces

Easily generate EIC (Extracted Ion Chromatogram):
Easily generate Extracted Ion Chromatogram for a given mass range or a certain m/z value. Compare these EICs with the peaks in the TIC for better information on overlapped peaks.

Automatic molecule matching for structure confirmation
Structure confirmation is a common objective when working with analytical chemistry data. Often, several techniques are combined for this purpose, most commonly NMR and LC/GC/MS. In addition to its many tools for structure confirmation by NMR, implemented in the NMR plugin, Mnova also implements tools for automatic structure confirmation by LC/GC/MS. This functionality is extremely fast and easy to use, making this capability available to all users, even complete novices. Import chemical structures from MOL or SD file formats, or copy/paste from ChemDraw, Isis/Draw and ChemSketch, and let the software confirm which ones match your experimental data. The assign match criteria can be customized by selecting the adducts and losses, mass accuracy and score thresholds.

The 'Molecule Match' feature is very useful to see if a mass spectrum and a GC or LC chromatogram peak match with a proposed molecular structure (or a group of proposed molecular structures). It is also possible to run a Molecular Match with a MS/MS spectrum and see the result directly in the MS/MS.

The 'Molecule Match' table with the results will contain information about the 'Retention Time' (RT), Scan (number of spectrum), Match Score, Similarity, MS Purity, etc.

Besides, Mnova MS shows you in the chromatogram the retention time of the match (with a blue vertical line) and displays the corresponding MS spectrum (the number 467 in this case) overlaid with the theoretical one (in green at a M/Z around 278, in this case).

New Featured added: It is also possible to run a Molecular Match with a MS/MS spectrum and see the result directly in the MS/MS. Here you can see an example.

Automatically compute potential Elemental Compositions for a given mass ion peak
With high accuracy mass spectral data, determine potential elemental compositions for a given molecular ion. Using Mnova MS it is possible to do an 'Elemental Composition' analysis of any peak of the Mass spectrum. Just define your constraints and click on the desired peak to obtain a table like this one with proposed elemental composition sorted by goodness of fit.

Create reports combining NMR and MS in full automation
Once the processing and analysis of LC/GC/MS data have been completed, frequently it will be necessary to report on such analysis, very often in combination with similar analysis carried out by NMR. Mnova allows the user to combine both techniques seamlessly for reporting, even within the same document.

In addition, Mnova also makes it possible to automate most of any organization's repetitive and non-value-adding tasks using Mnova Scripting Capabilities and its multi-technique environment (which allows our users to combine NMR LC GC MS in the same document).

In this example we show how it's possible to start from an LC/MS dataset and expected structures (or MW) and automatically end up with a report similar to the one on the right. This functionality can also be run in batch mode and exported as PDF or any other format. Watch the video to see how the automation works.

Auto analysis and reports the following results.

TIC, with peak integrals
UV traces, with peak integrals
Structures and their Selected Ion Chromatograms, and Mol Match
results
Lists of TIC and UV peaks with area% > 5
Co-added MS spectra for each of the TIC peaks with area% > 5

 Software Link: Mnova MS - Spectroscopy Software

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