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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Agilent Mass Profiler Professional - Mass Spectrometry software

Explore relationships in complex mass spectral data

Agilent Mass Profiler Professional software is the only chemometrics software package designed to exploit the high information content of mass spectrometry data. Researchers can easily import, analyze and visualize GC/MS, LC/MS, CE/MS and ICP-MS data from large sample sets and complex MS data sets.

Mass Profiler Professional integrates smoothly with Agilent MassHunter Workstation and ChemStation software, and is ideal for any MS-based application where you need to determine relationships among sample group and variables, including metabolomics, proteomics, food safety, environmental, forensics and toxicology.

For metabolomics and proteomics studies, the optional Pathway Architect helps you evaluate MS data in biological context.

Features:

• Allows comparison of multiple samples and/or multiple MS analysis platforms in a single project
• Designed for both scientists and statisticians, with guided and advanced workflows
• Provides comprehensive statistical tools including ANOVA, PCA, t-tests, volcano plots, hierarchical trees, SOMs, QT clustering, and SVMs for class prediction
• Generates inclusion list for subsequent MS/MS-based analyses to facilitate protein and metabolite identification
• Integrated ID Browser mirrors MassHunter Qualitative Software to allow identification using LC/MS Personal Compound Databases (METLIN, pesticides, forensics) and GC/MS libraries (NIST and Agilent Fiehn Metabolomics)
• R Scripting compatibility within Mass Profiler Professional allows you to further extend and customize statistical analysis and visualization capabilities 

Software Link: Agilent Mass Profiler Professional - Mass Spectrometry 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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Agilent MassHunter Workstation software

Making MS operation easier-from tuning to final report

The all new Agilent MassHunter Workstation software provides intuitive, yet powerful, instrument control, data acquisition, qualitative and quantitative data analysis, and reporting for Agilent time-of-flight (TOF), quadrupole time-of-flight (Q-TOF), ICP-MS, and triple quadrupole systems. Designed from the ground up to make MS analyses easier-from tuning to final report-MassHunter Workstation software can be complemented by application-specific MassHunter software packages that provide even more power and stream-lined operation for specialized analytical tasks such as expression profiling.

Features:

• MassHunter software is now used consistently across Agilent LC/MS, GC/MS, and ICP-MS instruments allowing you to reduce your staff training time.
• Fast, easy setup and operation with automated tuning for both triple quadrupole and Q-TOF instruments. Import worklists from spreadsheets, saving time in method development and high throughput screening.
• Powerful yet simple data analysis with separate, specialized modules for instrument control and data acquisition, qualitative identification of unknowns, and quantitation of target-compounds
• Fast, flexible data reporting with preconfigured reports that simplify basic analyses, or completely customized reports courtesy of Microsoft® Excel and XML. 

Software Link: Agilent MassHunter Workstation software

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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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MatrixAnalyzer - Spectroscopy Softwares

MatrixAnalyzer is a plug-in application to AnalyzerPro. It enables fast and accurate comparison to be made across multiple sample acquisitions and helps to determine key sample changes. Relative changes can be determined by including an internal injection standard.

MatrixAnalyzer extends the capabilies of AnalyzerPro to enable a fast and accurate comparison of a data set.

Accurate Mass Capable - handles high precision data as well as integer mass
Unlimited Matrix size - large data sets can be handled
Internal Standard option - relative and absolute variations can be tracked together
Component Base Peak Processing - allows for broad matching criteria
Exportable Data Sets - allows use of third party statistical analysis tools
Responses calculated on height or area - provides flexibility
Retention Index Compatible - where a Target Component Library has been created using retention indices.

Software Link: MatrixAnalyzer - Spectroscopy Softwares

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Spectrum Mill - Spectroscopy software

Faster, more accurate protein identification

Large-scale proteome characterization frequently leads to bottlenecks in data interpretation and review. Spectrum Mill for MassHunter Workstation quickly identifies proteins and peptides via fast database searches, with automatic or manual match validation and unique algorithms that minimize false positives. It also offers de novo spectral interpretation for proteins not found in any database. Spectrum Mill software can identify relative abundance differences of twofold or greater without complicated isotope labeling. And Spectrum Mill summarizes and correlates results in ways that provide maximum insight and convenience.

Features:

• Version A.03.03 now released
• Spectral extraction and quality assessment speeds protein identification
• Database searching provides multiple options for protein identification add flexibility
• Automatic and manual results validation
• De novo spectral interpretation for proteins not found in any database
• Quantitative and qualitative information
• Result summaries and review to make complex data accessible
• Compatible with multiple data formats from a variety of mass spectrometers 

Software Link: Spectrum Mill - Spectroscopy software

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Mass Spec Calculator™ Professional - Mass Spectroscopy software

Mass Spec Calculator™ Professional
A Utility for Assistance in Mass Spectral Interpretation

Draw chemical structures on screen quickly and easily
Fragment structures on screen using either manual or automated routines
Compare Predicted Fragmentations with Observed Mass Spectra
Instantly calculate & display isotopic profiles of molecules or fragment ions
Calculate possible elemental compositions for a given mass
Automatically digitize a graphical mass spectrum to a mass-intensity data file
All modules now support 79 elements, including essentially any element likely to be encountered in mass spectrometry.
All elemental data including mass, number of isotopes, and each isotope's mass and relative abundance can be easily edited if desired.
MS Calc Pro automatically adjusts to the available screen resolution to maximize the drawing space;
additional virtual screen space can be accessed by activating scrollbars.
The drawing routines have been improved, several new options have been added, a tool bar and pop-up menu are included
for additional ease of use, and a new alkyl chain tool and a user-defined "R-group" tool have been added to further speed the drawing process.
MS Calc Pro includes an enhanced Isotopic Profile utility based on a completely new algorithm that provides essentially
unrestricted analyses regardless of the number of polyisotopic atoms present in the structure.
Includes an enhanced Elemental Formula utility that supports all 79 elements and provides additional analysis and display features
Includes a new utility that can automatically digitize a scanned spectrum and import it for use within MS Calc Pro.
Includes improved spectrum and printing capabilities.

1. To begin using MS Calc Pro, one would generally first draw a structure. The MS Calc Pro drawing editor is designed to be very simple and easy to use, and a variety of preformed rings, functional groups and other structures are available to assist in this process. For example, the structure of nicotine can be drawn on screen in seconds in just six steps. This compound was drawn by placing two preformed rings on screen, then adding the bond, two N atoms and the methyl group as added objects.

2. The structure could be saved to disk, then converted to cotinine by adding =O in one step to form the lactam structure. The two structures shown here could thus be drawn and saved for later use by using just 7 steps and in less than 30 seconds.

3. Once a structure has been drawn, it can be analyzed in a number of ways. The most fundamental operation is manual fragmentation. This is done just as you would do using paper and pencil, but with electronic speed and accuracy. For example, to examine a homolytic break of the bond linking the two ring structures of nicotine, you would simply draw a line through the bond using the mouse; the program will instantly calculate and display the resulting two fragment masses. The display is color-coded to clearly link the fragment atoms with the associated mass.

This instant manual fragmentation process is interactive and can be repeated as often as desired. Manual fragmentation draws upon your knowledge of likely fragmentation routes to focus your time and effort on the most likely possibilities. There are three different manual fragmentation modes available including a 'free-form' option to accommodate any sort of fragmentation you might wish to examine. Multiple and sub-fragmentations of compounds can also be examined, and the display can be instantly switched between nominal and accurate mass resolution.

Auto-fragmentation results are only a mouse-click away. In the screen shown below, nicotine has been auto-fragmented by MSC and the user has selected mass 39 in the fragment list ... this automatically redraws the structure with the three atoms present in the fragment (C3H3) indicated on screen. This process of identifying specific fragments in the structure can be repeated as often as desired. These results can also be directly compared with the actual mass spectrum, either imported as an ASCII file or recreated within MSC; also, fragment isotope profiles can be instantly calculated and displayed; additional possible fragments including major rearrangement products such as McLafferty or tropylium ions can be identified; etc.

Once a molecule has been auto-fragmented, it can also be compared with an observed mass spectrum by choosing the 'Match' option button. This enables you to essentially overlay the projected and observed spectra, match predicted and observed isotopic profiles for the molecular ion, and calculate an overall 'Match Index' for the actual and predicted spectra.

MSC also includes utilities for determining Isotopic Profiles, for calculating possible elemental compositions given a mass, and for importing user spectral data in a variety of text formats, or creating spectral files directly from data entered onto an internal 'spreadsheet'.

The screen below demonstrates the Isotopic Profile utility. The user has drawn the structure of dioxin (TCDD) and then clicked on the Isotopic Profile Speedbutton. MSC Pro automatically incorporated the elemental 
composition for the TCDD structure, carried out the calculations, and instantly displayed the window shown here displaying the theoretical profile in both text and bar graph form. Compositions can also be entered and edited directly, and additional options such as to display the results in accurate mass form are available.

MS Calc Pro includes an enhanced Elemental Composition utility. With this tool you can enter a mass and tolerance, select the elements to be considered (with additional constraints if desired such as to specify the range of an element to include; or only show possible molecular ions; only formulae adhering to the 'Nitrogen Rule', etc.), and then click on the 'Calculate' button to have MSC calculate all possible elemental compositions fitting those conditions.

Software Link : Mass Spec Calculator™ Professional - Mass Spectroscopy software

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Agilent MassHunter BioConfirm software

Easily confirm protein and peptide identities

Agilent MassHunter BioConfirm software is ideally suited for scientists who need to support recombinant protein expression and process development, known-protein characterization, or synthetic peptide confirmation. BioConfirm software will help you confirm identities and identify variants before you start expensive testing.

Features:

• Interactive software allows analysis of both protein and peptide spectra using separate, optimized deconvolution algorithms
• Protein sequence editor/matcher enables creation of new protein, protein digest, or synthetic peptide sequences and comparison of theoretical masses with mass spectral data
• Superior feature extraction with a unique algorithm that finds all components-not just all peaks-in each sample
• Automated batch processing and reporting on the fly
• Import mass lists from the bioconfirmation software into a database search program, such as Agilent's Spectrum Mill for MassHunter Workstation for fast identification 

Software Link: Agilent MassHunter BioConfirm software

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Mnova Suite - Spectroscopy software

NMR AND LC/GC/MS PROCESSING, ANALYSIS, MANAGING AND REPORTING

Mnova is a multipage, multivendor, multitechnique and multiplatform analytical chemistry software suite designed as a container for our NMR & MS modules.

Learn more about the Mnova modules
The Mnova suite works as a container for all our specific plugins. This shared interface and its automation abilities allow our users to optimize their learning curve and workflows by combining different technique data on the same application.

Spectral database
A new concept for the shared storage of molecules, NMR and LC/GC/MS analytical data and other Mnova objects.

NMR processing and analysis
One single, powerful and intuitive environment for all your NMR data (all vendor formats supported) and users (from novice to expert).

NMR Prediction
Prediction of 1D (1H, 13C, 15N, 19F, 31P, 17O, 29Si) and 2D spectra from molecular structure (mol file, ChemDraw, IsisDraw, ChemSketch) within the Mnova Suite.

LC/GC/MS processing and analysis Maximize the use of LC/GC/MS across your organization, for all data formats and users.

Software Link: Mnova Suite - Spectroscopy software

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MassHunter Metabolite ID Software

Streamlined Metabolite Identification with MassHunter Metabolite ID Software

The MassHunter Metabolite ID software vastly simplifies metabolite identification without taking away your choice or control. It is used with the Agilent 6510 Q-TOF LC/MS which delivers the MS and MS/MS data quality of a research-grade mass spectrometer with the reliability and ease of use of a single quadrupole or TOF instrument.

Features:

• Superior accurate-mass MS and MS/MS data results in better, more accurate identification
• A wide in-scan dynamic range and unsurpassed Q-TOF sensitivity help find low abundance metabolites in the presence of more abundant compounds
• Unique molecular feature extraction algorithms do a better job of finding metabolites
• Metabolite ID software increases productivity and throughput 

Software Link: MassHunter Metabolite ID Software

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Agilent MassHunter Profiling software - Expression profiling Software

Designed for expression profiling applications

The Agilent MassHunter Profiling software is specifically designed for expression profiling applications such as biomarker discovery. MassHunter Profiling software uses a unique feature extraction and correlation algorithm, that does a better job of locating all the components in even very complex peptide mixtures.

Features:
Unique feature extraction and correlation algorithm locates molecular features, not just chromatographic peaks
Visualization tools allow the identification of statistically meaningful differences between sample groups (e g., healthy versus disease)
Calculates abundance ratios and clearly identifies differentially expressed features
Flexible feature selection allows user selection of comparison criteria
Exports profile data for statistical data analysis by Agilent's GeneSpring MS software, other database search programs, identification environments, or statistical analysis packages
Supports additional workflows including pharmaceutical impurity analysis, forensic analysis, environmental analysis, and pesticide analysis

Software Link : Agilent MassHunter Profiling software - Expression profiling Software 

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PEAKS - Proteomic Mass Spectrometry Software

PEAKS is proteomic mass spectrometry software, designed for the researcher interested in highly confident results. Whether studying an unsequenced organism, sequencing synthetic peptides or analyzing known sequences, PEAKS will return optimal results.

Start with the raw (unprocessed) data straight from the mass spectrometer, use various workflows to streamline tasks at hand, and report results in a clear user interface. PEAKS will give greater coverage and confidence in one shot than many other tools combined. Even a novice can obtain publishable results within minutes.

Proteomic Tools

• de novo Sequencing: Sequence peptides without a database (automated and manual-assisted)
• PEAKS DB: Protein Identification with maximum accuracy and sensitivity
• inChorus: Validate your results with multiple search engines
• PTM Finder: Map PTMs efficiently
• SPIDER: Homology Search specialized for de novo sequencing
• PEAKS Q: Quantify your tandem mass spectrometer results

More Than Just Database Search!

Running a database search alone can be effective but often will give false positives or incorrect identifications.1 Since 2002, PEAKS has been the industry standard for de novo sequencing by leading mass spectrometry labs around the world. But there is more to PEAKS than just database search and de novo sequencing. The following pages will discuss a variety of tools that should be a part of daily practices.

Provide your lab with a complete solution for proteomic mass spectrometry investigation; provide it with PEAKS. Protein identification via database searching and de novo sequencing produces stable results worthy of discovery and publication foundations.

What Are Your Needs?

PEAKS is available as both desktop and server solutions. PEAKS Studio is the optimal desktop model and PEAKS Online is the vast server/cluster model. Once you have read about the multiple tools provided with PEAKS within this General Information section, choose the solution that best meets your lab's needs and start testing. Not only is there access to request a downloadable free trial of PEAKS Studio, the BSI website hosts a public server for PEAKS Online where users can submit their own data, free, on a daily basis.

Get Published!

PEAKS makes getting published easier than ever before. Summary reports are automatically produced giving viewers a detailed glimpse of the project's results. Detailed images are easily exported and are configurable to fit exactly into the spaces you want. You no longer need to spend time adjusting blurred or distorted images to suit a specific location. We take pride in our software so you can take pride in your research.

Software Link : PEAKS - Proteomic Mass Spectrometry Software

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GPMAWTM - Protein Mass Analysis Software

GPMAWTM General Protein Mass Analysis for Windows
Mass spectrometric analysis of proteins and peptides and more.

The GPMAW program is primarily intended as a tool for mass spectrometric analysis of proteins and peptides. However, a number of other bioinformatics tools have been included, so the use of the program extends far beyond simple mass analysis.

The program runs on all 32-bit versions of Windows since Windows 2000 (i.e. 2000, XP, Vista, Win7). It will also run on current 64-bit versions, but has not been thoroughly tested on these platforms. It can also run on Mac systems with a Windows emulator, but full compatibility is not guaranteed.

Except for the MS/MS Search, the program does not need a strong processor or fast hard disk but can run on any system. Running the MS/MS Search you need a screen with SVGA+ resolution, otherwise you may even run it on a netbook.


GPMAW™ General Protein Mass Analysis Program content

Sequence handling
Import of sequences from a number of different formats with direct database search in Entrez and in local databases (FastA format and Swiss-Prot). Sequences can be saved in local files (databases) for future reference.

From the sequence window a large number of actions can be performed. Sequences can be exported in FastA format (either singly or all sequences at once) for easy transfer to other programs.

Mass analysis
The protein can be cleaved by automatic methods (e.g. a flexible nomenclature for defining enzyme actions) or manually. The peptides are displayed with a number of parameters (various mass values - mono, ave, charges - Bull&Breese index, HPLC index, pI, charge) and can be further worked upon (e.g. cross-linked, new cleavage).

Peptide mass searches can be performed on any local database in FastA format.

Bioinformatics
A number of graphs can be displayed, hydrophobicity, dot-plot, secondary structure prediction. BLAST searches can be performed on local databases.


GPMAW™ General Protein Mass Analysis Program Features

Sequence window
The sequence window is the default view of a sequence. From here you can call most of other sequence related functions (either through the menu, the toolbar, or the pop-up menu).

The display can be configured in various ways, 1- or 3-letter display, average mass/monoisotopic mass, fixed residue width, sidebar with sequence information, show disulfide bridges etc. By highlighting part of the sequence you can easily obtain the mass of the given section. For easy navigation you can color specific residues (three different colors and underlining are available).

Most of the settings can easily be pre-set.

The sequence window is the parent window from which a large number of derived daughter windows can be created:

Peptide window
Ms/ms window
Mass search, composition search
Available graphs
Hydrophobicity
Secondary structure
Charge vs. pH
Dot-plot
Alpha-helical wheel
Peptide window
The peptide window is normally called from the sequence window through the automatic digest commend. However, there are alternative methods like manual or semi-automatic cleavage.

The peptide window lists all the peptides that will be generated from the given protein along with a large number of physical-chemical parameters (charge single/multiple/negative, peptide number, location, HPLC index, theoretical pI, Bull & Breese index, sequence - 1/3-letter etc.).

Peptides can be generated with partial cleavages, modified termini, modified residues (even partial modifications are supported in a limited way). Specific residues may be colored for easier referencing.

The actual parameters presented can be configured by the user.

Sorting and reverse sorting can take place on any column by clicking on the header.

Through the toolbar and/or the pop-up menu (right mouse click) you can access a large number of additional functions related either to the digest (like the simulated HPLC reversed phase chromatogram) or to the currently selected peptide (ms/ms cleavage, peptide information, charge vs. pH graph).

User Defined pI Values
How are these pKa values then used by GPMAW? For the modifications, it is quite simple, as the pKa values are taken into the calculations of pI and charge whenever they are defined in a sequence (i.e. whenever a residue is modified with the relevant modification).

However, for the mass file GPMAW has a user-defined table, as GPMAW has four different tables.

The first and third are values taken from the literature (references in the on-line help and the manual). The second option is based on the values for free amino acid residues. The fourth and last option is based on the definitions in the currently selected mass file and has to be checked in order to use these values.

Software Link : GPMAWTM General Protein Mass Analysis Software

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