Author Topic: mMass - Open Source Mass Spectrometry Tool for Windows / Mac X 10.4 / or LINUX  (Read 2369 times)

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mMass - Open Source Mass Spectrometry Tool for Windows / Mac X 10.4 / or LINUX

 :o EEP! If you don't mind: I'll not download and test the Macintosh X version. It's making my head hurt already ...

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mMass - Open Source Mass Spectrometry Tool

Program mMass presents an open source multi-platform package of simple tools for mass spectrometric data analysis. It consist of several modules and tools for protein sequence handling and mass spectrum interpretation with focus on common proteomic tasks. As the program is written in Python language, uses wxPython libraries for graphic user interface and is released under GNU General Public License, it is portable to many computer platforms and has a good potential to be easily modified or extended by modules of specific need.


Main Features
Free & Open Source



mMass belongs to the wide family of open source software. It is written in Python language, uses wxPython libraries for graphic user interface and is released under GNU General Public License. Therefore it is portable to many computer platforms and has a good potential to be easily modified or extended by module of specific need.


Multiple Format Support


mMass supports several mass spectrometry formats. Two of the most popular XML-based formats are mzData and mzXML. Mass spectra and peaklist data can also be easily imported from a simple ASCII file consisting of two columns (m/z values and intensity values) separated by a tab, space, comma or semicolon.

Since it is often impossible to obtain the manufacturer's description of their native file format, only native data from Bruker Daltonics Flex Series instruments is currently supported. We believe, however, that future versions of mMass will also support the native file formats of other manufacturers.


User Definable Peaklist


One of the popular features of mMass is the ability to open a blank document and create the peaklist manually. This feature is particularly useful in those cases where raw data is unavailable, and the user has only a spectrum image or printed list of labelled peaks.



Spectrum Viewer/Analyzer


The core of the software is the Mass Spectrum module. Since most time in data interpretation is spent manipulating spectra (moving, shifting, scaling, zooming etc.), we aimed to make these functions as easy and user friendly as possible.

Two methods are available for peak labelling, Label Point and Label Peak, the latter using a classical centroid with a user definable peak height. To compare the differences between mass spectra effectively, up to nine additional spectra can be simultaneously loaded into the currently open document. In addition, a gel-like view can be used to simplify the comparison of multiple spectra.



Data Recalibration


Two methods are available for data (re)calibration. Internal Calibration is the classic calibration method, using internal reference values. An extensive list of internal reference values is available, and new values can be easily added. Statistical calibration, sometimes called ‘self-calibration’, is a special method, used only for peptide mass spectra. It doesn’t require any external information because, as peptide monoisotopic masses are distributed in a highly regular way.

For both methods, it is possible to use either linear or quadratic fitting. Then, using the calibration graph, the calibration can be checked before being applied to the measured data.



Sequence Editor


mMass provides an internal Sequence Editor, which can be used to make any protein or peptide sequence available to other modules. A sequence can be either written manually or imported from ASCII and FASTA files. Any post-translational modification can be applied to a single amino acid or to a selected type.



Sequence Search


Two additional tools can be used to search a sub-sequence, either by specified mass or by sequence pattern. The Search for Mass tool enables the identification of peptides resulting from non-specific protein cleavage. The Search for Sequence tool can be used to find possible modification sites, as well as for MS/MS data interpretation.



Protein Digest


Many experiments, involving the detection of modifications, protein validation etc., apply the specific enzymatic digestion of a protein with a known sequence. The Protein Digest tool can be used to generate a list of peptides resulting from in silico enzymatic digestion or in silico chemical digestion of a sequence previously defined using the Sequence Editor. The masses of these peptides can then be compared with the current peaklist within a specified tolerance.



Peptide Fragmentation


Different types of fragmentation techniques can be used for the validation of a peptide sequence, as well as for the detection, localisation and characterisation of post-translational modifications. For these types of experiments, the common fragments of a peptide sequence previously defined using the Sequence Editor can be generated in silico using the Peptide Fragmentation tool. The masses of the generated fragments can then be compared with the current peaklist within a specified tolerance.


Check Differences


The interpretation of mass spectra typically involves a seemingly never-ending check of the differences between all peaks in a spectrum. However our Check Differences module is able to simply generate a table of all the differences between the peaks in the peaklist. This table can then be used to automatically compare, within a specified tolerance, each difference with the respective masses of all amino acids, calculated dipeptides, and pre-defined modifications, as well as with a specified mass value or molecular formula.



Compare Peaklists


Few experiments can be covered by just one measurement. In general, multiple samples and spectra are produced, and interpretation involves comparing the spectra. Using our Compare Peaklist tool, an unlimited number of peaklists can be loaded, and compared with the current peaklist within a specified tolerance.



Data Matching


As mentioned above, any teoretical data from Protein Digest or Peptide Fragmentation tool, as well as additional loaded peaklists can be compared with the current peaklist within a specified tolerance. Matched values are highlighted in the list, and peaklist annotation can be generated automatically. Results can also be viewed in the Match Info dialog box, which displays basic information, such as sequence coverage, matched fragments or the number of matched/missed peaks, as well as an error distribution graph.



On-line Search


Although mass spectrometry is a very popular tool for protein identification, it would not be possible without the tools publicly available on the Internet. mMass provides an interface that allows data to be directly sent to the three main tools available on the Mascot website; Peptide Mass Fingerprint, Sequence Query and MS/MS Ion Search.


 ::)  Double EEP!  :o   :o  Sounds expensive ....  Looks expensive too ...

http://www.mmass.org/

Categories: Business - Protein Sequencer - Peptide Sequencer - Mass Spectrometry - Mac System X - Tiger - PPC - MacIntel - LINUX - Windows
« Last Edit: November 24, 2010, 02:47:16 PM by Software Santa »