Mass Spec Tools - Mass Spectrometry Software

Mass Spec ToolsTM
Exact-mass spectra and common calculations related to mass spectrometry

An essential toolkit of 11 programs for the mass spectrometrist, Mass Spec (MS)Tools process exact-mass spectra and perform common calculations related to mass spectrometry. Display and processing functions are intended to make use of exact-mass data, but integer mass spectra can also be displayed.

Listed below are brief descriptions of each program

MS Tools includes
Elemental Composition Workshop
Individual masses or an entire high resolution mass spectrum may be rendered to generate a list of elemental compositions that can be used to assist spectral interpretation or to search NIST or other nominal mass spectral libraries for compound identification.

Calculate elemental compositions from exact masses, isotopic abundances, or both. This utility has a direct link to the NIST MS Search Program if present and will search for the best match based on the number of synonyms and presences in other databases.

SearchFromList
Search exact-mass spectra against your own custom mass spectral database or identify components in a complex spectrum by exact mass measurements. Lists are easily created in comma-delimited text or Microsoft Excel format.

Mass Spec Periodic Table
A periodic table with information that is relevant to mass spectrometry. Clicking on an element produces a graphical display of the isotopic abundances for that element along with a table of exact masses and abundances for each element.

MassSpec To Metafile
Generate vector graphic (metafile) displays from mass spectra or mass chromatogram files saved in text format. The output can be imported into reports, presentations, or graphic editors for preparing publication-quality figures.

Isotope Ratio Calculator
A means for simulating the isotopic abundances and masses average mass and the appearance of single-charge or multiple-charge isotopic clusters at any given resolving power. Supports isotope enrichment calculations and simulates overlapping isotopic distributions.

Mass Series Calculator
Useful for calculating reference tables based on polymers or clusters with repeating subunits. The program can also calculate ionic clusters and multiple-charge ions (including multimers).

Simple ESI Calculator
Calculate multiple-charge ion m/z's for a given composition, or estimate molecular weight from two successive charge states or a measured m/z and a known adduct.

Interactive Peak Integrator
Permits manual peak integration for text-format chromatograms or peaks in a segment of a mass spectrum.

PPM Calc
Interactively view the relationship between parts-per-million, resolving power, and mass differences.

Batch Composition to Mass Converter
Rapid calculation of monoisotopic average, nominal, and/or lowest m/z for large compound lists. Convert thousands of elemental compositions in spreadsheet form within seconds.

Subtract Composition
Subtract one elemental composition from another and view the resultant composition and masses for each composition.

 Software Link: Mass Spec Tools - Mass Spectrometry Software

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SmileMS - Mass spectrometry Software

Mass spectrometry is a recognized powerful analytical technique used to screen and identify a wide range of chemical compounds. It is used routinely in many laboratories in fields such as Laboratory Medicine, Forensic Toxicology, Doping Control, Food Testing, and Metabolomics research. The rapid introduction of LC-MS and LC-MSMS provides access to an extended range of molecules, complementing the well-established GC-MS methods. Current identification methods for both targeted and unknown screening increasingly rely on MSMS spectra library searches. A number of challenges are however still to be addressed:
Fragmentation spectra of a given compound can vary a lot depending on the selected instrument and acquisition method.
Currently available MSMS spectral libraries only cover a subset of these experimental conditions for the available molecules.
Algorithms offered in dedicated software solutions originate from the GC-MS development and do not show appropriate performances for LC-MSMS data.
In routine applications, there is a need for a robust, easy-to-use, MS vendor-independent and integrated solution for rapid screening of large sets of molecules with confidence.

SmileMS meets these needs and proposes a unique LC-MSMS library search solution.
SmileMS software is designed to identify analytes from MS spectra of fragmented molecules via a spectral library search approach. It can be used both for targeted and untargeted screening methods.

The intuitive interface makes SmileMS appropriate for routine applications and allows experts to evaluate the results in detail.
Results are delivered in aggregated lists of identified analytes, supported with chromatogram and annotated spectra.
A robust and innovative algorithm allows for confident identification of molecules across different instrumental architectures and acquisition methods.
The software can handle MSMS and MSn data from a wide range of LC-MSMS vendors and takes advantage of accurate mass MSMS.
Different spectral libraries can be uploaded and queried simultaneously or separately, e.g. from NIST, AB SCIEX, Wiley-VCH, etc., as well as privately created libraries.

Key Features:
Outstanding compound identification with highest levels of confidence
Easy to use and intuitive interface
Two-step workflow designed for routine technicians
Interactive result review for in-depth analysis
Filters for identification of metabolites and other unknown compounds
Compatible with LC-MSMS instruments from major vendors (AB Sciex, Agilent, Bruker, Thermo, Waters)
Library search against multiple LC-MSMS libraries, provided by NIST, AB Sciex, Wiley, as well as home made libraries

Advanced Functionalities:
Take advantage of accurate mass MSMS from high resolution instruments, e.g. QqTOF, FT, etc.
Efficient spectra library management (edition, visualization, sharing, etc.)
Analysis workspace for organization of results and analyses
Login system and user rights for enhanced traceability and privileges
Automation with SmileMS submission module" for greater productivity with Bruker and Thermo instruments"

 Software Link: SmileMS - Mass spectrometry 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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Phenyx - MS/MS protein identification software

Working closely with proteomics scientists to understand their current challenges and expectations, we have created Phenyx, the next generation of MS/MS protein identification software. Phenyx is available in multiple formats and installation configurations to insure its availability to the entire scientific community.

Developed in collaboration with the Swiss Institute of Bioinformatics (SIB), Phenyx is GeneBio's renowned software platform for the identification, characterization and quantitation of proteins and peptides from mass spectrometry data. Specifically designed to meet the concurrent demands of high-throughput MS data analysis and dynamic results assessment, it offers a highly flexible user interface and an adaptable architecture that help instill confidence in results assessment.

Phenyx enables proteomics scientists to 1) submit MS/MS data and identify peptides and proteins 2) visualize and evaluate results using various dynamic views, 3) manually validate results and compare Phenyx runs and those of other database search engines (like Mascot, SEQUEST and X!Tandem), 4) perform quantitative analysis with the Phenyx quantitation module, and 5) export results and generate reports into various formats and integrate Phenyx into your laboratory workflow.

Through its import feature, its advanced Results Comparison functionality and its quantitation module, Phenyx goes beyond being a single search engine tool to become a comprehensive identification platform allowing users to import, compare, quantify and validate their Phenyx results but progressively also their Mascot, SEQUEST and X!Tandem results while visualizing them in various levels of granularity and easily exporting their comparative results in one click for publication.

 Software Link: Phenyx - MS/MS protein identification software

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GC and GCMS File Translator Professional - Mass spec Program

Read files from a variety of popular GC Mass Spec programs without worrying about incompatibilities.

Now you can share, import, and export your gas chromatography (GC) and GC-Mass Spec data files easily without worrying about file incompatibilities. This program reads files from a variety of popular GC Mass Spec programs including Hewlett Packard Chemstation GC, Agilent (Hewlett Packard) Chemstation MS, Finnigan Xcalibur (on systems with Xcalibur software), Finnigan ITDS, Finnigan Magnum MS, Finnigan Incos MS, Finnigan GCQ, Finnigan ICIS, Shimadzu MS, EasyChrom, Chromperfect, Beckman Gold, netCDF GC, netCDF MS, Inficon Hapsite, Shrader, JCAMP-DX GC, JCAMP-DX MS, and ASCII. Data can be saved in the following formats: Chemstation GC, Agilent (Hewlett Packard) Chemstation MS, Finnigan ITDS, Finnigan GCQ, Varian Saturn, Galactic Grams, EasyChrom, Chromperfect, netCDF GC, netCDF MS, JCAMP-DX GC, JCAMP-DX MS, and ASCII. In addition, users of recent versions of Excel can export data to spreadsheet. Customizable to perform extractions of spectral records, total ion chromatograms, and selected ion traces. Data filter, batch and command line processing options exist.

Using GC, GC/MS File Translator ProTM During Preparation of High Quality Graphics
Your data is only as impressive as your presentations. Poor export capabilities of commercial processing packages restrict your ability to produce high quality slides, publications, etc. Only one native software package supports graphics exports in vector format for colored, high resolution images. This limits you to fuzzy, bit-mapped images, screen capture, or dot matrix printouts, which require extensive cutting and pasting. GC, GC/MS File Translator ProTM allows you to extract whatever data you need to produce professional quality graphics, either in ASCII format for import into your favorite graphics package, or for import into a chromatographic processing packages which satisfies your needs.

GC, GC/MS File Translator ProTM in Research: Complete Access to all Data Aids Evaluation of Experimental Processing Strategies
Experimental data processing objectives such as pattern recognition, comparative library evaluation, or advanced signal filtering can now be tested for data collected with a variety of popular acquisition packages. Such tests necessitate complete access to all data, which often is limited by capabilities of data processing software rather than information contained in data files (e.g. display may be graphic, while actual numeric data are inaccessible). With GC, GC/MS File Translator ProTM numeric data can be recovered from data files for further processing as required.

Delayed Processing and Background Processing
GC, GC/MS File TranslatorTM allows you to process data in background while you are simultaneously working on other tasks. Instead, you may chose to add several lengthy translations to the program's job list and delay their execution until your system is idle. All translation jobs can be configured independently.

Configuration Options and Integrated Data FilterM
The Translation Settings dialog shown here allows you to review information contained in source file headers, and to customize format translations according to your specific needs. Options include partial extraction of selected retention time windows or record ranges, review and modification of comment and operator text entry fields, and data editing via customized y axis factor and offset values. For export in ASCII format, data sets can be reduced to accommodate limitations of commercial spread sheets and graphics programs (which typically are limited to 8000 data points).

Software Link : GC and GCMS File Translator Professional - Mass spec Program 

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